Computational study of the pK a values of a modified G·C base pair in duplex DNA

2021 ◽  
Author(s):  
Hyeonjun Kim ◽  
Youngshang Pak
Keyword(s):  
Base Pair ◽  
Computational Study ◽  
Duplex Dna

scholarly journals Isosteric and fluorescent DNA base pair formed by 4-amino-phthalimide and 2,4-diaminopyrimidine: melting, structure, and THz polar solvation dynamics

2016 ◽  
Vol 18 (9) ◽  
pp. 6813-6820 ◽  
Author(s):  
L. Dehmel ◽  
F. Berndt ◽  
M. Weinberger ◽  
M. Sajadi ◽  
I. Ioffe ◽  
...  
Keyword(s):  
Base Pair ◽  
Solvation Dynamics ◽  
Duplex Dna ◽  
Dna Base ◽  
Dna Base Pair ◽  
Polar Solvation

An artificial base pair in duplex DNA, formed by 2,4-diaminopyrimidine and fluorescent 4-aminophthalimide C-nucleosides, is characterized spectroscopically, for use in femtosecond solvation dynamics.

scholarly journals Importance of base-pair opening for mismatch recognition

2020 ◽  
Vol 48 (20) ◽  
pp. 11322-11334
Author(s):  
Tomáš Bouchal ◽  
Ivo Durník ◽  
Viktor Illík ◽  
Kamila Réblová ◽  
Petr Kulhánek
Keyword(s):  
Base Pair ◽  
Computational Study ◽  
Minor Groove ◽  
Base Pairs ◽  
Theoretical Support ◽  
Molecular Pattern ◽  
Anti Cancer ◽  
Mismatch Recognition ◽  
Base Pair Opening

Abstract Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.

HgIIIon Specifically Binds with T:T Mismatched Base Pair in Duplex DNA

2010 ◽  
Vol 16 (44) ◽  
pp. 13218-13225 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Base Pair ◽  
Duplex Dna ◽  
Mismatched Base Pair

Unraveling the B to A Conformational Transition in Duplex DNA at Single Base Pair Resolution

2020 ◽  
Vol 34 (S1) ◽  
pp. 1-1
Author(s):  
Davis Jose ◽  
Michal Kalisz ◽  
Kirsten Lawson
Keyword(s):  
Base Pair ◽  
Conformational Transition ◽  
Duplex Dna ◽  
Single Base ◽  
Single Base Pair

scholarly journals One-Electron Reduction Potential of the Neutral Guanyl Radical in the GC Base Pair of Duplex DNA

2009 ◽  
Vol 131 (14) ◽  
pp. 5203-5207 ◽  
Author(s):  
Sujata S. Shinde ◽  
Andrej Maroz ◽  
Michael P. Hay ◽  
Robert F. Anderson
Keyword(s):  
Base Pair ◽  
Reduction Potential ◽  
Duplex Dna ◽  
Electron Reduction

Parallel-stranded duplex DNA formed by a new base pair between guanine and 5-aza-7-deazaguanine

1997 ◽  
Vol 7 (17) ◽  
pp. 2173-2176 ◽  
Author(s):  
Frank Seela ◽  
Alexander Melenewski ◽  
Changfu Wei
Keyword(s):  
Base Pair ◽  
Duplex Dna

Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand

2020 ◽  
Vol 22 (26) ◽  
pp. 14875-14888 ◽  
Author(s):  
Yan Sun ◽  
May Myat Moe ◽  
Jianbo Liu
Keyword(s):  
Mass Spectrometry ◽  
Proton Transfer ◽  
Radical Cation ◽  
Base Pair ◽  
Hydrogen Transfer ◽  
Theoretical Study ◽  
Computational Study ◽  
Collision Induced Dissociation ◽  
Water Ligand

A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.

A duplex DNA model with regular inter-base-pair hydrogen bonds

2010 ◽  
Vol 266 (3) ◽  
pp. 374-379 ◽  
Author(s):  
Xu-Qing Li ◽  
Ping Fan
Keyword(s):  
Hydrogen Bonds ◽  
Base Pair ◽  
Duplex Dna
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