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- W2012015946 abstract "DNA carries an inherent polymorphism, which surfaces under various external conditions. While B-form remains predominant under normal physiological conditions for most of the DNA sequences, low humidity and increased ion concentration cause B- to A-form transition. Certain proteins and molecules also sometimes cause local deformation of the DNA to the specific A-form. Previous experimental and computational studies focused on the overall B- to A-form transition. Here for the first time we investigated thermodynamics and mechanism of B- to A-form transition in water for various DNA sequences at a local dinucleotide base pair level. We introduced a new reaction coordinate Zp', based on the unique order parameter Zp, to drive B- to A-form transition locally and thereby calculate free energy profiles for the same for all the ten different dinucleotide steps embedded in a twelve base pair DNA. Results show that the trend of A and B philicity observed in experiment is preserved even at this local dinucleotide level, indicating its localized origin. Higher free energy cost obtained here is attributed to the cost of creating B∕A junctions along with formation of B->A transition at dimer level. We find that while water energetically stabilizes A-form for all the ten different dinucleotide steps to various extents, entropy acts against it. Therefore, we find that the stability of B-form DNA in water is entropic in origin. Mechanism of the conversion appears to be triggered by Slide; however, backbone parameters change concertedly." @default.
- W2012015946 created "2016-06-24" @default.
- W2012015946 creator A5026772468 @default.
- W2012015946 creator A5074886886 @default.
- W2012015946 date "2013-10-21" @default.
- W2012015946 modified "2023-10-02" @default.
- W2012015946 title "Sequence dependent free energy profiles of localized B- to A-form transition of DNA in water" @default.
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- W2012015946 doi "https://doi.org/10.1063/1.4825175" @default.
- W2012015946 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24160545" @default.
- W2012015946 hasPublicationYear "2013" @default.
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