1
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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2
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Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun 2023; 14:8219. [PMID: 38086811 PMCID: PMC10716388 DOI: 10.1038/s41467-023-43735-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Artificially Expanded Genetic Information Systems (AEGIS) add independently replicable unnatural nucleotide pairs to the natural G:C and A:T/U pairs found in native DNA, joining the unnatural pairs through alternative modes of hydrogen bonding. Whether and how AEGIS pairs are recognized and processed by multi-subunit cellular RNA polymerases (RNAPs) remains unknown. Here, we show that E. coli RNAP selectively recognizes unnatural nucleobases in a six-letter expanded genetic system. High-resolution cryo-EM structures of three RNAP elongation complexes containing template-substrate UBPs reveal the shared principles behind the recognition of AEGIS and natural base pairs. In these structures, RNAPs are captured in an active state, poised to perform the chemistry step. At this point, the unnatural base pair adopts a Watson-Crick geometry, and the trigger loop is folded into an active conformation, indicating that the mechanistic principles underlying recognition and incorporation of natural base pairs also apply to AEGIS unnatural base pairs. These data validate the design philosophy of AEGIS unnatural basepairs. Further, we provide structural evidence supporting a long-standing hypothesis that pair mismatch during transcription occurs via tautomerization. Together, our work highlights the importance of Watson-Crick complementarity underlying the design principles of AEGIS base pair recognition.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA.
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
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3
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Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA. Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. Nat Commun 2023; 14:6820. [PMID: 37884513 PMCID: PMC10603101 DOI: 10.1038/s41467-023-42406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
The 4-letter DNA alphabet (A, T, G, C) as found in Nature is an elegant, yet non-exhaustive solution to the problem of storage, transfer, and evolution of biological information. Here, we report on strategies for both writing and reading DNA with expanded alphabets composed of up to 12 letters (A, T, G, C, B, S, P, Z, X, K, J, V). For writing, we devise an enzymatic strategy for inserting a singular, orthogonal xenonucleic acid (XNA) base pair into standard DNA sequences using 2'-deoxy-xenonucleoside triphosphates as substrates. Integrating this strategy with combinatorial oligos generated on a chip, we construct libraries containing single XNA bases for parameterizing kmer basecalling models for commercially available nanopore sequencing. These elementary steps are combined to synthesize and sequence DNA containing 12 letters - the upper limit of what is accessible within the electroneutral, canonical base pairing framework. By introducing low-barrier synthesis and sequencing strategies, this work overcomes previous obstacles paving the way for making expanded alphabets widely accessible.
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Affiliation(s)
- Hinako Kawabe
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Logan Miessner
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas Kaplan
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA, 98195, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, 32615, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, 32615, USA
| | - Jorge A Marchand
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, 98195, USA.
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4
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Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. ACS Synth Biol 2023; 12:2750-2763. [PMID: 37671922 PMCID: PMC10510751 DOI: 10.1021/acssynbio.3c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/07/2023]
Abstract
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1'-β-d-2'-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find G-Z pairs have stability comparable to that of A-T pairs and should therefore be included as base pairs in structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing it with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases in which Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.
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Affiliation(s)
- Tuan M. Pham
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Terrel Miffin
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Hongying Sun
- Department
of Surgery, University of Rochester Medical
Center, Rochester, New York 14642, United States
| | - Kenneth K. Sharp
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Xiaoyu Wang
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Mingyi Zhu
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Shuichi Hoshika
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | | | - Steven A. Benner
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Jason D. Kahn
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - David H. Mathews
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
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5
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. bioRxiv 2023:2023.07.14.548955. [PMID: 37503021 PMCID: PMC10369999 DOI: 10.1101/2023.07.14.548955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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6
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Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. bioRxiv 2023:2023.06.06.543917. [PMID: 37333404 PMCID: PMC10274641 DOI: 10.1101/2023.06.06.543917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo-[1,2- a ]-1,3,5-triazin-(8 H )-4-one and 6-amino-3-(1'-β-D-2'-deoxyribofuranosyl)-5-nitro-(1 H )-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases where Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.
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Affiliation(s)
- Tuan M. Pham
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
| | - Terrel Miffin
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Hongying Sun
- Department of Surgery, University of Rochester Medical Center, Rochester, NY
| | - Kenneth K. Sharp
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Xiaoyu Wang
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
| | | | | | | | - Jason D. Kahn
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
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7
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Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
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Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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8
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Shukla MS, Hoshika S, Benner SA, Georgiadis MM. Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220028. [PMID: 36633282 PMCID: PMC9835606 DOI: 10.1098/rstb.2022.0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The first structural model of duplex DNA reported in 1953 by Watson & Crick presented the double helix in B-form, the form that genomic DNA exists in much of the time. Thus, artificial DNA seeking to mimic the properties of natural DNA should also be able to adopt B-form. Using a host-guest system in which Moloney murine leukemia virus reverse transcriptase serves as the host and DNA as the guests, we determined high-resolution crystal structures of three complexes including 5'-CTTBPPBBSSZZSAAG, 5'-CTTSSPBZPSZBBAAG and 5'-CTTZZPBSBSZPPAAG with 10 consecutive unnatural nucleobase pairs in B-form within self-complementary 16 bp duplex oligonucleotides. We refer to this ALternative Isoinformational ENgineered (ALIEN) genetic system containing two nucleobase pairs (P:Z, pairing 2-amino-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one with 6-amino-5-nitro-(1H)-pyridin-2-one, and B:S, 6-amino-4-hydroxy-5-(1H)-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one) as ALIEN DNA. We characterized both position- and sequence-specific helical, nucleobase pair and dinucleotide step parameters of P:Z and B:S pairs in the context of B-form DNA. We conclude that ALIEN DNA exhibits structural features that vary with sequence. Further, Z can participate in alternative stacking modes within a similar sequence context as captured in two different structures. This finding suggests that ALIEN DNA may have a larger repertoire of B-form structures than natural DNA. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Madhura S. Shukla
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, no. 7, Alachua, FL 32615, USA
| | - Millie M. Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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9
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Hoshika S, Shukla MS, Benner SA, Georgiadis MM. Visualizing "Alternative Isoinformational Engineered" DNA in A- and B-Forms at High Resolution. J Am Chem Soc 2022; 144:15603-15611. [PMID: 35969672 DOI: 10.1021/jacs.2c05255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A fundamental property of DNA built from four informational nucleotide units (GCAT) is its ability to adopt different helical forms within the context of the Watson-Crick pair. Well-characterized examples include A-, B-, and Z-DNA. For this study, we created an isoinformational biomimetic polymer, built (like standard DNA) from four informational "letters", but with the building blocks being artificial. This ALternative Isoinformational ENgineered (ALIEN) DNA was hypothesized to support two nucleobase pairs, the P:Z pair matching 2-amino-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one with 6-amino-3-5-nitro-1H-pyridin-2-one and the B:S pair matching 6-amino-4-hydroxy-5-1H-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one. We report two structures of ALIEN DNA duplexes at 1.2 Å resolution and a third at 1.65 Å. All of these are built from a single self-complementary sequence (5'-CTSZZPBSBSZPPBAG) that includes 12 consecutive ALIEN nucleotides. We characterized the helical, nucleobase pair, and dinucleotide step parameters of ALIEN DNA in these structures. In addition to showing that ALIEN pairs retain basic Watson-Crick pairing geometry, two of the ALIEN DNA structures are characterized as A-form DNA and one as B-form DNA. We identified parameters that map differences effecting the transition between the two helical forms; these same parameters distinguish helical forms of isoinformational natural DNA. Collectively, our analyses suggest that ALIEN DNA retains essential structural features of natural DNA, not only its information density and Watson-Crick pairing but also its ability to adopt two canonical forms.
