1
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Deal BR, Ma R, Narum S, Ogasawara H, Duan Y, Kindt JT, Salaita K. Heteromultivalency enables enhanced detection of nucleic acid mutations. Nat Chem 2024; 16:229-238. [PMID: 37884668 DOI: 10.1038/s41557-023-01345-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/15/2023] [Indexed: 10/28/2023]
Abstract
Detecting genetic mutations such as single nucleotide polymorphisms (SNPs) is necessary to prescribe effective cancer therapies, perform genetic analyses and distinguish similar viral strains. Traditionally, SNP sensing uses short oligonucleotide probes that differentially bind the SNP and wild-type targets. However, DNA hybridization-based techniques require precise tuning of the probe's binding affinity to manage the inherent trade-off between specificity and sensitivity. As conventional hybridization offers limited control over binding affinity, here we generate heteromultivalent DNA-functionalized particles and demonstrate optimized hybridization specificity for targets containing one or two mutations. By investigating the role of oligo lengths, spacer lengths and binding orientation, we reveal that heteromultivalent hybridization enables fine-tuned specificity for a single SNP and dramatic enhancements in specificity for two non-proximal SNPs empowered by highly cooperative binding. Capitalizing on these abilities, we demonstrate straightforward discrimination between heterozygous cis and trans mutations and between different strains of the SARS-CoV-2 virus. Our findings indicate that heteromultivalent hybridization offers substantial improvements over conventional monovalent hybridization-based methods.
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Affiliation(s)
- Brendan R Deal
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Steven Narum
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - James T Kindt
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
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2
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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3
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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs. Biophys J 2023; 122:3323-3339. [PMID: 37469144 PMCID: PMC10465710 DOI: 10.1016/j.bpj.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/21/2023] Open
Abstract
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, Chicago, Illinois
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, Chicago, Illinois; The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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4
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Ashwood B, Jones MS, Radakovic A, Khanna S, Lee Y, Sachleben JR, Szostak JW, Ferguson AL, Tokmakoff A. Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536266. [PMID: 37090657 PMCID: PMC10120721 DOI: 10.1101/2023.04.10.536266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Hybridization of short nucleic acid segments (<4 nucleotides) to single-strand templates occurs as a critical intermediate in processes such as non-enzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood due to experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential non-canonical base pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2 to 40 µs depending on the template and temperature. Dinucleotide hybridization and dehybridization involves a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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Affiliation(s)
- Brennan Ashwood
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
| | - Michael S Jones
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | | | - Smayan Khanna
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Yumin Lee
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Joseph R Sachleben
- Biomolecular NMR Core Facility, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, United States
| | - Jack W Szostak
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry, The University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637
- The James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, Illinois 60637, United States
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5
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Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess. Molecules 2022; 27:molecules27206831. [PMID: 36296424 PMCID: PMC9610079 DOI: 10.3390/molecules27206831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.
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6
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Kashida H, Nishikawa K, Shi W, Miyagawa T, Yamashita H, Abe M, Asanuma H. A helical amplification system composed of artificial nucleic acids. Chem Sci 2021; 12:1656-1660. [PMID: 34163925 PMCID: PMC8179025 DOI: 10.1039/d0sc05245k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Herein we report an amplification system of helical excess triggered by nucleic acid hybridization for the first time. It is usually impossible to prepare achiral nanostructures composed of nucleic acids because of their intrinsic chirality. We used serinol nucleic acid (SNA) oligomers for the preparation of achiral nanowires because SNA oligomers with symmetrical sequences are achiral. Nanowire formation was confirmed by atomic force microscopy and size exclusion chromatography. When a chiral nucleic acid with a sequence complementary to SNA was added to the nanostructure, helicity was induced and a strong circular dichroism signal was observed. The SNA nanowire could amplify the helicity of chiral nucleic acids through nucleobase stacks. The SNA nanostructures have potential for use as platforms to detect chiral biomolecules under aqueous conditions because SNA can be readily functionalized and is water-soluble. Herein we report an amplification system of helical excess triggered by nucleic acid hybridization for the first time.![]()
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Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Nishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Wenjing Shi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Toshiki Miyagawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University 1-3, Machikaneyama Toyonaka Osaka 560-8531 Japan
| | - Masayuki Abe
- Graduate School of Engineering Science, Osaka University 1-3, Machikaneyama Toyonaka Osaka 560-8531 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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7
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Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res 2020; 48:5147-5156. [PMID: 32282905 PMCID: PMC7229855 DOI: 10.1093/nar/gkaa207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.
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Affiliation(s)
- Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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8
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Li T, Wu X, Tao G, Yin H, Zhang J, Liu F, Li N. A simple and non-amplification platform for femtomolar DNA and microRNA detection by combining automatic gold nanoparticle enumeration with target-induced strand-displacement. Biosens Bioelectron 2018; 105:137-142. [DOI: 10.1016/j.bios.2018.01.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 12/11/2022]
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9
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Golyshev VM, Abramova TV, Pyshnyi DV, Lomzov AA. A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines. Biophys Chem 2018; 234:24-33. [PMID: 29407768 DOI: 10.1016/j.bpc.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/28/2017] [Accepted: 12/28/2017] [Indexed: 10/18/2022]
Abstract
The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.
