Proton exchange in DNA-luzopeptin and DNA-echinomycin bisintercalation complexes: rates and processes of base-pair opening

Biochemistry ◽  
1992 ◽  
Vol 31 (5) ◽  
pp. 1407-1415 ◽  
Author(s):  
Jean Louis Leroy ◽  
Xiaolian Gao ◽  
Vinod Misra ◽  
Maurice Gueron ◽  
Dinshaw J. Patel
Keyword(s):  
Base Pair ◽  
Proton Exchange ◽  
Base Pair Opening

Proton Exchange and Base Pair Opening in a DNA Triple Helix†

Biochemistry ◽  
2001 ◽  
Vol 40 (37) ◽  
pp. 11065-11072 ◽  
Author(s):  
Stephen W. Powell ◽  
Lihong Jiang ◽  
Irina M. Russu
Keyword(s):  
Base Pair ◽  
Triple Helix ◽  
Proton Exchange ◽  
Dna Triple Helix ◽  
Base Pair Opening

A single mode of DNA base-pair opening drives imino proton exchange

Nature ◽  
1987 ◽  
Vol 328 (6125) ◽  
pp. 89-92 ◽  
Author(s):  
Maurice Guéron ◽  
Michel Kochoyan ◽  
Jean-Louis Leroy
Keyword(s):  
Base Pair ◽  
Single Mode ◽  
Proton Exchange ◽  
Imino Proton ◽  
Dna Base ◽  
Imino Proton Exchange ◽  
Dna Base Pair ◽  
Base Pair Opening

Processes of base-pair opening and proton exchange in Z-DNA

Biochemistry ◽  
1990 ◽  
Vol 29 (20) ◽  
pp. 4799-4805 ◽  
Author(s):  
Michel Kochoyan ◽  
Jean Louis Leroy ◽  
Maurice Gueron
Keyword(s):  
Base Pair ◽  
Proton Exchange ◽  
Z Dna ◽  
Base Pair Opening

Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR 1 1Edited by I. Tinoco

1999 ◽  
Vol 288 (4) ◽  
pp. 659-671 ◽  
Author(s):  
Gauri M. Dhavan ◽  
Jon Lapham ◽  
Shuwei Yang ◽  
Donald M. Crothers
Keyword(s):  
Base Pair ◽  
Proton Exchange ◽  
Imino Proton ◽  
Imino Proton Exchange ◽  
Dna Complex ◽  
Base Pair Opening

scholarly journals Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

2021 ◽  
Vol 22 (6) ◽  
pp. 3234
Author(s):  
Juhyun Lee ◽  
Si-Eun Sung ◽  
Janghyun Lee ◽  
Jin Young Kang ◽  
Joon-Hwa Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Nmr Spectroscopy ◽  
Bacillus Cereus ◽  
Base Pair ◽  
Noncoding Rna ◽  
Hydrogen Exchange ◽  
Magnesium Ion ◽  
Fluoride Ion ◽  
Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

scholarly journals Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

Biochemistry ◽  
2013 ◽  
Vol 52 (51) ◽  
pp. 9275-9285 ◽  
Author(s):  
Belinda B. Wenke ◽  
Leah N. Huiting ◽  
Elisa B. Frankel ◽  
Benjamin F. Lane ◽  
Megan E. Núñez
Keyword(s):  
Base Pair ◽  
Cyclobutane Dimer ◽  
Base Pair Opening

scholarly journals Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer

2020 ◽  
Vol 119 (6) ◽  
pp. 1147-1156
Author(s):  
Zachary R. Churcher ◽  
Devid Garaev ◽  
Howard N. Hunter ◽  
Philip E. Johnson
Keyword(s):  
Ligand Binding ◽  
Base Pair ◽  
Base Pair Opening
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