Biopolym. Cell. 2005; 21(6):559-561.
http://dx.doi.org/10.7124/bc.000714
Short Communications
Mechanism of 6-azacytosine N1-glycosides interaction with catalytic site of phage T7 DNA-dependent RNA-polymerase: model quantum-chemical study
1Palchikovska L. H., 1Platonov M. O., 1Alexeeva I. V., 1Shved A. D.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

By the quantum-chemistry approach at the HF/6-31G (d, p) theory level for the first time considerable increase in the charge value of the atom N6 of azanucleosides in the model of catalytic site of phage T7 DNA-dependent RNA-polymerase was recorded. The blocking of Mg2+ ion by the additional interaction with N6 atom in the azanucleoside–metal–Tyr639 complex seems to reduce the rate of elongation, that was confirmed experimentally by the significant decrease in the amount of synthesized RNA in a unit of time.
Keywords: phage T7 DNA-dependent RNA polymerase, azanucleosides, 6-azacytosine N1-glycosides
Full text: (PDF, in Ukrainian)

References

[1] Palchikovs'ka LG, Garmanchouk LV, Alexeeva IV, Usenko LS, Shestakova TS, Solyanik GI, Shved AD, Chekhun VF. The N1-glycosilic analogues of 6-azacytidine. Cytotoxic effect and influence on transcription in vitro. Biopolym Cell. 2005; 21(5):433-9.
[2] Alexeeva I, Dyachenko N, Nosach L, Zhovnovataya V, Rybalko S, Lozitskaya R, Fedchuk A, Lozitsky V, Gridina T, Shalamay A, Palchikovskaja L, Povnitsa O. 6-azacytidine--compound with wide spectrum of antiviral activity. Nucleosides Nucleotides Nucleic Acids. 2001;20(4-7):1147-52.
[3] Platonov MO, Hovorun DM, Alexeeva IV, Sudakov OO, Boiko YuV, Pal'chykovs'ka LG. Nonempirical quantum-chemical conformational analysis of 6-azacytidine, a modified nucleoside with a wide spectrum of biological activities. Dopovidi Nats Akad Nauk Ukrainy. 2004;(3):163-9.
[4] Temiakov D, Patlan V, Anikin M, McAllister WT, Yokoyama S, Vassylyev DG. Structural basis for substrate selection by t7 RNA polymerase. Cell. 2004;116(3):381-91.
[5] Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, et al. General atomic and molecular electronic structure system. J Comp hem. 1993;14(11):1347–63.