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Madhura S Shukla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Steven A Benner
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
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10
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Georgiadis MM, Hoshika S, Benner SA. Structural properties of alien DNA, an alternative genetic system. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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11
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019; 59:663-668. [PMID: 31650689 DOI: 10.1002/anie.201909691] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six-letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six-letter DNA library to selectively bind liver cancer cells; and 2) in a six-letter self-assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer-nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer-targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Sai Wang
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.,Current address: College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xigao Chen
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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12
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Sai Wang
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
- Current address: College of Food Science and Engineering Ocean University of China Qingdao Shandong 266003 China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Xigao Chen
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Shuo Wan
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Long Li
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
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13
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Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J, Georgiadis MM, Benner SA. Hachimoji DNA and RNA: A genetic system with eight building blocks. Science 2019; 363:884-887. [PMID: 30792304 DOI: 10.1126/science.aat0971] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/25/2018] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
We report DNA- and RNA-like systems built from eight nucleotide "letters" (hence the name "hachimoji") that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. Three crystal structures show that the synthetic building blocks do not perturb the aperiodic crystal seen in the DNA double helix. Hachimoji DNA was then transcribed to give hachimoji RNA in the form of a functioning fluorescent hachimoji aptamer. These results expand the scope of molecular structures that might support life, including life throughout the cosmos.
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Affiliation(s)
- Shuichi Hoshika
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Nicole A Leal
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Myong-Jung Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA
| | - Nilesh B Karalkar
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA.,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA
| | - Alison M Bates
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | | | - Adam J Meyer
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78703, USA
| | - Saurja DasGupta
- Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, University of Texas, Austin, TX 78703, USA
| | | | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, FL 32615, USA. .,Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
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14
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Yang Z, Kim HJ, Le JT, McLendon C, Bradley KM, Kim MS, Hutter D, Hoshika S, Yaren O, Benner SA. Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection. Nucleic Acids Res 2019; 46:5902-5910. [PMID: 29800323 PMCID: PMC6159519 DOI: 10.1093/nar/gky392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/02/2018] [Indexed: 01/18/2023] Open
Abstract
Described here are the synthesis, enzymology and some applications of a purine nucleoside analog (H) designed to have two tautomeric forms, one complementary to thymidine (T), the other complementary to cytidine (C). The performance of H is compared by various metrics to performances of other 'biversal' analogs that similarly rely on tautomerism to complement both pyrimidines. These include (i) the thermodynamic stability of duplexes that pair these biversals with various standard nucleotides, (ii) the ability of the biversals to support polymerase chain reaction (PCR), (iii) the ability of primers containing biversals to equally amplify targets having polymorphisms in the primer binding site, and (iv) the ability of ligation-based assays to exploit the biversals to detect medically relevant single nucleotide polymorphisms (SNPs) in sequences flanked by medically irrelevant polymorphisms. One advantage of H over the widely used inosine 'universal base' and 'mixed sequence' probes is seen in ligation-based assays to detect SNPs. The need to detect medically relevant SNPs within ambiguous sequences is especially important when probing RNA viruses, which rapidly mutate to create drug resistance, but also suffer neutral drift, the second obstructing simple methods to detect the first. Thus, H is being developed to detect variants of viruses that are rapidly mutating.