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Affiliation(s)
- Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia.
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
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10
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Chen Z, Miao L, Liu Y, Dong T, Ma X, Guan X, Zhou G, Zou B. A universal genotyping–microarray constructed by ligating a universal fluorescence-probe with SNP-encoded flaps cleaved from multiplex invasive reactions. Chem Commun (Camb) 2017; 53:12922-12925. [PMID: 29152636 DOI: 10.1039/c7cc06649j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The universal chip and fluorescence probe enable genotyping multiple SNPs more labor-saving and cost-saving.
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Affiliation(s)
- Zhiyao Chen
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Liyan Miao
- Department of Clinical Pharmacology Research Lab
- The First Affiliated Hospital of Soochow University
- Suzhou 215006
- China
| | - Yunlong Liu
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Tianhui Dong
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Xueping Ma
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Xiaoxiang Guan
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Guohua Zhou
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
| | - Bingjie Zou
- Department of Pharmacology
- Jinling Hospital
- Medical School of Nanjing University
- Nanjing 210002
- China
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11
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Liu W, Zhu M, Liu H, Wei J, Zhou X, Xing D. Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants. Biosens Bioelectron 2016; 81:309-316. [PMID: 26985583 DOI: 10.1016/j.bios.2016.02.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/15/2016] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays.
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Affiliation(s)
- Weipeng Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Minjun Zhu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Hongxing Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Jitao Wei
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China.
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China.
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12
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Hofmann S, Huang Y, Paulicka P, Kappel A, Katus HA, Keller A, Meder B, Stähler CF, Gumbrecht W. Double-Stranded Ligation Assay for the Rapid Multiplex Quantification of MicroRNAs. Anal Chem 2015; 87:12104-11. [DOI: 10.1021/acs.analchem.5b02850] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stefan Hofmann
- Department
of Bioinformatics, University of Würzburg, Würzburg, 97074, Germany
| | - Yiwei Huang
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Peter Paulicka
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Andreas Kappel
- Technology Center,
Siemens Healthcare, Erlangen, 91058, Germany
| | - Hugo A. Katus
- Internal
Medicine III, University Hospital Heidelberg, Heidelberg, 69120, Germany
| | - Andreas Keller
- Clinical
Bioinformatics, Medical Faculty, Saarland University, Saarbrücken, 66123, Germany
| | - Benjamin Meder
- Internal
Medicine III, University Hospital Heidelberg, Heidelberg, 69120, Germany
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13
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McGinley JT, Wang Y, Jenkins IC, Sinno T, Crocker JC. Crystal-Templated Colloidal Clusters Exhibit Directional DNA Interactions. ACS NANO 2015; 9:10817-10825. [PMID: 26439813 DOI: 10.1021/acsnano.5b03272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Spherical colloids covered with grafted DNA have been used in the directed self-assembly of a number of distinct crystal and gel structures. Simulation suggests that the use of anisotropic building blocks greatly augments the variety of potential colloidal assemblies that can be formed. Here, we form five distinct symmetries of colloidal clusters from DNA-functionalized spheres using a single type of colloidal crystal as a template. The crystals are formed by simple sedimentation of a binary mixture containing a majority "host" species that forms close-packed crystals with the minority "impurity" species occupying substitutional or interstitial defect sites. After the DNA strands between the two species are hybridized and enzymatically ligated, the results are colloidal clusters, one for each impurity particle, with a symmetry determined by the nearest neighbors in the original crystal template. By adjusting the size ratio of the two spheres and the timing of the ligation, we are able to generate clusters having the symmetry of tetrahedra, octahedra, cuboctahedra, triangular orthobicupola, and icosahedra, which can be readily separated from defective clusters and leftover spheres by centrifugation. We further demonstrate that these clusters, which are uniformly covered in DNA strands, display directional binding with spheres bearing complementary DNA strands, acting in a manner similar to patchy particles or proteins having multiple binding sites. The scalable nature of the fabrication process, along with the reprogrammability and directional nature of their resulting DNA interactions, makes these clusters suitable building blocks for use in further rounds of directed self-assembly.
