Model Studies Directed toward a General Triplex DNA Recognition Scheme: A Novel DNA Base That Binds a CG Base-Pair in an Organic Solvent

1995 ◽  
Vol 117 (43) ◽  
pp. 10769-10770 ◽  
Author(s):  
Steven C. Zimmerman ◽  
Philippe Schmitt
Keyword(s):  
Organic Solvent ◽  
Base Pair ◽  
Dna Recognition ◽  
Triplex Dna ◽  
Model Studies ◽  
Dna Base

Varying DNA Base-Pair Size in Subangstrom Increments:  Evidence for a Loose, Not Large, Active Site in Low-Fidelity Dpo4 Polymerase

Biochemistry ◽  
2006 ◽  
Vol 45 (9) ◽  
pp. 2772-2778 ◽  
Author(s):  
Shin Mizukami ◽  
Tae Woo Kim ◽  
Sandra A. Helquist ◽  
Eric T. Kool
Keyword(s):  
Active Site ◽  
Base Pair ◽  
Dna Base ◽  
Dna Base Pair

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 rhodium(III) complex for high-affinity DNA base-pair mismatch recognition

2003 ◽  
Vol 100 (7) ◽  
pp. 3737-3742 ◽  
Author(s):  
H. Junicke ◽  
J. R. Hart ◽  
J. Kisko ◽  
O. Glebov ◽  
I. R. Kirsch ◽  
...  
Keyword(s):  
Base Pair ◽  
High Affinity ◽  
Base Pair Mismatch ◽  
Dna Base ◽  
Mismatch Recognition ◽  
Dna Base Pair

Interaction between the Guanine−Cytosine Watson−Crick DNA Base Pair and Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and Group IIb (Zn2+, Cd2+, Hg2+) Metal Cations

1998 ◽  
Vol 102 (29) ◽  
pp. 5951-5957 ◽  
Author(s):  
Jiří Šponer ◽  
Jaroslav V. Burda ◽  
Michal Sabat ◽  
Jerzy Leszczynski ◽  
Pavel Hobza
Keyword(s):  
Base Pair ◽  
Metal Cations ◽  
Dna Base ◽  
Dna Base Pair

DNA Base Pair Stacking Crystallization of Gold Colloids

Langmuir ◽  
2020 ◽  
Vol 36 (19) ◽  
pp. 5118-5125 ◽  
Author(s):  
Jaewon Lee ◽  
Ji-Hyeok Huh ◽  
Seungwoo Lee
Keyword(s):  
Base Pair ◽  
Gold Colloids ◽  
Dna Base ◽  
Dna Base Pair ◽  
Base Pair Stacking

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.

140 Attacking mechanism of H and OH radicals to DNA base pair: DFT calculations in water

2015 ◽  
Vol 33 (sup1) ◽  
pp. 91-92
Author(s):  
Naoko Okutsu ◽  
Eisuke Shimizu ◽  
Victor I. Danilov ◽  
Sergiy Shulga ◽  
Noriyuki Kurita
Keyword(s):  
Dft Calculations ◽  
Base Pair ◽  
Oh Radicals ◽  
Dna Base ◽  
Dna Base Pair

ChemInform Abstract: Design and Synthesis of Heterocyclic Cations for Specific DNA Recognition: From AT-Rich to Mixed-Base-Pair DNA Sequences.

ChemInform ◽  
2014 ◽  
Vol 45 (29) ◽  
pp. no-no
Author(s):  
Yun Chai ◽  
Ananya Paul ◽  
Michael Rettig ◽  
W. David Wilson ◽  
David W. Boykin
Keyword(s):  
Dna Sequences ◽  
Base Pair ◽  
Dna Recognition ◽  
Design And Synthesis ◽  
Heterocyclic Cations
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