Effects of DNA sequence and structure on binding of RecA to single-stranded DNA

被引:62
作者
Bar-Ziv, R [1 ]
Libchaber, A [1 ]
机构
[1] Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10021 USA
关键词
RecA-DNA interaction; DNA secondary structure; fluorescence anisotropy; single nucleotide polymorphism; molecular beacon;
D O I
10.1073/pnas.151242898
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Fluorescence anisotropy is used to follow the binding of RecA to short single-stranded DNA (ssDNA) sequences (39 bases) at low DNA and RecA concentration where the initial phase of polymerization occurs. We observe that RecA condensation is extremely sensitive to minute changes in DNA sequences. RecA binds strongly to sequences that are rich in pyrimidines and that Pack significant secondary structure and base stacking. We find a correlation between the DNA folding free energy and the onset concentration for RecA binding. These results suggest that the folding of ssDNA and base stacking represent a barrier for RecA binding. The link between secondary structure and binding affinity is further analyzed with two examples: discrimination between two naturally occurring polymorphisms differing by one base and RecA binding on a molecular beacon. A self-assembly model is introduced to explain these observations. We propose that RecA may be used to sense ssDNA sequence and structure.
引用
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页码:9068 / 9073
页数:6
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