Base pairing patterns of DNA base lesion spiroiminodihydantoin: A DFT study

2013 ◽  
Vol 113 (24) ◽  
pp. 2600-2604 ◽  
Author(s):  
Pradeep Kumar Shukla ◽  
P.C. Mishra
Keyword(s):  
Dft Study ◽  
Base Pairing ◽  
Dna Base ◽  
Base Lesion

The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study

2001 ◽  
Vol 3 (19) ◽  
pp. 4404-4411 ◽  
Author(s):  
Jaroslav V. Burda ◽  
Jiří Šponer ◽  
Jerzy Leszczynski
Keyword(s):  
Ab Initio ◽  
Platinum Complexes ◽  
Dft Study ◽  
Base Pairing ◽  
Dna Base ◽  
Square Planar ◽  
Ab Initio Dft

Effect of N7-methylation on base pairing patterns of guanine: a DFT study

2021 ◽  
Vol 27 (6) ◽  
Author(s):  
Swarnadeep Biswas ◽  
Pradeep Kumar Shukla
Keyword(s):  
Dft Study ◽  
Base Pairing

scholarly journals Supercoiling and looping promote DNA base accessibility and coordination among distant sites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan M. Fogg ◽  
Allison K. Judge ◽  
Erik Stricker ◽  
Hilda L. Chan ◽  
Lynn Zechiedrich
Keyword(s):  
Mechanical Stress ◽  
Genomic Instability ◽  
Base Pair ◽  
Base Pairing ◽  
Complex Interplay ◽  
Site Specific ◽  
Torsional Strain ◽  
Dna Base ◽  
Dna Backbone ◽  
Negative Supercoiling

AbstractDNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.

scholarly journals A Deep Dive into DNA Base Pairing Interactions Under Water

2020 ◽  
Vol 124 (27) ◽  
pp. 5559-5570
Author(s):  
Rongpeng Li ◽  
Chi H. Mak
Keyword(s):  
Base Pairing ◽  
Deep Dive ◽  
Dna Base ◽  
Pairing Interactions

scholarly journals Creating the protein version of DNA base pairing

Science ◽  
2019 ◽  
Vol 366 (6468) ◽  
pp. 965.3-965
Author(s):  
Zibo Chen
Keyword(s):  
Base Pairing ◽  
Dna Base

Unnatural Covalent DNA Base Pairing:  Quantum Chemical Study

2002 ◽  
Vol 106 (40) ◽  
pp. 9319-9324 ◽  
Author(s):  
Eugene S. Kryachko ◽  
Minh Tho Nguyen
Keyword(s):  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Base Pairing ◽  
Dna Base

scholarly journals Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways

2020 ◽  
Vol 49 (14) ◽  
pp. 4266-4276
Author(s):  
Reza Latifi ◽  
Jennifer L. Minnick ◽  
Matthew G. Quesne ◽  
Sam P. de Visser ◽  
Laleh Tahsini
Keyword(s):  
Nonheme Iron ◽  
Dna Bases ◽  
Dft Study ◽  
Computational Studies ◽  
Repair Enzymes ◽  
Dna Base ◽  
Repair Mechanisms ◽  
High Valent

A detailed QM/MM and DFT study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases is reported. In particular, we investigate the aliphatic hydroxylation and CC epoxidation mechanisms of the enzymes by a high-valent iron(iv)–oxo intermediate.

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