scholarly journals Roles of the Amino Group of Purine Bases in the Thermodynamic Stability of DNA Base Pairing

Molecules ◽  
2014 ◽  
Vol 19 (8) ◽  
pp. 11613-11627 ◽  
Author(s):  
Shu-ichi Nakano ◽  
Naoki Sugimoto
Keyword(s):  
Thermodynamic Stability ◽  
Amino Group ◽  
Base Pairing ◽  
Purine Bases ◽  
Dna Base

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 Effect of Base-Pairing Partner on the Thermodynamic Stability of the Diastereomeric Spiroiminodihydantoin Lesion

2016 ◽  
Vol 29 (3) ◽  
pp. 279-284 ◽  
Author(s):  
Brian Gruessner ◽  
Megana Dwarakanath ◽  
Elizabeth Stewart ◽  
Yoon Bae ◽  
Elizabeth R. Jamieson
Keyword(s):  
Thermodynamic Stability ◽  
Base Pairing
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