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Unraveling the B to A Conformational Transition in Duplex DNA at Single Base Pair Resolution
Author(s) -
Jose Davis,
Kalisz Michal,
Lawson Kirsten
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.03108
Subject(s) - dna , transition (genetics) , conformational change , oligonucleotide , chemistry , dna supercoil , helix (gastropod) , z dna , base pair , crystallography , conformational isomerism , duplex (building) , biophysics , stereochemistry , dna replication , biochemistry , biology , molecule , ecology , organic chemistry , snail , gene
DNA shows conformational heterogeneity and the interest in non‐canonical DNA conformations is increasing as these conformers are found to be involved in many important biological process. Although triple helices, quadruple helices and supercoils are the most studied structures, the conformational transition of the standard B‐form DNA helix to A‐form DNA was the first observed one. The transition of B‐DNA double helix to A‐form is essential for biological functions as recognized by the presence of A‐form DNA in many protein‐DNA complexes. Even though it is known that the B to A conformational transition occurs, the specifics like where in the DNA it originates, how it propagates, and the detailed step‐by‐step mechanism involved is still unknown. By using site specifically positioned fluorescent oligonucleotides, we explored the local and global conformational changes in this transition. Our results showed that by using 2‐Aminopurine (2‐AP), a fluorescent analogue of Adenine, we could monitor the local and global conformational change simultaneously. As a next step our aim is to introduce spermine or spermidine to the system at different ethanol percentages and monitor the spectral changes at various intervals of this transition. This will help us to understand the fundamentals of the long known B to A DNA conformational transition.