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Affiliation(s)
- James T McGinley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Yifan Wang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Ian C Jenkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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14
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Dannenberg F, Dunn KE, Bath J, Kwiatkowska M, Turberfield AJ, Ouldridge TE. Modelling DNA origami self-assembly at the domain level. J Chem Phys 2015; 143:165102. [DOI: 10.1063/1.4933426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frits Dannenberg
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom
| | - Katherine E. Dunn
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
- Department of Electronics, University of York, York YO10 5DD, United Kingdom
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Marta Kwiatkowska
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom
| | - Andrew J. Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas E. Ouldridge
- Department of Physics, University of Oxford, Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
- Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ, United Kingdom
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15
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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16
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Wang J, Lu J, Su S, Gao J, Huang Q, Wang L, Huang W, Zuo X. Binding-induced collapse of DNA nano-assembly for naked-eye detection of ATP with plasmonic gold nanoparticles. Biosens Bioelectron 2014; 65:171-5. [PMID: 25461154 DOI: 10.1016/j.bios.2014.10.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/06/2014] [Accepted: 10/13/2014] [Indexed: 11/20/2022]
Abstract
The detection of small molecules depends heavily on complicated GC-MS (Gas chromatography-mass spectrometry), HPLC (High-performance liquid chromatography) and some other complicated instruments that are not suitable for point of care detection. Here, we have demonstrated a fast (in 10min), simple (instrument-free) and effective detection platform for small molecule-ATP. In our design, we engineered the hybridization region of aptamer and assembled it into a superstructure to avoid the exposed flexible ends. The binding of ATP triggered the collapse of the superstructures to produce single stranded DNA that can obviously tune the plasmonic coupling of unmodified gold nanoparticles (AuNPs). Compared to detection platforms based on fully hybridized aptamer double helix, the detection time was significantly decreased to 10min. The resulting color change can be recognized by naked eyes. Our detection is highly specific and selective. Furthermore, a logic gate with multiplexed detection capability for ATP and DNA were demonstrated.
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Affiliation(s)
- Jingjing Wang
- School of Medical Lab Science and Life Science, Wenzhou Medical University, Wenzhou 325035, China; Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jianxin Lu
- School of Medical Lab Science and Life Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing, China
| | - Jimin Gao
- School of Medical Lab Science and Life Science, Wenzhou Medical University, Wenzhou 325035, China.
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing, China
| | - Wei Huang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
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17
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Yu CY, Yin BC, Ye BC. A universal real-time PCR assay for rapid quantification of microRNAs via the enhancement of base-stacking hybridization. Chem Commun (Camb) 2014; 49:8247-9. [PMID: 23925039 DOI: 10.1039/c3cc44125c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Via the base-stacking hybridization strategy, we have developed a universal, one-step real-time quantitative PCR assay for sensitive and selective detection of microRNAs. This proposed assay has several intrinsic features including rapid response, low cost, simple handling procedures, etc.
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Affiliation(s)
- Cui-Yuan Yu
- Lab of Biosystem and Microanalysis, East China University of Science & Technology, Shanghai 200237, PR China
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18
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Liu W, Zhou X, Xing D. Rapid and reliable microRNA detection by stacking hybridization on electrochemiluminescent chip system. Biosens Bioelectron 2014; 58:388-94. [PMID: 24705177 DOI: 10.1016/j.bios.2014.02.082] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/12/2014] [Accepted: 02/24/2014] [Indexed: 01/09/2023]
Abstract
MicroRNAs play pivotal roles in many fundamental aspects of life. Because microRNAs have the characteristics of small size, similar sequence, and low abundance, it is challenging to identify microRNAs rapidly and specifically with high sensitivity. Herein, we developed an electrochemiluminescent (ECL) chip system for microRNA detection based on base-stacking hybridization and magnetic microparticle enrichment technology. In the designed system, the integration of the microfluidic system with ECL detection made it easy to assemble the multiple assay steps and allowed the construction of a device that is convenient to carry. A limit of detection of 1fmol was achieved with this assay. The proposed direct optical microRNA detection technique demonstrated an acceptable sensitivity combined with the advantages of reliability and rapidity.
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Affiliation(s)
- Weipeng Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Xiaoming Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
| | - Da Xing
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China.
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19
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Valentini P, Fiammengo R, Sabella S, Gariboldi M, Maiorano G, Cingolani R, Pompa PP. Gold-nanoparticle-based colorimetric discrimination of cancer-related point mutations with picomolar sensitivity. ACS NANO 2013; 7:5530-8. [PMID: 23697628 DOI: 10.1021/nn401757w] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Point mutations in the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene are being increasingly recognized as important diagnostic and prognostic markers in cancer. In this work, we describe a rapid and low-cost method for the naked-eye detection of cancer-related point mutations in KRAS based on gold nanoparticles. This simple colorimetric assay is sensitive (limit of detection in the low picomolar range), instrument-free, and employs nonstringent room temperature conditions due to a combination of DNA-conjugated gold nanoparticles, a probe design which exploits cooperative hybridization for increased binding affinity, and signal enhancement on the surface of magnetic beads. Additionally, the scheme is suitable for point-of-care applications, as it combines naked-eye detection, small sample volumes, and isothermal (PCR-free) amplification.
