Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 17, Issue 3, Pages 1308-1317Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.0c01116
Keywords
-
Funding
- Samsung Science and Technology Foundation [SSTF-BA1601-11]
Ask authors/readers for more resources
The study proposes a theoretical model and performs molecular dynamics simulations to quantify the sequence-dependent kink probability of strongly bent DNA. Results show that sequences with TA dinucleotide repeats flanked by GC steps increase kink propensity, and the number of base pairs involved in local opening is coupled with sequence-specific bubble formation free energy.
Kink formation is essential in highly bent DNA complexed with gene regulatory proteins such as histones to release the bending stress stored within the DNA duplex. Local opening of the double-stranded DNA creates a sharp turn along the specific sequence, which leads to the global bending of the DNA strand. Despite the critical role of kink formation, it is still challenging to predict the position of kink formation for a given DNA sequence. In this study, we propose a theoretical model and perform molecular dynamics simulations to quantify the sequence-dependent kink probability of a strongly bent DNA. By incorporating the elastic bending energy and the sequence-specific thermodynamic parameters, we investigate the importance of the DNA sequence on kink formation. We find that the sequence with TA dinucleotide repeats flanked by GC steps increases the kink propensity by more than an order of magnitude under the same bending stress. The number of base pairs involved in the local opening is found to be coupled with the sequence-specific bubble formation free energy. Our study elucidates the molecular origin of the sequence heterogeneity on kink formation, which is fundamental to understanding protein-DNA recognition.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available