Literature DB >> 25932960

How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

Ol'ha O Brovarets'1,2, Dmytro M Hovorun1,2.   

Abstract

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

Entities:  

Keywords:  DPT; incorporation error; mutagenic tautomerization; spontaneous point mutation; structural switching; zwitterionic transition state

Mesh:

Substances:

Year:  2015        PMID: 25932960     DOI: 10.1080/07391102.2015.1046936

Source DB:  PubMed          Journal:  J Biomol Struct Dyn        ISSN: 0739-1102


  12 in total

1.  Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

Authors:  Pengfei Li; Atul Rangadurai; Hashim M Al-Hashimi; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2020-06-11       Impact factor: 15.419

2.  Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.

Authors:  Eric S Szymanski; Isaac J Kimsey; Hashim M Al-Hashimi
Journal:  J Am Chem Soc       Date:  2017-03-20       Impact factor: 15.419

3.  Constraints on error rate revealed by computational study of G•U tautomerization in translation.

Authors:  Andriy Kazantsev; Zoya Ignatova
Journal:  Nucleic Acids Res       Date:  2021-11-18       Impact factor: 16.971

4.  Effects of Environmental Factors and Metallic Electrodes on AC Electrical Conduction Through DNA Molecule.

Authors:  S Abdalla; A Obaid; F M Al-Marzouki
Journal:  Nanoscale Res Lett       Date:  2017-04-27       Impact factor: 4.703

5.  Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Dmytro M Hovorun
Journal:  Front Chem       Date:  2018-02-27       Impact factor: 5.221

6.  Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Dmytro M Hovorun
Journal:  PLoS One       Date:  2018-06-27       Impact factor: 3.240

7.  Unexpected Routes of the Mutagenic Tautomerization of the T Nucleobase in the Classical A·T DNA Base Pairs: A QM/QTAIM Comprehensive View.

Authors:  Ol'ha O Brovarets'; Kostiantyn S Tsiupa; Andrii Dinets; Dmytro M Hovorun
Journal:  Front Chem       Date:  2018-11-27       Impact factor: 5.221

8.  A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization.

Authors:  Ol'ha O Brovarets'; Alona Muradova; Dmytro M Hovorun
Journal:  Front Chem       Date:  2020-11-26       Impact factor: 5.221

9.  Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey.

Authors:  Ol'ha O Brovarets'; Timothy A Oliynyk; Dmytro M Hovorun
Journal:  Front Chem       Date:  2019-09-18       Impact factor: 5.221

10.  Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion.

Authors:  Atul Rangadurai; Eric S Szymanski; Isaac Kimsey; Honglue Shi; Hashim M Al-Hashimi
Journal:  J Biomol NMR       Date:  2020-08-12       Impact factor: 2.835

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