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Affiliation(s)
- Paola Valentini
- Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano (Lecce), Italy
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20
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Howell C, Hamoudi H, Zharnikov M. Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study. Biointerphases 2013; 8:6. [PMID: 24706119 DOI: 10.1186/1559-4106-8-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 02/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The establishment of spectroscopic analysis techniques for complex, surface-bound biological systems is an important step toward the further application of these powerful experimental tools to new questions in biology and medicine. METHODS We use a combination of the complementary spectroscopic techniques of X-ray photoelectron spectroscopy, Infrared reflection-absorption spectroscopy, and near-edge x-ray absorption fine structure spectroscopy to monitor the composition and molecular orientation in adenine/thymine diblock oligonucleotide films and their hybridized brushes on gold. RESULTS We demonstrate that the surface-bound probe molecules, consisting of a binding adenine block, d(A), and a sensing thymine block, d(T), deviate from the ideal L-shape model due to the internal intra- and intermolecular hybridization. This effect becomes more pronounced with increasing length of the d(A) block. Nevertheless, these films were found to hybridize well with the complementary target d(A) strands, especially if they were treated in advance to reduce internal interaction between the molecules. In spite of the structural complexity of these films, the hybridization efficiency correlated well with the potential accessibility of the sensing d(T) blocks, defined by their lateral spacing. CONCLUSIONS These findings are a good demonstration of the strength of multi-technique spectroscopic analysis when applied to assemblies of biological molecules intrinsically prone to complex interactions.
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Affiliation(s)
- Caitlin Howell
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany,
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21
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Chang CC, Wei SC, Wu TH, Lee CH, Lin CW. Aptamer-based colorimetric detection of platelet-derived growth factor using unmodified gold nanoparticles. Biosens Bioelectron 2012. [PMID: 23202340 DOI: 10.1016/j.bios.2012.10.072] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We developed a simple method for the detection of platelet-derived growth factors (PDGFs) based on base stacking effect coupled with an unmodified gold nanoparticle (AuNP) indicator. In the absence of a target, an aptamer probe and a capture probe stably co-exist in a solution, as it is difficult to sustain an interaction between both these probes due to the short 8bp duplex. However, when a target protein binds to the aptamer probe, the strong base stacking effect can lead to a favorable and stable interaction between the aptamer and capture probes. Hence, the capture probe dissociates from the AuNP surfaces, inducing AuNP aggregation. Compared with other AuNP-based aptasensors for PDGFs, using this base stacking effect can overcome a structured-aptamer method's limitation of requiring thiolated-aptamer-modified AuNPs. Under optimal detection conditions, this label-free colorimetric sensor could detect PDGFs down to 6nM with high selectivity in the presence of other interferring proteins. This simple detection approach provides viable methods for a structured-aptamer sensing protocol.
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Affiliation(s)
- Chia-Chen Chang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan
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22
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Bichenkova EV, Lang Z, Yu X, Rogert C, Douglas KT. DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:1-23. [PMID: 21111076 DOI: 10.1016/j.bbagrm.2010.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/07/2010] [Accepted: 11/12/2010] [Indexed: 11/25/2022]
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23
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Halpern MD, Ballantyne J. An STR Melt Curve Genotyping Assay for Forensic Analysis Employing an Intercalating Dye Probe FRET*. J Forensic Sci 2010; 56:36-45. [DOI: 10.1111/j.1556-4029.2010.01549.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Lymperopoulos K, Crawford R, Torella JP, Heilemann M, Hwang LC, Holden SJ, Kapanidis AN. Single-molecule DNA biosensors for protein and ligand detection. Angew Chem Int Ed Engl 2010; 49:1316-20. [PMID: 20077444 DOI: 10.1002/anie.200904597] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Konstantinos Lymperopoulos
- Biological Physics Research Group, Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, United Kingdom
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25
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Lymperopoulos K, Crawford R, Torella J, Heilemann M, Hwang L, Holden S, Kapanidis A. Einzelmolekül-DNA-Biosensoren zur Detektion von Proteinen und Liganden. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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A single nucleotide polymorphism melt curve assay employing an intercalating dye probe fluorescence resonance energy transfer for forensic analysis. Anal Biochem 2009; 391:1-10. [DOI: 10.1016/j.ab.2009.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 04/30/2009] [Accepted: 05/02/2009] [Indexed: 11/20/2022]
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27
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Wang A, Zocchi G. Elastic energy driven polymerization. Biophys J 2009; 96:2344-52. [PMID: 19289060 DOI: 10.1016/j.bpj.2008.11.065] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 09/11/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022] Open
Abstract
We present a molecular system where polymerization is controlled externally by tuning the elastic energy of the monomers. The elastic energy, provided by a DNA molecular spring, destabilizes the monomer state through a process analogous to domain swapping. This energy can be large (of approximately 10 kT) and thus drive polymerization at relatively low monomer concentrations. The monomer-dimer equilibrium provides a measurement of the elastic energy of the monomer, which in this construction appears limited by kink formation in the DNA molecular spring, in accord with previous theoretical and experimental investigations of the elasticity of sharply bent DNA.