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Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jennifer T Le
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Daniel Hutter
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
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15
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Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM. Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. Nucleic Acids Res 2019; 46:7977-7988. [PMID: 29986111 PMCID: PMC6125688 DOI: 10.1093/nar/gky552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/15/2018] [Indexed: 01/20/2023] Open
Abstract
The next challenge in synthetic biology is to be able to replicate synthetic nucleic acid sequences efficiently. The synthetic pair, 2-amino-8-(1-beta-d-2′- deoxyribofuranosyl) imidazo [1,2-a]-1,3,5-triazin-[8H]-4-one (trivially designated P) with 6-amino-3-(2′-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one (trivially designated Z), is replicated by certain Family A polymerases, albeit with lower efficiency. Through directed evolution, we identified a variant KlenTaq polymerase (M444V, P527A, D551E, E832V) that incorporates dZTP opposite P more efficiently than the wild-type enzyme. Here, we report two crystal structures of this variant KlenTaq, a post-incorporation complex that includes a template-primer with P:Z trapped in the active site (binary complex) and a pre-incorporation complex with dZTP paired to template P in the active site (ternary complex). In forming the ternary complex, the fingers domain exhibits a larger closure angle than in natural complexes but engages the template-primer and incoming dNTP through similar interactions. In the binary complex, although many of the interactions found in the natural complexes are retained, there is increased relative motion of the thumb domain. Collectively, our analyses suggest that it is the post-incorporation complex for unnatural substrates that presents a challenge to the natural enzyme and that more efficient replication of P:Z pairs requires a more flexible polymerase.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Roberto Laos
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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16
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Hoshika S, Singh I, Switzer C, Molt RW, Leal NA, Kim MJ, Kim MS, Kim HJ, Georgiadis MM, Benner SA. "Skinny" and "Fat" DNA: Two New Double Helices. J Am Chem Soc 2018; 140:11655-11660. [PMID: 30148365 DOI: 10.1021/jacs.8b05042] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
According to the iconic model, the Watson-Crick double helix exploits nucleobase pairs that are both size complementary (big purines pair with small pyrimidines) and hydrogen bond complementary (hydrogen bond donors pair with hydrogen bond acceptors). Using a synthetic biology strategy, we report here the discovery of two new DNA-like systems that appear to support molecular recognition with the same proficiency as standard Watson-Crick DNA. However, these both violate size complementarity (big pairs with small), retaining hydrogen bond complementarity (donors pair with acceptors) as their only specificity principle. They exclude mismatches as well as standard Watson-Crick DNA excludes mismatches. In crystal structures, these "skinny" and "fat" systems form the expected hydrogen bonds, while conferring novel minor groove properties to the resultant duplex regions of the DNA oligonucleotides. Further, computational tools, previously tested primarily on natural DNA, appear to work well for these two new molecular recognition systems, offering a validation of the power of modern computational biology. These new molecular recognition systems may have application in materials science and synthetic biology, and in developing our understanding of alternative ways that genetic information might be stored and transmitted.
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Boulevard, Box 7 , Alachua , Florida 32615 , United States
| | - Isha Singh
- Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana 46202 , United States
| | - Christopher Switzer
- Department of Chemistry , University of California , Riverside , California 92521 , United States
| | - Robert W Molt
- Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana 46202 , United States.,ENSCO, Inc. , 4849 North Wickham Road , Melbourne , Florida 32940 , United States
| | - Nicole A Leal
- Firebird Biomolecular Sciences LLC , 13709 Progress Boulevard, Box 17 , Alachua , Florida 32615 , United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Boulevard, Box 7 , Alachua , Florida 32615 , United States
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC , 13709 Progress Boulevard, Box 17 , Alachua , Florida 32615 , United States
| | - Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC , 13709 Progress Boulevard, Box 17 , Alachua , Florida 32615 , United States
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana 46202 , United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME) , 13709 Progress Boulevard, Box 7 , Alachua , Florida 32615 , United States.,Firebird Biomolecular Sciences LLC , 13709 Progress Boulevard, Box 17 , Alachua , Florida 32615 , United States
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17
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Singh I, Kim MJ, Molt RW, Hoshika S, Benner SA, Georgiadis MM. Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K). ACS Synth Biol 2017; 6:2118-2129. [PMID: 28752992 DOI: 10.1021/acssynbio.7b00150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson-Crick pair between imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-diaminopyrimidine (K) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. Here, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X:K pairs in GATCXK DNA determined as a host-guest complex at 1.75 Å resolution. X:K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X:K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X:K pairs locally and energetically more closely resemble A:T pairs.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Robert W. Molt
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, and the Westheimer Institute of Science & Technology, 13709 Progress Boulevard, Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Millie M. Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
- Department
of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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18
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Takahashi N, Sugaya H, Matsuki K, Miyauchi H, Matsumoto M, Tokai M, Onishi K, Hoshika S, Ueda Y. Hypertrophy of the extra-articular tendon of the long head of biceps correlates with the location and size of a rotator cuff tear. Bone Joint J 2017; 99-B:806-811. [DOI: 10.1302/0301-620x.99b6.bjj-2016-0885.r1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 01/30/2017] [Indexed: 12/19/2022]
Abstract
Aims The aim of this study was to assess hypertrophy of the extra-articular tendon of the long head of biceps (LHB) in patients with a rotator cuff tear. Patients and Methods The study involved 638 shoulders in 334 patients (175 men, 159 women, mean age 62.6 years; 25 to 81) with unilateral symptomatic rotator cuff tears. The cross-sectional area (CSA) of the LHB tendon in the bicipital groove was measured pre-operatively in both shoulders using ultrasound. There were 154 asymptomatic rotator cuff tears in the contralateral shoulder. Comparisons were made between those with a symptomatic tear, an asymptomatic tear and those with no rotator cuff tear. In the affected shoulders, the CSAs were compared in relation to the location and size of the rotator cuff tear. Results The mean CSA was 21.0 mm2 (4 to 71) in those with a symptomatic rotator cuff tear, 19.9 mm2 (4 to 75) in those with an asymptomatic rotator cuff tear and 14.1 mm2 (5 to 43) in those with no rotator cuff tear. The mean CSA in patients with both symptomatic and asymptomatic rotator cuff tears was significantly larger than in those with no rotator cuff tear (p < 0.001). In the affected shoulders, there were significant differences between patients with more than a medium sized posterosuperior cuff tear and those with an antero-superior cuff tear. Conclusion Regardless of the symptoms, there was significant hypertrophy of the extra-articular LHB tendon in patients with a rotator cuff tear. The values were significantly related to the size of the tear. Cite this article: Bone Joint J 2017;99-B:806–11.
