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Improved methods of analysis for CD data applied to single‐strand stacking
Author(s) -
Causley Gary C.,
Staskus Paul W.,
Johnson W. Curtis
Publication year - 1983
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.360220315
Subject(s) - chemistry , stacking , degenerate energy levels , basis (linear algebra) , singular value decomposition , thermodynamics , domain (mathematical analysis) , space (punctuation) , least squares function approximation , mathematical analysis , mathematics , physics , algorithm , geometry , statistics , quantum mechanics , linguistics , philosophy , organic chemistry , estimator
CD spectra of ApA, Poly(A), CpC, and poly(C), measured as a function of tempeature, are used to demonstrate improved methods of analysis for this type of data. Each of the four sets of temperature‐dependent CD spectra are decomposed using singular value deocmposition. This method demonstrates that there are only two independnet parameters in each set of data. The two basis curves in the wavelength domain for each set of data are use to average the CD curves even though they are taken at different temperatures. Each of the four sets of temperature‐dependent data, smoothed in this way, is decomposed in the Taylor series to separate degenerate interactions due to stacking from the intrinsic CD of the chromophores and nondegenerate interactions. Such a decomposition allow the comparison of corresponding interactions whose relative magnitudes are not obvious in the data. The CD due to degenrate interactions fits the van't Hoff equation well in all four cases and thermodynamic parameters are determined. A simplex routine is used to search the space before performing the least‐squares fit of the data of the van't Hoff equation. This guarantees a global solution rather than a local solution. The first of the two basis curves in the temperature domain derived by singular value decomposition also fits the van't Hoff equation well and gives comparable thermodynamic parameters, although the basis curves derived in this manner have no a priori physical significance. Rather than comparing room temperature CD curves, we compare CD curves of the various compounds at their melting temperature where the populations of the stacked conformation are equivalent. We use the Cantor‐Tinoco equation, which relates the CD of a polymer to the CD of the corresponding dimer, to show that the secondary structure of ApA is not the same as poly(A), and the secondary structure of CpC is not the same as poly(C). However, the two dimers have similar degenerate stacking interactions as do the two polymers. A sound theoretical basis is provided for the semiempirical Cantor‐Tonoco equation.