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Affiliation(s)
- Andrew Wang
- Department of Physics & Astronomy, University of California, Los Angeles, California, USA
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28
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Pöhlmann C, Wang Y, Humenik M, Heidenreich B, Gareis M, Sprinzl M. Rapid, specific and sensitive electrochemical detection of foodborne bacteria. Biosens Bioelectron 2009; 24:2766-71. [PMID: 19278848 DOI: 10.1016/j.bios.2009.01.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/22/2009] [Accepted: 01/28/2009] [Indexed: 10/21/2022]
Abstract
Electrochemical biochips are an emerging tool for point-of-care diagnostic systems in medicine, food and environmental monitoring. In the current study, a thermostable reporter enzyme, esterase 2 (EST2) from Alicyclobacillus acidocaldarius, is used for specific and sensitive detection of bacteria by one-step rRNA/DNA hybridization between a bacterium-specific capture oligodeoxynucleotide (ODN), bacterial 16S rRNA and an uniform EST2-ODN reporter conjugate. The detection limit corresponds to approximately 500 colony forming units (cfu) Escherichia coli. Beside high sensitivity, the application of electrochemical biochips allows discrimination of two gram-negative and two gram-positive bacteria demonstrating the specificity and the potential for parallel detection of microorganisms. The feasibility of identification of foodborne bacteria was studied with meat juice contaminated with E. coli. This detection system has the capability to be applied for monitoring of bacterial food contamination.
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Affiliation(s)
- Christopher Pöhlmann
- Laboratorium für Biochemie, Universität Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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29
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Quantification of microRNAs, splicing isoforms, and homologous mRNAs with the invader assay. Methods Mol Biol 2009; 488:279-318. [PMID: 18982299 DOI: 10.1007/978-1-60327-475-3_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The understanding of physiology and pathology requires accurate quantification of intracellular concentrations of important molecules such as unique RNA species. Accurate quantification of highly homologous messenger RNAs (mRNAs) (1-3), alternatively spliced mRNAs (4), and the short microRNAs (miRNAs) (5,6) has been successfully achieved using the Invader assay. This method directly detects specific RNA molecules in preparations of pure total cellular RNA (1- 100 ng) or in crude cell lysate (10(3)-10(4) cells) samples using an isothermal signal amplification process with a fluorescence resonance energy transfer (FRET)-based fluorescence readout. Features of the Invader assay include the ability to detect 1-10 RNA molecules per cell, to discriminate between RNAs that differ by a single base, and to precisely measure 1.2-fold changes in RNA expression. Further, an isothermal format and the ability to detect two different RNA molecules with a biplex format make the Invader assay suitable for high-throughput screening applications.
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30
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Lucarelli F, Capponcelli S, Marrazza G, Sangiorgi L, Mascini M. Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms. Analyst 2008; 134:52-9. [PMID: 19082174 DOI: 10.1039/b806514d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.
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Affiliation(s)
- Fausto Lucarelli
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto F.no, Florence, Italy
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31
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Lutay AV, Grigoriev IV, Zenkova MA, Chernolovskaya EL, Vlassov VV. Nonenzymatic recombination of RNA by means of transesterification. Russ Chem Bull 2008. [DOI: 10.1007/s11172-007-0398-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Tanaka A, Matsuo Y, Niikura K, Ijiro K. Stabilization of DNA Multiassembly by Addition of a Phosphate Group at the 5′-Sticky End. CHEM LETT 2008. [DOI: 10.1246/cl.2008.758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Walsh L, Gbaj A, Etchells LL, Douglas KT, Bichenkova EV. SNP detection for cytochrome P450 alleles by target-assembled tandem oligonucleotide systems based on exciplexes. J Biomol Struct Dyn 2008; 25:629-40. [PMID: 18399696 DOI: 10.1080/07391102.2008.10507209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We report the first use of exciplex-based split-probes for detection of the wild type and *3 mutant alleles of human cytochrome P450 2C9. A tandem 8-mer split DNA oligonucleotide probe system was designed that allows detection of the complementary target DNA sequence. This exciplex-based fluorescence detector system operates by means of a contiguous hybridization of two oligonucleotide exciplex split-probes to a complementary target nucleic acid target. Each probe oligonucleotide is chemically modified at one of its termini by a potential exciplex-forming partner, each of which is fluorescently silent at the wavelength of detection. Under conditions that ensure correct three-dimensional assembly, the chemical moieties on suitable photoexcitation form an exciplex that fluoresces with a large Stokes shift (in this case 130 nm). Preliminary proof-of-concept studies used two 8-mer probe oligonucleotides, but in order to give better specificity for genomic applications, probe length was extended to give coverage of 24 bases. Eight pairs of tandem 12-mer oligonucleotide probes spanning the 2C9*3 region were designed and tested to find the best set of probes. Target sequences tested were in the form of (i) synthetic oligonucleotides, (ii) embedded in short PCR products (150 bp), or (iii) inserted into plasmid DNA (approximately 3 Kbp). The exciplex system was able to differentiate wild type and human cytochrome P450 2C9 *3 SNP (1075 A-->C) alleles, based on fluorescence emission spectra and DNA melting curves, indicating promise for future applications in genetic testing and molecular diagnostics.