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Affiliation(s)
- N. Takahashi
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - H. Sugaya
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - K. Matsuki
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - H. Miyauchi
- Funabashi Orthopaedic Hospital, 1-833
Hazama, Funabashi, 2740082, Japan
| | - M. Matsumoto
- Funabashi Orthopaedic Hospital, 1-833
Hazama, Funabashi, 2740082, Japan
| | - M. Tokai
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - K. Onishi
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - S. Hoshika
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
| | - Y. Ueda
- Funabashi Orthopaedic Hospital Sports Medicine & Joint Center, 1-833 Hazama, Funabashi, 2740082, Japan
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19
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Wang X, Hoshika S, Peterson RJ, Kim MJ, Benner SA, Kahn JD. Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P). ACS Synth Biol 2017; 6:782-792. [PMID: 28094993 DOI: 10.1021/acssynbio.6b00224] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthetic nucleobases presenting non-Watson-Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2'-deoxyriboside (presenting a {donor-donor-acceptor} hydrogen bonding pattern on the Watson-Crick face of the small component, trivially designated Z) and imidazo[1,2-a]-1,3,5-triazin-4(8H)one 2'-deoxyriboside (presenting an {acceptor-acceptor-donor} hydrogen bonding pattern on the large component, trivially designated P) is one of these extra pairs for which a substantial amount of molecular biology has been developed. Here, we report the results of UV absorbance melting measurements and determine the energetics of binding of DNA strands containing Z and P to give short duplexes containing Z:P pairs as well as various mismatches comprising Z and P. All measurements were done at 1 M NaCl in buffer (10 mM Na cacodylate, 0.5 mM EDTA, pH 7.0). Thermodynamic parameters (ΔH°, ΔS°, and ΔG°37) for oligonucleotide hybridization were extracted. Consistent with the Watson-Crick model that considers both geometric and hydrogen bonding complementarity, the Z:P pair was found to contribute more to duplex stability than any mismatches involving either nonstandard nucleotide. Further, the Z:P pair is more stable than a C:G pair. The Z:G pair was found to be the most stable mismatch, forming either a deprotonated mismatched pair or a wobble base pair analogous to the stable T:G mismatch. The C:P pair is less stable, perhaps analogous to the wobble pair observed for C:O6-methyl-G, in which the pyrimidine is displaced into the minor groove. The Z:A and T:P mismatches are much less stable. Parameters for predicting the thermodynamics of oligonucleotides containing Z and P bases are provided. This represents the first case where this has been done for a synthetic genetic system.
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Affiliation(s)
- Xiaoyu Wang
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Raymond J. Peterson
- Celadon Laboratories, 6525 Belcrest
Road, Hyattsville, Maryland 20782, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 17, Alachua, Florida 32615, United States
| | - Jason D. Kahn
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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20
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Benner SA, Karalkar NB, Hoshika S, Laos R, Shaw RW, Matsuura M, Fajardo D, Moussatche P. Alternative Watson-Crick Synthetic Genetic Systems. Cold Spring Harb Perspect Biol 2016; 8:a023770. [PMID: 27663774 PMCID: PMC5088529 DOI: 10.1101/cshperspect.a023770] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In its "grand challenge" format in chemistry, "synthesis" as an activity sets out a goal that is substantially beyond current theoretical and technological capabilities. In pursuit of this goal, scientists are forced across uncharted territory, where they must answer unscripted questions and solve unscripted problems, creating new theories and new technologies in ways that would not be created by hypothesis-directed research. Thus, synthesis drives discovery and paradigm changes in ways that analysis cannot. Described here are the products that have arisen so far through the pursuit of one grand challenge in synthetic biology: Recreate the genetics, catalysis, evolution, and adaptation that we value in life, but using genetic and catalytic biopolymers different from those that have been delivered to us by natural history on Earth. The outcomes in technology include new diagnostic tools that have helped personalize the care of hundreds of thousands of patients worldwide. In science, the effort has generated a fundamentally different view of DNA, RNA, and how they work.
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Affiliation(s)
- Steven A Benner
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Nilesh B Karalkar
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Shuichi Hoshika
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Roberto Laos
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Ryan W Shaw
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Mariko Matsuura
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Diego Fajardo
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
| | - Patricia Moussatche
- The Westheimer Institute for Science and Technology, The Foundation for Applied Molecular Evolution, Alachua, Florida 32615
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21
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Biondi E, Lane JD, Das D, Dasgupta S, Piccirilli JA, Hoshika S, Bradley KM, Krantz BA, Benner SA. Laboratory evolution of artificially expanded DNA gives redesignable aptamers that target the toxic form of anthrax protective antigen. Nucleic Acids Res 2016; 44:9565-9577. [PMID: 27701076 PMCID: PMC5175368 DOI: 10.1093/nar/gkw890] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 11/16/2022] Open
Abstract
Reported here is a laboratory in vitro evolution (LIVE) experiment based on an artificially expanded genetic information system (AEGIS). This experiment delivers the first example of an AEGIS aptamer that binds to an isolated protein target, the first whose structural contact with its target has been outlined and the first to inhibit biologically important activities of its target, the protective antigen from Bacillus anthracis. We show how rational design based on secondary structure predictions can also direct the use of AEGIS to improve the stability and binding of the aptamer to its target. The final aptamer has a dissociation constant of ∼35 nM. These results illustrate the value of AEGIS-LIVE for those seeking to obtain receptors and ligands without the complexities of medicinal chemistry, and also challenge the biophysical community to develop new tools to analyze the spectroscopic signatures of new DNA folds that will emerge in synthetic genetic systems replacing standard DNA and RNA as platforms for LIVE.
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Affiliation(s)
- Elisa Biondi
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Joshua D Lane
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Debasis Das
- School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA
| | - Saurja Dasgupta
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Joseph A Piccirilli
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Bryan A Krantz
- School of Dentistry, The University of Maryland, Baltimore, MD 21201, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA .,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
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22
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Yaren O, Glushakova LG, Bradley KM, Hoshika S, Benner SA. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus. J Virol Methods 2016; 236:54-61. [PMID: 27421627 PMCID: PMC5010982 DOI: 10.1016/j.jviromet.2016.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/17/2016] [Accepted: 07/12/2016] [Indexed: 11/21/2022]
Abstract
This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Lyudmyla G Glushakova
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615 USA; Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL 32615, USA.
