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Merritt KK, Bradley KM, Hutter D, Matsuura MF, Rowold DJ, Benner SA. Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance. Beilstein J Org Chem 2014; 10:2348-60. [PMID: 25383105 PMCID: PMC4222377 DOI: 10.3762/bjoc.10.245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 09/18/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide "letters", the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson-Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so. RESULTS We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson-Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2'-deoxyisocytidine and 2'-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted. CONCLUSION AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.
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Affiliation(s)
- Kristen K Merritt
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Daniel Hutter
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 17, Alachua, FL 32615, USA
| | - Mariko F Matsuura
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Diane J Rowold
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville, FL, 32604, USA ; The Westheimer Institute for Science and Technology, 720 S. W. 2nd Avenue, Suites 201-208, Gainesville, FL, 32601, USA ; Firebird Biomolecular Sciences LLC, 13709 Progress Blvd. Box 17, Alachua, FL 32615, USA
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Sivaraman K, Seshasayee A, Tarwater PM, Cole AM. Codon choice in genes depends on flanking sequence information--implications for theoretical reverse translation. Nucleic Acids Res 2008; 36:e16. [PMID: 18203741 PMCID: PMC2241905 DOI: 10.1093/nar/gkm1181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75% (c-NCM). The algorithms, their applications and implications are discussed herein.
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Affiliation(s)
- Karthikeyan Sivaraman
- Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
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Benner SA, Sassi SO, Gaucher EA. Molecular paleoscience: systems biology from the past. ACTA ACUST UNITED AC 2007; 75:1-132, xi. [PMID: 17124866 DOI: 10.1002/9780471224464.ch1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Experimental paleomolecular biology, paleobiochemistry, and paleogenetics are closely related emerging fields that infer the sequences of ancient genes and proteins from now-extinct organisms, and then resurrect them for study in the laboratory. The goal of paleogenetics is to use information from natural history to solve the conundrum of modern genomics: How can we understand deeply the function of biomolecular structures uncovered and described by modern chemical biology? Reviewed here are the first 20 cases where biomolecular resurrections have been achieved. These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
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Matousek J, Soucek J, Ríha J, Zankel TR, Benner SA. Immunosuppressive activity of angiogenin in comparison with bovine seminal ribonuclease and pancreatic ribonuclease. Comp Biochem Physiol B Biochem Mol Biol 1995; 112:235-41. [PMID: 7584854 DOI: 10.1016/0305-0491(95)00075-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Angiogenin, a member of the pancreatic-like ribonuclease family with a special biological action (RISBAses), is a basic protein that induces blood vessel formation. Another member of these special ribonucleases, bovine seminal ribonuclease (BS RNase), displays biological properties, including aspermatogenic, embryotoxic, antitumor and immunosuppressive activities. The effects of two angiogenin preparations tested on the biological activities mentioned above are reported and compared with those of BS RNase and RNase A. In contrast to RNase A, which was ineffective in all biological activities tested, angiogenin suppressed significantly the proliferation of human lymphocytes stimulated by phytohemagglutinin or concanavalin A or by allogenic human lymphocytes (mixed lymphocyte culture). However, angiogenin did not affect the growth of human tumor cell lines, development of cow and mouse embryos and spermatogenicity in mice. On the basis of these results, angiogenin is the first monomeric ribonuclease described so far that displays immunosuppressive activity similar to that of the dimeric BS RNase. The immunosuppressive activity of angiogenin might synergize with the effect on neovascularization of tumor tissues and thus contribute to the development of tumor.
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Affiliation(s)
- J Matousek
- Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, Libĕchov, Czech Republic
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