Ludmila A. Alexandrova

Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases β and λ

A novel class of non-nucleoside triphosphate analogues, bearing hydrophobic groups sterically similar to nucleosides linked to the α-phosphate but lacking the chemical functional groups of nucleic acids, were tested against six different DNA polymerases (polymerases). Human polymerases α, β and λ, and Saccharomyces cerevisiae polymerase IV, were inhibited with different potencies by these analogues. On the contrary, Escherichia coli polymerase I and HIV-1 reverse transcriptase were not. Polymerase β incorporated these derivatives in a strictly Mn++-dependent manner. On the other hand, polymerase λ could incorporate some alkyltriphosphate derivatives with both Mg++ and Mn++, but only opposite to an abasic site on the template strand. The active site mutant polymerase λ Y505A showed an increased ability to incorporate the analogues. These results show for the first time that neither the base nor the sugar moieties of nucleotides are required for incorporation by family X DNA polymerases.

dNTP modified at triphosphate residues: substrate properties towards DNA polymerases and stability in human serum.

Substrate and terminating substrate properties of dNTP with phosphate groups replaced by phosphonates at alpha-, gamma-, beta, gamma-, and alpha, beta, gamma-positions towards different human DNA polymerases and retroviral reverse transcriptases are reviewed. Substitution of the phosphate group by the phosphonate at any of the three phosphate positions of dNTP increased their stability towards dephosphorylating enzymes of human blood. In some cases hydrophobicity of these compounds was markedly enhanced.

Furano- and pyrrolo [2,3-d] pyrimidine nucleosides and their 5'-O-triphospates: synthesis and enzymatic activity.

A series of bicyclic [2,3-d]furano- and pyrrolopyrimidine ribonucleosides were synthesized and converted chemically into corresponding 5′-O-triphosphates. Substrate properties of the triphosphates toward some RNA and DNA polymerases are reported

Human DNA polymerases and retroviral reverse transcriptases: selectivity in respect to dNTPs modified at triphosphate residues.

Abstract A series of dTTP and ddTTP(3′N3) γ-phosphonates and β,γ-diphosphonates are studied as substrates or terminating substrates towards different human DNA polymerases and retroviral reverse transcriptases.

Aryl-Containing Esters Of Triphosphoric Acid As Substrates Of Terminal Deoxynucleotidyl Transferase

A new group of terminal deoxynucleotidyltransferase (TDT) substrates, namely, non-nucleoside triphosphates (NNTP) bearing 5-substituted 2,4-dinitrophenyl fragments instead of nucleoside residues was synthesized.

Synthesis of Novel Alkyl Triphosphates and Their Substrate Properties Toward Terminal Deoxynucleotidyltransferase

Novel triphosphate derivatives bearing bulky or small groups at α-position attached to the triphosphate residue through linkers of different structures and lengths were synthesized and studied as substrates toward terminal deoxynucleotidyltransferase. The substrate efficacy depends on the structure of substituents, linker length, and nature of metal activator. The replacement of hydrophobic groups by small substituents decreased the substrate efficacy by about 20 times in respect to hydrophobic residues. The dependence on metal activator is the following: Co2+ > Mn2+ >> Mg2+. The model of interaction of alkyl triphosphates with linkers of different lengths bearing TdT active site is presented.

Base-Modified Ribonucleosides as Potential Anti-Hepatitis C virus Agents

Four novel series of base modified ribonucleoside analogues were synthesized and evaluated as potential anti-HCV agents. For two compounds notable anti-HCV activity was observed The triphosphates of bicyclic pyrimidine ribonucleosides were studied as substrates/inhibitors of HCV RNA-dependent RNA polymerase (RdRp, NS5B protein) and RNA helicase/NTPase (NS3 protein).

2′-Deoxynucleoside 5′-Triphosphates with Reporter Groups Modified at α-, β,γ- or γ-Phosphates as Substrates for DNA Polymerases

Abstract The presence of reporter or ligand groups in 2′-deoxynucleoside 5′-triphosphates (dNTP) makes it possible to monitor the diffusion of these compounds into cell and to observe their incorporation into DNA. Here we present the synthesis of new dNTPs modified at α-, β,γ- or γ-phosphates of types I-IV, and containing reporter or ligand groups at the C5 position of dUTP.