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23
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Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angew Chem Int Ed Engl 2016; 55:12372-5. [PMID: 27601357 DOI: 10.1002/anie.201605058] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/01/2016] [Indexed: 01/11/2023]
Abstract
Laboratory in vitro evolution (LIVE) might deliver DNA aptamers that bind proteins expressed on the surface of cells. In this work, we used cell engineering to place glypican 3 (GPC3), a possible marker for liver cancer theranostics, on the surface of a liver cell line. Libraries were then built from a six-letter genetic alphabet containing the standard nucleobases and two added nucleobases (2-amino-8H-imidazo[1,2-a][1,3,5]triazin-4-one and 6-amino-5-nitropyridin-2-one), Watson-Crick complements from an artificially expanded genetic information system (AEGIS). With counterselection against non-engineered cells, eight AEGIS-containing aptamers were recovered. Five bound selectively to GPC3-overexpressing cells. This selection-counterselection scheme had acceptable statistics, notwithstanding the possibility that cells engineered to overexpress GPC3 might also express different off-target proteins. This is the first example of such a combination.
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Affiliation(s)
- Liqin Zhang
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Thu Le Trinh
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA
| | - I-Ting Teng
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Sai Wang
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Qunfeng Wu
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA
| | - Sena Cansiz
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Diane J Rowold
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Christopher McLendon
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Yuan Wu
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Cheng Cui
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Yuan Liu
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weijia Hou
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Kimberly Stewart
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA.
| | - Weihong Tan
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA. .,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China.
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24
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Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Liqin Zhang
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Thu Le Trinh
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - I-Ting Teng
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Sai Wang
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Qunfeng Wu
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - Sena Cansiz
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Diane J. Rowold
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Christopher McLendon
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Myong-Sang Kim
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Yuan Wu
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
| | - Cheng Cui
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Yuan Liu
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Weijia Hou
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Kimberly Stewart
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Shuo Wan
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Weihong Tan
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
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25
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Yaren O, Bradley KM, Moussatche P, Hoshika S, Yang Z, Zhu S, Karst SM, Benner SA. A norovirus detection architecture based on isothermal amplification and expanded genetic systems. J Virol Methods 2016; 237:64-71. [PMID: 27546345 DOI: 10.1016/j.jviromet.2016.08.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
Abstract
Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel.
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Affiliation(s)
- Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Patricia Moussatche
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA
| | - Shu Zhu
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville FL 32611, USA; The Emerging Pathogens Institute, University of Florida, Gainesville FL 32611, USA
| | - Stephanie M Karst
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville FL 32611, USA; The Emerging Pathogens Institute, University of Florida, Gainesville FL 32611, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA.
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26
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Winiger CB, Kim MJ, Hoshika S, Shaw RW, Moses JD, Matsuura MF, Gerloff DL, Benner SA. Polymerase Interactions with Wobble Mismatches in Synthetic Genetic Systems and Their Evolutionary Implications. Biochemistry 2016; 55:3847-50. [DOI: 10.1021/acs.biochem.6b00533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian B. Winiger
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Blvd., Box 17, Alachua, Florida 32615, United States
| | - Shuichi Hoshika
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Blvd., Box 17, Alachua, Florida 32615, United States
| | - Ryan W. Shaw
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Blvd., Box 17, Alachua, Florida 32615, United States
| | - Jennifer D. Moses
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Blvd., Box 17, Alachua, Florida 32615, United States
| | - Mariko F. Matsuura
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Dietlind L. Gerloff
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for
Applied Molecular Evolution (FfAME), 13709 Progress Blvd., Box 7, Alachua, Florida 32615, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Blvd., Box 17, Alachua, Florida 32615, United States
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27
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Matsuura MF, Shaw RW, Moses JD, Kim HJ, Kim MJ, Kim MS, Hoshika S, Karalkar N, Benner SA. Assays To Detect the Formation of Triphosphates of Unnatural Nucleotides: Application to Escherichia coli Nucleoside Diphosphate Kinase. ACS Synth Biol 2016; 5:234-40. [PMID: 26829203 DOI: 10.1021/acssynbio.5b00172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One frontier in synthetic biology seeks to move artificially expanded genetic information systems (AEGIS) into natural living cells and to arrange the metabolism of those cells to allow them to replicate plasmids built from these unnatural genetic systems. In addition to requiring polymerases that replicate AEGIS oligonucleotides, such cells require metabolic pathways that biosynthesize the triphosphates of AEGIS nucleosides, the substrates for those polymerases. Such pathways generally require nucleoside and nucleotide kinases to phosphorylate AEGIS nucleosides and nucleotides on the path to these triphosphates. Thus, constructing such pathways focuses on engineering natural nucleoside and nucleotide kinases, which often do not accept the unnatural AEGIS biosynthetic intermediates. This, in turn, requires assays that allow the enzyme engineer to follow the kinase reaction, assays that are easily confused by ATPase and other spurious activities that might arise through "site-directed damage" of the natural kinases being engineered. This article introduces three assays that can detect the formation of both natural and unnatural deoxyribonucleoside triphosphates, assessing their value as polymerase substrates at the same time as monitoring the progress of kinase engineering. Here, we focus on two complementary AEGIS nucleoside diphosphates, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one. These assays provide new ways to detect the formation of unnatural deoxyribonucleoside triphosphates in vitro and to confirm their incorporation into DNA. Thus, these assays can be used with other unnatural nucleotides.
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Affiliation(s)
- Mariko F. Matsuura
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
| | - Ryan W. Shaw
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Jennifer D. Moses
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Myong-Sang Kim
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Nilesh Karalkar
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box
17, Alachua, Florida 32615, United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
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28
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Glushakova LG, Sharma N, Hoshika S, Bradley AC, Bradley KM, Yang Z, Benner SA. Detecting respiratory viral RNA using expanded genetic alphabets and self-avoiding DNA. Anal Biochem 2015; 489:62-72. [PMID: 26299645 PMCID: PMC4733849 DOI: 10.1016/j.ab.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 08/07/2015] [Accepted: 08/13/2015] [Indexed: 11/23/2022]
Abstract
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround, they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems (AEGISs), which enable low-noise PCR. These are supplemented by “transliteration” technology, which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10 MERS virions in a 20-μl sample.