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Affiliation(s)
- Lindsey Walsh
- Wolfson Center for Rational Structure-Based Design of Molecular Diagnostics, School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester, M13 9PL, U.K
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34
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Bettazzi F, Lucarelli F, Palchetti I, Berti F, Marrazza G, Mascini M. Disposable electrochemical DNA-array for PCR amplified detection of hazelnut allergens in foodstuffs. Anal Chim Acta 2008; 614:93-102. [PMID: 18405686 DOI: 10.1016/j.aca.2008.03.027] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Revised: 03/05/2008] [Accepted: 03/07/2008] [Indexed: 11/28/2022]
Abstract
An electrochemical low-density DNA-array has been designed and implemented to be used in combination with polymerase chain reaction (PCR) in order to investigate the presence of hazelnut major allergens (Cor a 1.04, Cor a 1.03) in foodstuff. Unmodified PCR products were captured at the sensor interface via sandwich hybridization with surface-tethered probes and biotinylated signalling probes. The resulting biotinylated hybrids were coupled with a streptavidin-alkaline phosphatase conjugate and then exposed to a alpha-naphthyl phosphate solution. Differential pulse voltammetry was finally used to detect the alpha-naphthol signal. The detection limits for Cor a 1.03 and Cor a 1.04 were 0.3 and 0.1 nmol L(-1), respectively (R.S.D. 10%). The optimized conditions were used to test several commercially available foodstuffs, claiming to contain or not the targeted nuts. The results were compared with those obtained with classical ELISA tests.
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Affiliation(s)
- Francesca Bettazzi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
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35
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Improved sandwich-hybridization assay for an electrical DNA-chip-based monitoring of bioprocess-relevant marker genes. Appl Microbiol Biotechnol 2008; 78:719-28. [DOI: 10.1007/s00253-008-1347-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 12/22/2007] [Accepted: 12/30/2007] [Indexed: 10/22/2022]
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36
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Channel Glass-based Detection of Human Short Insertion/Deletion Polymorphisms by Tandem Hybridization. Mol Biotechnol 2007; 38:145-53. [DOI: 10.1007/s12033-007-9004-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 09/05/2007] [Indexed: 10/23/2022]
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37
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Meijer HA, Bushell M, Hill K, Gant TW, Willis AE, Jones P, de Moor CH. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res 2007; 35:e132. [PMID: 17933768 PMCID: PMC2095794 DOI: 10.1093/nar/gkm830] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The length of the poly(A) tail of an mRNA plays an important role in translational efficiency, mRNA stability and mRNA degradation. Regulated polyadenylation and deadenylation of specific mRNAs is involved in oogenesis, embryonic development, spermatogenesis, cell cycle progression and synaptic plasticity. Here we report a new technique to analyse the length of poly(A) tails and to separate a mixed population of mRNAs into fractions dependent on the length of their poly(A) tails. The method can be performed on crude lysate or total RNA, is fast, highly reproducible and minor changes in poly(A) tail length distribution are easily detected. We validated the method by analysing mRNAs known to undergo cytoplasmic polyadenylation during Xenopus laevis oocyte maturation. We then separated RNA from NIH3T3 cells into two fractions with short and long poly(A) tails and compared them by microarray analysis. In combination with the validation experiments, the results indicate that ∼25% of the expressed genes have a poly(A) tail of less than 30 residues in a significant percentage of their transcripts.
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Affiliation(s)
- Hedda A Meijer
- RNA Biology Group, Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham, UK
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Carter DJ, Cary RB. Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography. Nucleic Acids Res 2007; 35:e74. [PMID: 17478499 PMCID: PMC1904290 DOI: 10.1093/nar/gkm269] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on a miniaturized lateral flow device that makes use of hybridization-mediated target capture. The miniaturization of lateral flow nucleic acid detection provides multiple advantages over traditional lateral flow devices. Ten-microliter sample volumes reduce reagent consumption and yield analyte detection times, excluding sample preparation and amplification, of <120 s while providing sub-femtomole sensitivity. Moreover, the use of microarray technology increases the potential information capacity of lateral flow. Coupled with a hybridization-based detection scheme, the lateral flow microarray (LFM) enables sequence-specific detection, opening the door to highly multiplexed implementations for broad-range assays well suited for point-of-care and other field applications. The LFM system is demonstrated using an isothermal amplification strategy for detection of Bacillus anthracis, the etiologic agent of anthrax. RNA from as few as two B. anthracis cells was detected without thermocycling hardware or fluorescence detection systems.
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Affiliation(s)
| | - R. Bruce Cary
- *To whom correspondence should be addressed. Tel: 505 665 6874; Fax: 505 665 3024;
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39
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Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006; 34:564-74. [PMID: 16449200 PMCID: PMC1360284 DOI: 10.1093/nar/gkj454] [Citation(s) in RCA: 615] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the first time, DNA stacking parameters are obtained directly (without extrapolation) for temperatures from below room temperature to close to melting temperature. We also obtain DNA stacking parameters for different salt concentrations ranging from 15 to 100 mM Na+. From stacking parameters of individual contacts, we calculate base-stacking contribution to the stability of A•T- and G•C-containing DNA polymers. We find that temperature and salt dependences of the stacking term fully determine the temperature and the salt dependence of DNA stability parameters. For all temperatures and salt concentrations employed in present study, base-stacking is the main stabilizing factor in the DNA double helix. A•T pairing is always destabilizing and G•C pairing contributes almost no stabilization. Base-stacking interaction dominates not only in the duplex overall stability but also significantly contributes into the dependence of the duplex stability on its sequence.
