Effect of triphosphate modifications in 2′‐deoxynucleoside 5′‐triphosphates on their specificity towards various DNA polymerases

Martynov, B. I.; Shirokova, Elena A.; Jasko, Maxim V.; Victorova, Lyubov S.; Krayevsky, Alexander A.

doi:10.1016/s0014-5793(97)00577-2

Cited by 23 publications

(22 citation statements)

References 6 publications

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“…Current models suggest that the geometry of the active site plays a role in fidelity by distinguishing the dimensions of a correct versus and an incorrect base pair (8,12,31,32). Nucleotide analogs containing base (33–36), sugar (37–42), or phosphate (43–46) modifications have been designed to probe the active site architecture. Incorporation analyses demonstrate that each polymerase has a defined tolerance for a particular nucleotide modification.…”

Section: Discussionmentioning

confidence: 99%

Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

Mulder¹,

Anaya²,

Yu³

et al. 2005

Nucleic Acids Research

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The mechanism by which HIV-1 reverse transcriptase (HIV-RT) discriminates between the correct and incorrect nucleotide is not clearly understood. Chemically modified nucleotides containing 1-aminonaphthalene-5-sulfonate (ANS) attached to their γ-phosphate were synthesized and used to probe nucleotide selection by this error prone polymerase. Primer extension reactions provide direct evidence that the polymerase is able to incorporate the gamma-modified nucleotides. Forward mutation assays reveal a 6-fold reduction in the mutational frequency with the modified nucleotides, and specific base substitutions are dramatically reduced or eliminated. Molecular modeling illustrates potential interactions between critical residues within the polymerase active site and the modified nucleotides. Our data demonstrate that the fidelity of reverse transcriptase is improved using modified nucleotides, and we suggest that specific modifications to the γ-phosphate may be useful in designing new antiviral therapeutics or, more generally, as a tool for defining the structural role that the polymerase active site has on nucleotide selectivity.

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Section: Discussionmentioning

confidence: 99%

Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

Mulder¹,

Anaya²,

Yu³

et al. 2005

Nucleic Acids Research

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“…Historically, the specificities of DNA polymerases toward γ-phosphate modified dNTPs are found to be very different, due to the various degrees of steric effects of substituted chemical groups on each enzyme’s dNTP binding pocket (Arzumanov et al, 1996; Martynov et al, 1997). For instance, a bulky 2, 4-dinitrophenyl group substitution at the γ-phosphate of dNTP is a good substrate for the RT-family AMV RT, but is not acceptable for A or B-family DNA polymerases (Alexandrova et al, 1998).…”

Section: Challenges Of Rapidly Evolving Nucleotide Substrates On Dna mentioning

confidence: 99%

DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present

Chen

2014

Front. Microbiol.

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Next-generation sequencing (NGS) technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized in Sanger's dideoxy chain-terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE) and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage φ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphatelabeled nucleoside polyphosphates. Furthermore, φ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistorbased sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.

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“…Their deprotonation constants (pK a ) are usually lower compared to phosphate group, which improves their ability to penetrate through cell walls. The compounds with substitutions at α-(I) [70,71], γ-(II) [72], β,γ-(III) [73], and α,β and γ-phosphates (IV-VI) [74,75] have been synthesized during last years.…”

Section: Design Of Hydrogenphosphonate Derivatives Of Nucleoside Analogsmentioning

confidence: 99%

Design of Anti-HIV Compounds from Nucleoside to Nucleoside 5-Triphosphate Analogs. Problems and Perspectives

Kukhanova¹,

Krayevsky²,

Prusoff³

et al. 2000

CPD

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To date, human immunodeficiency virus infection remains incurable although a variety of antiviral agents have been identified and characterized. Even though nucleoside analogs have been the most successful prodrugs, there remains the need to develop new compounds that exhibit a more favorable toxicity profile, less susceptible to cross-resistance, and greater efficacy. As prodrugs, the nucleoside analogs should be sequentially phosphorylated by cellular kinases to yield triphosphate form before they can inhibit HIV replication at the reverse transcriptase level. The efficiency of phosphorylation of nucleoside analogs is a key factor in their antiviral activity and strongly depends on nucleoside structure and cell type. In recent years, several attempts have been made to improve therapeutic potential of nucleoside analogs by the use of nucleotide prodrugs (pronucleotides), that can avoid the first step of phosphorylation. This review focuses on problems of intracellular phosphorylation of nucleoside analogs and perspectives of developing of a new class of nucleotide analogs modified at phosphate group as a form for the delivery of nucleotide analogs into the cell.

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Effect of triphosphate modifications in 2′‐deoxynucleoside 5′‐triphosphates on their specificity towards various DNA polymerases

Cited by 23 publications

References 6 publications

Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

Nucleotide modification at the -phosphate leads to the improved fidelity of HIV-1 reverse transcriptase

DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present

Design of Anti-HIV Compounds from Nucleoside to Nucleoside 5-Triphosphate Analogs. Problems and Perspectives

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