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Affiliation(s)
| | - Nidhi Sharma
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Andrea C Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA
| | - Steven A Benner
- Firebird Biomolecular Sciences, Alachua, FL 32615, USA; Foundation for Applied Molecular Evolution (FfAME), Alachua, FL 32615, USA.
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29
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Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim H, Kim M, Piccirilli JA, Benner SA. Inside Back Cover: A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair (Angew. Chem. Int. Ed. 34/2015). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201506280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Armando R. Hernandez
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Sandip A. Shelke
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Hyo‐Joong Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Myong‐Jung Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
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30
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Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA. Innenrücktitelbild: A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair (Angew. Chem. 34/2015). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA. A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair. Angew Chem Int Ed Engl 2015. [PMID: 26223188 DOI: 10.1002/anie.201504731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As one of its goals, synthetic biology seeks to increase the number of building blocks in nucleic acids. While efforts towards this goal are well advanced for DNA, they have hardly begun for RNA. Herein, we present a crystal structure for an RNA riboswitch where a stem C:G pair has been replaced by a pair between two components of an artificially expanded genetic-information system (AEGIS), Z and P, (6-amino-5-nitro-2(1H)-pyridone and 2-amino-imidazo[1,2-a]-1,3,5-triazin-4-(8H)-one). The structure shows that the Z:P pair does not greatly change the conformation of the RNA molecule nor the details of its interaction with a hypoxanthine ligand. This was confirmed in solution by in-line probing, which also measured a 3.7 nM affinity of the riboswitch for guanine. These data show that the Z:P pair mimics the natural Watson-Crick geometry in RNA in the first example of a crystal structure of an RNA molecule that contains an orthogonal added nucleobase pair.
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Affiliation(s)
- Armando R Hernandez
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA)
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Myong-Jung Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA)
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of Chicago, Chicago, IL 60637 (USA).
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL 32615 (USA).
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32
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Hernandez AR, Shao Y, Hoshika S, Yang Z, Shelke SA, Herrou J, Kim HJ, Kim MJ, Piccirilli JA, Benner SA. A Crystal Structure of a Functional RNA Molecule Containing an Artificial Nucleobase Pair. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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33
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Yang Z, McLendon C, Hutter D, Bradley KM, Hoshika S, Frye CB, Benner SA. Helicase-Dependent Isothermal Amplification of DNA and RNA by Using Self-Avoiding Molecular Recognition Systems. Chembiochem 2015; 16:1365-70. [PMID: 25953623 PMCID: PMC4489552 DOI: 10.1002/cbic.201500135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 11/06/2022]
Abstract
Assays that detect DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low-resource environments, and requires equipment and power that might not be available in these environments. Isothermal procedures, which avoid thermal cycling, are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a "self avoiding molecular recognition system" (SAMRS) eliminates these artifacts and gives clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3'-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, difficult to achieve with HDA using standard primers. Thus, SAMRS-HDA is a more versatile approach than standard HDA, with a broader applicability for xNA-targeted diagnostics and research.
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Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org.
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org
| | - Daniel Hutter
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, N112, Alachua, FL 32615 (USA)
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org
| | - Carole B Frye
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, N112, Alachua, FL 32615 (USA)
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601 (USA) http://ffame.org.
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, N112, Alachua, FL 32615 (USA).
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Zhang L, Yang Z, Sefah K, Bradley KM, Hoshika S, Kim MJ, Kim HJ, Zhu G, Jiménez E, Cansiz S, Teng IT, Champanhac C, McLendon C, Liu C, Zhang W, Gerloff DL, Huang Z, Tan W, Benner SA. Evolution of functional six-nucleotide DNA. J Am Chem Soc 2015; 137:6734-7. [PMID: 25966323 DOI: 10.1021/jacs.5b02251] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add functional groups not found in natural DNA, but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to pair via complete Watson-Crick geometry. These were added to a library of oligonucleotides used in a laboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Zs and Ps. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries.
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Affiliation(s)
- Liqin Zhang
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Zunyi Yang
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Kwame Sefah
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Kevin M Bradley
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Shuichi Hoshika
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Myong-Jung Kim
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Hyo-Joong Kim
- §Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
| | - Guizhi Zhu
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States.,∥Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Elizabeth Jiménez
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Sena Cansiz
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - I-Ting Teng
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Carole Champanhac
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Christopher McLendon
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Chen Liu
- ⊥Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida 32610, United States
| | - Wen Zhang
- #Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,∇SeNA Research, Inc., Atlanta, Georgia 30303, United States
| | - Dietlind L Gerloff
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States
| | - Zhen Huang
- #Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States.,∇SeNA Research, Inc., Atlanta, Georgia 30303, United States
| | - Weihong Tan
- †Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, Florida 32611, United States.,∥Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha 410082, China
| | - Steven A Benner
- ‡Foundation for Applied Molecular Evolution, Gainesville, Florida 32601, United States.,§Firebird Biomolecular Sciences LLC, Alachua, Florida 32615, United States
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35
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Georgiadis MM, Singh I, Kellett WF, Hoshika S, Benner SA, Richards NGJ. Structural basis for a six nucleotide genetic alphabet. J Am Chem Soc 2015; 137:6947-55. [PMID: 25961938 DOI: 10.1021/jacs.5b03482] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form. Another contained six consecutive Z:P pairs; it crystallized without a host in an A-form. In both structures, Z:P pairs fit canonical nucleobase hydrogen-bonding parameters and known DNA helical forms. Unique features include stacking of the nitro group on Z with the adjacent nucleobase ring in the A-form duplex. In both B- and A-duplexes, major groove widths for the Z:P pairs are approximately 1 Å wider than those of comparable G:C pairs, perhaps to accommodate the large nitro group on Z. Otherwise, ZP-rich DNA had many of the same properties as CG-rich DNA, a conclusion supported by circular dichroism studies in solution. The ability of standard duplexes to accommodate multiple and consecutive Z:P pairs is consistent with the ability of natural polymerases to biosynthesize those pairs. This, in turn, implies that the GACTZP synthetic genetic system can explore the entire expanded sequence space that additional nucleotides create, a major step forward in this area of synthetic biology.