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40
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Kitamura Y, Ihara T, Okada K, Tsujimura Y, Shirasaka Y, Tazaki M, Jyo A. Asymmetric cooperativity in tandem hybridization of enantiomeric metal complex-tethered short fluorescent DNA probes. Chem Commun (Camb) 2005:4523-5. [PMID: 16158101 DOI: 10.1039/b505632b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex [Ru(phen)(2)(dppz)](2+)(phen = 1,10-phenanthroline, dppz = dipyrido[3,2-aratio2',3'-c]phenazine) was attached to the 5' end of a short oligonucleotide to form conjugates, the Delta-isomer of which showed a high cooperativity during the recognition of the repetitive sequence, while the Lambda-isomer did not.
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Affiliation(s)
- Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
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41
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Abstract
Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623–631] is added to the 5′-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3′-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5′- and 3′-terminal OH ends and other oligonucleotides with 5′-phosphorylated and 3′-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.
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Affiliation(s)
- Richard T Pon
- Department of Biochemistry and Molecular Biology, University of Calgary Calgary, AB, Canada T2N 4N1.
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42
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Murphy D, Redmond G. Optical detection and discrimination of cystic fibrosis-related genetic mutations using oligonucleotide-nanoparticle conjugates. Anal Bioanal Chem 2005; 381:1122-9. [PMID: 15744517 DOI: 10.1007/s00216-004-3030-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2004] [Revised: 10/14/2004] [Accepted: 12/16/2004] [Indexed: 11/30/2022]
Abstract
Novel methods for application of oligonucleotide-gold nanoparticle conjugates to selective colorimetric detection and discrimination of cystic fibrosis (CF) related genetic mutations in model oligonucleotide systems are presented. Three-strand oligonucleotide complexes are employed, wherein two probe oligonucleotide-gold nanoparticle conjugates are linked together by a third target oligonucleotide strand bearing the CF-related mutation(s). By monitoring the temperature dependence of the optical properties of the complexes, either in solution or on silica gel plates, melting behaviors may be accurately and reproducibly compared. Using this approach, fully complementary sequences are successfully distinguished from mismatched sequences, with single base mismatch resolution, for Delta F 508, M470V, R74W and R75Q mutations.
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Affiliation(s)
- Deirdre Murphy
- Nanotechnology Group, Tyndall National Institute, Lee Maltings, Cork, Ireland
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43
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Murphy D, Doyle H, Eritja R, Redmond G. Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study. J Biomol Struct Dyn 2005; 22:195-204. [PMID: 15317480 DOI: 10.1080/07391102.2004.10506995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches is monitored using temperature-dependent optical absorption spectroscopy. A sequential three-state equilibrium model is used to analyze the measured melting profiles and evaluate thermodynamic parameters associated with dissociation of the complexes. The free-energy of stabilization of a nick complex compared to a gap complex due to base stacking is determined to be -1.9 kcal/mol. The influence of a mispaired base in these systems is shown to destabilize a nick complex by 3.1 kcal/mol and a gap complex by 2.8 kcal/mol, respectively.
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Affiliation(s)
- Dierdre Murphy
- Nanotechnology Group, NMRC, Lee Maltings, Prospect Row, Cork, Ireland
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44
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Sarkar T, Conwell CC, Harvey LC, Santai CT, Hud NV. Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery. Nucleic Acids Res 2005; 33:143-51. [PMID: 15640449 PMCID: PMC546144 DOI: 10.1093/nar/gki156] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The condensation of nucleic acids into well-defined particles is an integral part of several approaches to artificial cellular delivery. Improvements in the efficiency of nucleic acid delivery in vivo are important for the development of DNA- and RNA-based therapeutics. Presently, most efforts to improve the condensation and delivery of nucleic acids have focused on the synthesis of novel condensing agents. However, short oligonucleotides are not as easy to condense into well-defined particles as gene-length DNA polymers and present particular challenges for discrete particle formation. We describe a novel strategy for improving the condensation and packaging of oligonucleotides that is based on the self-organization of half-sliding complementary oligonucleotides into long duplexes (ca. 2 kb). These non-covalent assemblies possess single-stranded nicks or single-stranded gaps at regular intervals along the duplex backbones. The condensation behavior of nicked- and gapped-DNA duplexes was investigated using several cationic condensing agents. Transmission electron microscopy and light-scattering studies reveal that these DNA duplexes condense much more readily than short duplex oligonucleotides (i.e. 21 bp), and more easily than a 3 kb plasmid DNA. The polymeric condensing agents, poly-l-lysine and polyethylenimine, form condensates with nicked- and gapped-DNA that are significantly smaller than condensates formed by the 3 kb plasmid DNA. These results demonstrate the ability for DNA structure and topology to alter nucleic acid condensation and suggest the potential for the use of this form of DNA in the design of vectors for oligonucleotide and gene delivery. The results presented here also provide new insights into the role of DNA flexibility in condensate formation.
