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Circular dichroism of polynucleotides: Dimers as a function of conformation
Author(s) -
Johnson W. C.,
Itzkowitz M. S.,
Tinoco I.
Publication year - 1972
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1972.360110117
Subject(s) - chemistry , circular dichroism , polynucleotide , glycosidic bond , helix (gastropod) , crystallography , base pair , dna , base (topology) , stereochemistry , biochemistry , ecology , mathematical analysis , enzyme , mathematics , snail , biology
Working within the restrictions of a model, we have calculated the circular dichroism of the dinucleoside phosphates ApA, CpC, and CpA for various conformations. Comparing the calculated curves with those measured in aqueous solution we find agreement for ( 1 ) ApA as a right‐handed helix with both bases either as in B‐form DNA, or else rotated 180° around the glycosidic bond, ( 2 ) CpC as the right‐handed conformation with both bases as in DNA, ( 3 ) ApC as either the right‐handed conformation with both bases as in DNA, or else as a left‐handed helix with both bases rotated 180°, and ( 4 ) CpA as either a left‐handed helix with both bases in a left‐handed DNA, or else in the right‐handed conformation with both bases rotated 180°. In addition, we have investigated circular dichroism as a measure of unstacking. We find that opening the bases to a 90° total angle (base planes perpendicular) reduces the intensity of the calculated bands to 20% of their original value. Further, we find that allowing the sliding of one base past the other does not lead to a temperature dependence consistent with experiment.