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36
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Leal NA, Kim HJ, Hoshika S, Kim MJ, Carrigan MA, Benner SA. Transcription, reverse transcription, and analysis of RNA containing artificial genetic components. ACS Synth Biol 2015; 4:407-13. [PMID: 25137127 DOI: 10.1021/sb500268n] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the synthetic biology of artificially expanded genetic information systems (AEGIS) requires tools to make and analyze RNA molecules having added nucleotide "letters". We report here the development of T7 RNA polymerase and reverse transcriptase to catalyze transcription and reverse transcription of xNA (DNA or RNA) having two complementary AEGIS nucleobases, 6-amino-5-nitropyridin-2-one (trivially, Z) and 2-aminoimidazo[1,2a]-1,3,5-triazin-4(8H)-one (trivially, P). We also report MALDI mass spectrometry and HPLC-based analyses for oligomeric GACUZP six-letter RNA and the use of ribonuclease (RNase) A and T1 RNase as enzymatic tools for the sequence-specific degradation of GACUZP RNA. We then applied these tools to analyze the GACUZP and GACTZP products of polymerases and reverse transcriptases (respectively) made from DNA and RNA templates. In addition to advancing this 6-letter AEGIS toward the biosynthesis of proteins containing additional amino acids, these experiments provided new insights into the biophysics of DNA.
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Affiliation(s)
- Nicole A. Leal
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Hyo-Joong Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Shuichi Hoshika
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Myong-Jung Kim
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
| | - Matthew A. Carrigan
- Department
of Natural Sciences, Santa Fe College, 3000 NW 83rd Street L209, Gainesville, Florida 32606, United States
| | - Steven A. Benner
- Foundation
for
Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
- Firebird Biomolecular
Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, Florida 32615, United States
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Wang X, Sharp KK, Hoshika S, Bellaousov S, Zhang X, Mathews DH, Benner SA, Peterson RJ, Kahn JD. Structure and Thermodynamics of Aegis Nucleotides P and Z in DNA. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.2165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Sharma N, Hoshika S, Hutter D, Bradley KM, Benner SA. Recombinase-based isothermal amplification of nucleic acids with self-avoiding molecular recognition systems (SAMRS). Chembiochem 2014; 15:2268-74. [PMID: 25209570 PMCID: PMC7162014 DOI: 10.1002/cbic.201402250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/27/2022]
Abstract
Recombinase polymerase amplification (RPA) is an isothermal method to amplify nucleic acid sequences without the temperature cycling that classical PCR uses. Instead of using heat to denature the DNA duplex, RPA uses recombination enzymes to swap single-stranded primers into the duplex DNA product; these are then extended using a strand-displacing polymerase to complete the cycle. Because RPA runs at low temperatures, it never forces the system to recreate base-pairs following Watson-Crick rules, and therefore it produces undesired products that impede the amplification of the desired product, complicating downstream analysis. Herein, we show that most of these undesired side products can be avoided if the primers contain components of a self-avoiding molecular recognition system (SAMRS). Given the precision that is necessary in the recombination systems for them to function biologically, it is surprising that they accept SAMRS. SAMRS-RPA is expected to be a powerful tool within the range of amplification techniques available to scientists.
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Affiliation(s)
- Nidhi Sharma
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604 (USA)
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39
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Abstract
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Rearranging hydrogen bonding groups
adds nucleobases to an artificially
expanded genetic information system (AEGIS), pairing orthogonally
to standard nucleotides. We report here a large-scale synthesis of
the AEGIS nucleotide carrying 2-amino-3-nitropyridin-6-one (trivially
Z) via Heck coupling and a hydroboration/oxidation sequence.
RiboZ is more stable against epimerization than its 2′-deoxyribo
analogue. Further, T7 RNA polymerase incorporates ZTP opposite its
Watson–Crick complement, imidazo[1,2-a]-1,3,5-triazin-4(8H)one (trivially P), laying grounds for using this “second-generation”
AEGIS Z:P pair to add amino acids encoded by mRNA.
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Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution (FfAME), 720 SW Second Avenue, Suite 201, Gainesville, Florida 32601, United States
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Shibata S, Baratieri L, Vieria L, Fu J, Hoshika S, Matsuda Y, Sano H. Microtensile bond strength of self-etching adhesives on caries affected dentin and normal dentin. Dent Mater 2013. [DOI: 10.1016/j.dental.2013.08.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Applied Molecular Evolution, The Westheimer Institute for Science and Technology, 720 SW 2nd Avenue, Suite 201, Gainesville, FL 32601, USA
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Abstract
Reported here is a "Self-Avoiding Molecular Recognition Systems" (SAMRS), a species of DNA that can bind via simple rules to natural DNA but cannot bind to other members of the same SAMRS species. A system having these properties has been achieved with 2-aminopurine-2'-deoxyriboside (A*), 2'-deoxy-2-thiothymidine (T*), 2'-deoxyinosine (G*) and N4-ethyl-2'-deoxycytidine. These were designed to form more stable base pairs with natural complements than with SAMRS complements, based on the number of hydrogen bonds. Thermal melting studies were performed using duplexes containing SAMRS components. All SAMRS species, A*, T*, G* and C*, formed more stable base pairs with natural complements, T, A, C and G than with SAMRS complements, T*, A*, C* and G* respectively. This property of SAMRS would be useful for avoiding to be produced undesired products derived from intra- and intermolecular interaction between primers in multiplexed polymerase chain reactions.
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Affiliation(s)
- Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 1115 NW 4 Street, Gainesville, FL 32601, USA.
