scholarly journals Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking

2019 ◽  
Vol 122 (21) ◽  
Author(s):  
Jiyoun Jeong ◽  
Harold D. Kim
Keyword(s):  
Base Pair ◽  
Dna Loops ◽  
Base Pair Mismatch

scholarly journals Base-pair mismatch can destabilize small DNA loops through cooperative kinking

2019 ◽  
Author(s):  
Jiyoun Jeong ◽  
Harold D. Kim
Keyword(s):  
Single Molecule ◽  
Base Pair ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Kinetic Stability ◽  
Bending Stress ◽  
Dna Loops ◽  
Bent Dna ◽  
Base Pair Mismatch ◽  
Three State Model

Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of tightly bent DNA loops with and without base pair mismatch. Surprisingly, for loops captured by stackable sticky ends, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings show that base pair mismatch transfers bending stress to the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability of DNA loops.

scholarly journals Hybridization of synthetic oligodeoxyribonucleotides to ΦX174 DNA: the effect of single base pair mismatch

1979 ◽  
Vol 6 (11) ◽  
pp. 3543-3558 ◽  
Author(s):  
R. Bruce Wallace ◽  
J. Shaffer ◽  
R.F. Murphy ◽  
J. Bonner ◽  
T. Hirose ◽  
...  
Keyword(s):  
Base Pair ◽  
Single Base ◽  
Base Pair Mismatch ◽  
Single Base Pair

scholarly journals Genetic and physical analysis of the M26 recombination hotspot of Schizosaccharomyces pombe.

Genetics ◽  
1988 ◽  
Vol 119 (3) ◽  
pp. 491-497
Author(s):  
A S Ponticelli ◽  
E P Sena ◽  
G R Smith
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Meiotic Recombination ◽  
Base Pair ◽  
Initiation Site ◽  
Mitotic Recombination ◽  
Physical Analysis ◽  
Nucleotide Change ◽  
Recombination Hotspot ◽  
Base Pair Mismatch

Abstract The ade6-M26 mutation of Schizosaccharomyces pombe has previously been reported to stimulate ade6 intragenic meiotic recombination. We report here that the ade6-M26 mutation is a single G----T nucleotide change, that M26 stimulated recombination within ade6 but not at other distinct loci, and that M26 stimulated meiotic but not mitotic recombination. In addition, M26 stimulated recombination within ade6 when M26 is homozygous; this result demonstrates that a base-pair mismatch at the M26 site was not required for the stimulation. These results are consistent with the ade6-M26 mutation creating a meiotic recombination initiation site.

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

scholarly journals Amplified Single Base-Pair Mismatch Detection via Aggregation of Exonuclease-Sheared Gold Nanoparticles

2014 ◽  
Vol 86 (7) ◽  
pp. 3461-3467 ◽  
Author(s):  
Shuo Wu ◽  
Pingping Liang ◽  
Haixiang Yu ◽  
Xiaowen Xu ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Base Pair ◽  
Single Base ◽  
Mismatch Detection ◽  
Base Pair Mismatch ◽  
Single Base Pair
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