Acyclic nucleoside triphosphate analogs as terminators in biocatalytic DNA replication

Martinez, Carlos I.; El-Ansari, Mohamed A.; Gibbs, Richard A.; Burgess, Kevin

doi:10.1016/s0960-894x(97)10135-4

Cited by 12 publications

(8 citation statements)

References 4 publications

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“…Natural DNA polymerases are significantly less tolerant toward chemical modifications made to the sugar moiety than the nucleobase. One of the few early reports on sugar recognition is an acyclic peptide nucleic acid derivative that functions as a chain terminator of DNA synthesis (Martinez et al ., 1997). However, despite facile preparation, this analog is less efficient compared to 2′,3′-dideoxyribonucleoside triphosphates, which is the standard reagent set used for Sanger sequencing (Sanger et al ., 1977).…”

Section: Engineering Polymerase Functions By Rational Designmentioning

confidence: 99%

Engineering polymerases for applications in synthetic biology

Nikoomanzar

Chim

Yik

et al. 2020

Quart. Rev. Biophys.

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DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.

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Section: Engineering Polymerase Functions By Rational Designmentioning

confidence: 99%

Engineering polymerases for applications in synthetic biology

Nikoomanzar

Chim

Yik

et al. 2020

Quart. Rev. Biophys.

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“…Especially analogues altered in the 3′-position (32)(33)(34)37), 2′-position (35,36,38), or both (35) have been studied. But also acyclic analogues (49,50) and analogues with modifications in the 4′-position of the ring (51) were the subject of incorporation assays. Results from these experiments support a hypothesis that modified nucleosides and nucleotides can be accepted on the conditions that they possess a partly flattened sugar residue of limited flexibility (52).…”

mentioning

confidence: 99%

Enzymatic Incorporation in DNA of 1,5-Anhydrohexitol Nucleotides

et al. 2000

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The ability of several DNA polymerases to catalyze the template-directed synthesis of duplex oligonucleotides containing a base pair between a nucleotide with anhydrohexitol ring and its natural complement has been investigated. All DNA polymerases were able to accept the chemically synthesized anhydrohexitol triphosphate as substrate and to catalyze the incorporation of one anhydrohexitol nucleotide. However, only family B DNA polymerases succeeded in elongating the primer after the incorporation of an anhydrohexitol nucleotide. In this family, Vent (exo(-)) DNA polymerase is the most successful one and was therefore selected for further investigation. Results revealed that at high enzyme concentrations six hATPs could be incorporated; however, a selective incorporation proved only feasible under experimental conditions where no more than two analogues could be inserted. Also the synthesis of a mixed HNA-DNA sequence was examined. Kinetic parameters for incorporation of one anhydrohexitol adenine nucleoside were similar to those of its natural analogue.

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“…Nevertheless, limited incorporation of these modified NTPs by DNA polymerases was observed. 106,107 Reversible terminators modified at the 3 0 -position with a hydroxylamine have shown potential for next-generation sequencing. 108 In this context, Chen et al discusses the use of NTPs containing reversible terminators with diverse DNA polymerases for sequencing by synthesis.…”

Section: Chemical Biology Applications Of Sugar-modified Ntpsmentioning

confidence: 99%