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Affiliation(s)
| | | | - Lilia C. Harvey
- Department of Chemistry, Agnes Scott CollegeDecatur, GA 30030, USA
| | | | - Nicholas V. Hud
- To whom correspondence should be addressed. Tel: +1 404 385 1162; Fax: +1 404 894 2295;
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45
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Zhao Y, Truhlar DG. How well can new-generation density functional methods describe stacking interactions in biological systems? Phys Chem Chem Phys 2005; 7:2701-5. [PMID: 16189582 DOI: 10.1039/b507036h] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA
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46
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Protozanova E, Yakovchuk P, Frank-Kamenetskii MD. Stacked-unstacked equilibrium at the nick site of DNA. J Mol Biol 2004; 342:775-85. [PMID: 15342236 DOI: 10.1016/j.jmb.2004.07.075] [Citation(s) in RCA: 203] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2004] [Revised: 06/24/2004] [Accepted: 07/18/2004] [Indexed: 11/23/2022]
Abstract
Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.
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Affiliation(s)
- Ekaterina Protozanova
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
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47
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Tian H, Cao L, Tan Y, Williams S, Chen L, Matray T, Chenna A, Moore S, Hernandez V, Xiao V, Tang M, Singh S. Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis. Nucleic Acids Res 2004; 32:e126. [PMID: 15356286 PMCID: PMC519123 DOI: 10.1093/nar/gnh119] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe a novel multiplexing technology using a library of small fluorescent molecules, termed eTag molecules, to code and quantify mRNA targets. eTag molecules, which have the same fluorometric property, but distinct charge-to-mass ratios possess pre-defined electrophoretic characteristics and can be resolved using capillary electrophoresis. Coupled with primary Invader mRNA assay, eTag molecules were applied to simultaneously quantify up to 44 mRNA targets. This multiplexing approach was validated by examining a panel of inflammation responsive genes in human umbilical vein endothelial cells stimulated with inflammatory cytokine interleukin 1beta. The laser-induced fluorescence detection and electrokinetic sample injection process in capillary electrophoresis allows sensitive quantification of thousands of copies of mRNA molecules in a reaction. The assay is precise, as evaluated by measuring qualified Z' factor, a dimensionless and simple characteristic for applications in high-throughput screening using mRNA assays. Our data demonstrate the synergy between the multiplexing capability of eTag molecules by sensitive capillary electrophoresis detection and the isothermal linear amplification characteristics of the Invader assay. eTag multiplex mRNA assay presents a unique platform for sensitive, high sample throughput and multiplex gene expression analysis.
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Affiliation(s)
- Huan Tian
- ACLARA BioSciences, Inc., 1288 Pear Avenue, Mountain View, CA 94043, USA.
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48
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Pyshnyi DV, Goldberg EL, Ivanova EM. Efficiency of coaxial stacking depends on the DNA duplex structure. J Biomol Struct Dyn 2004; 21:459-68. [PMID: 14616040 DOI: 10.1080/07391102.2003.10506940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear regression analysis has revealed that the free-energy increments of interaction for the contacts GX*pYG/CZVC and CX*pYC/GZVG can be described by a set of uniform Delta G degrees(X*pY/ZV) values. The difference in the observed free-energy of the coaxial stacking between the two sets is defined by the contribution from the factors reflecting structural differences between compared DNA duplexes.
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Affiliation(s)
- Dmitrii V Pyshnyi
- Institute of Biological Chemistry and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090, Novosibirsk, Prospect Akad, Lavrentyeva 8.
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49
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Abstract
DNA secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected DNA catalysts, nanotechnology, and DNA-based computing. Accurate prediction of DNA secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including Watson-Crick base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe DNA. Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.
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Affiliation(s)
- John SantaLucia
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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50
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Barken KB, Gabig-Ciminska M, Holmgren A, Molin S. Effect of unlabeled helper probes on detection of an RNA target by bead-based sandwich hybridization. Biotechniques 2004; 36:124-32. [PMID: 14740494 DOI: 10.2144/04361rr03] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Unlabeled helper oligonucleotides assisting a bead-based sandwich hybridization assay were tested for the optimal placement of the capture and detection probes. The target used was a full-length in vitro synthesized mRNA molecule. Helper probes complementary to regions adjacent to the binding site of the 5′ end attached capture probe were found much more effective than helper probes targeting positions adjacent to the detection probe binding site. The difference is believed to be caused by a disruption of the RNA secondary structure in the area where the capture probe binds, thereby reducing structural interference from the bead. The use of additional helpers showed an additive effect. Using helpers at both sides of the capture and detection probes showed a 15- to 40-fold increase in hybridization efficiency depending on the target, thereby increasing the sensitivity of the hybridization assays. Using an electrical chip linked to the detection probe for the detection of p-aminophenol, which is produced by alkaline phosphatase, a detection limit of 2 × 10−13 M mRNA molecules was reached without the use of a nucleic acid amplification step.
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