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Benner SA, Hoshika S, Sukeda M, Hutter D, Leal N, Yang Z, Chen F. Synthetic Biology for Improved Personalized Medicine. ACTA ACUST UNITED AC 2008:243-4. [DOI: 10.1093/nass/nrn123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Havemann SA, Hoshika S, Hutter D, Benner SA. Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure. Nucleosides Nucleotides Nucleic Acids 2008; 27:261-78. [PMID: 18260010 DOI: 10.1080/15257770701853679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Thermal denaturation and circular dichroism studies suggested that multiple (up to 12), sequential pseudothymidines, a representative C-glycoside, do not perturb the structure of a representative DNA duplex. Further, various Family A and B DNA polymerases were found to extend a primer by incorporating four sequential pseudothymidine triphosphates, and then continue the extension to generate full-length product. Detailed studies showed that Taq polymerase incorporated up to five sequential C-glycosides, but not more. These results constrain architectures for sequencing, quantitating, and analyzing DNA analogs that exploit C-glycosides, and define better the challenge of creating a synthetic biology using these with natural polymerases.
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Affiliation(s)
- Stephanie A Havemann
- Department of Microbiology & Cell Science, Space Life Sciences Laboratory, Kennedy Space Center, University of Florida, FL, USA
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Hoshika S, Minakawa N, Shionoya A, Imada K, Ogawa N, Matsuda A. Study of modification pattern-RNAi activity relationships by using siRNAs modified with 4'-thioribonucleosides. Chembiochem 2008; 8:2133-8. [PMID: 17924376 DOI: 10.1002/cbic.200700342] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A detailed study of the modification pattern-RNAi activity relationships by using siRNAs that are modified with 4'-thioribonucleosides has been carried out against photinus luciferase and renilla luciferase genes in cultured mammalian NIH/3T3, HeLa, and MIA PaCa-2 cell lines. When the photinus luciferase gene was targeted, all of the modified siRNAs showed activity equal to, or less than the unmodifed siRNA. In contrast, all modified siRNAs that have a similar modification pattern showed activity equal to or much higher than the unmodified siRNA when tested with the renilla luciferase gene. These results indicated that siRNAs such as RNA33 and RNA53, which each have four residues of the 4'-thioribonucleoside unit on both ends of the sense strand and four residues on the 3'-end of the antisense strand, were the most effective. Accordingly, we succeeded in developing modified siRNAs that have the greatest number of 4'-thioribonucleosides without loss of RNAi activity, and that exhibit potent RNAi activity against two target genes in three different cell lines. Our findings also indicate the significance of target sequences and cell lines when RNAi activity is compared with that of the unmodified siRNA.
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Affiliation(s)
- Shuichi Hoshika
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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Shuto S, Tamura Y, Yamamoto Y, Kodama T, Hoshika S, Ichikawa S, Ueno Y, Ohtsuka E, Komatsu Y, Matsuda A. Stable hairpins having a loop consisting of 3'-deoxy-4'-C-(2-hydroxyethyl)thymidines. ACTA ACUST UNITED AC 2007:67-8. [PMID: 17150481 DOI: 10.1093/nass/48.1.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A novel sugar-modified thymidine analogue, 3'-deoxy-4'-C-(2-hydroxyethyl)thymidine (X), was designed and synthesized to show that it can stabilize hairpin structures when it is present in the loop moiety, probably due to the flexibility of the one-carbon-elongated 4'-branched structure.
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Affiliation(s)
- Satoshi Shuto
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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48
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Abstract
Short interfering RNAs (siRNAs) variously modified with 4'-thioribonucleosides against the photinus luciferase gene and the renilla luciferase gene were tested for their induction of the RNA interference (RNAi) activity in cultured NIH/3T3 cells. Results indicated that modifications with 4'-thioribonucleosides on siRNA against the photinus luciferase were as potent as natural siRNA. On the other hand, modifications with 4'-thioribonucleosides on natural siRNA against the renilla luciferase improved their RNAi activity. These results suggest that 4'-thioribonucleosides might be potentially useful in the development of novel and effective chemically modified siRNAs.
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Affiliation(s)
- Shuichi Hoshika
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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Hoshika S, Minakawa N, Kamiya H, Harashima H, Matsuda A. RNA interference induced by siRNAs modified with 4'-thioribonucleosides in cultured mammalian cells. FEBS Lett 2005; 579:3115-8. [PMID: 15919084 DOI: 10.1016/j.febslet.2005.04.073] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 04/26/2005] [Accepted: 04/27/2005] [Indexed: 12/01/2022]
Abstract
Short interfering RNAs (siRNAs) variously modified with 4'-thioribonucleosides against the Photinus luciferase gene were tested for their induction of the RNA interference (RNAi) activity in cultured NIH/3T3 cells. Results indicated that modifications at the sense-strand were well tolerated for RNAi activity except for full modification with 4'-thioribonucleosides. However, the activity of siRNAs modified at the antisense-strand was dependent on the position and the number of modifications with 4'-thioribonucleosides. Since modifications of siRNAs with 4'-thioribonucleosides were well tolerated in RNAi activity compared with that of 2'-O-methyl nucleosides, 4'-thioribonucleosides might be potentially useful in the development of novel and effective chemically modified siRNAs.
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Affiliation(s)
- Shuichi Hoshika
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-Ku, Sapporo 060-0812, Japan
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Hoshika S, Ueno Y, Kamiya H, Matsuda A. Nucleosides and nucleotides. Part 226: alternate-strand triple-helix formation by 3'-3'-linked oligodeoxynucleotides composed of asymmetrical sequences. Bioorg Med Chem Lett 2005; 14:3333-6. [PMID: 15149701 DOI: 10.1016/j.bmcl.2004.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 03/18/2004] [Indexed: 10/26/2022]
Abstract
In this paper, we describe the synthesis of the 3'-3'-linked oligonucleotides connected with pentaerythritol composed of asymmetrical sequences. Stability of the triplexes between these oligonucleotides and the DNA targets involving the adjacent oligopurine domains on alternate strands was investigated using the electrophoretic mobility shift assay (EMSA) and DNase I footprinting experiment. It was found that the 3'-3'-linked oligonucleotides composed of asymmetrical sequences formed the stable antiparallel triplexes with the DNA targets as compared with the unlinked oligonucleotides. Thus, oligonucleotides linked with pentaerythritol would be useful as antigene oligonucleotides for DNA targets consisting of the alternating oligopyrimidine-oligopurine sequences.
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Affiliation(s)
- Shuichi Hoshika
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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