Base inclinations in natural and synthetic DNAs Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/44558h51k

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  • A sophisticated computer program is developed to analyze flow linear dichroism data on nucleic acids for individual base inclinations. Measured absorption and linear dichroism data for synthetic AT and GC polymers and natural DNAs are analyzed. The reliability of the program is tested on data for the synthetic polymers, and the results are similar to earlier, more straightforward analyses. For the first time, specific base inclinations are derived for all bases individually from the linear dichroism data for natural deoxyribonucleic acids. For B-form DNA in aqueous solution at moderate salt concentrations, the inclinations from perpendicular are as follows: d(A)=16.1 ± 0.5; d(T)=25.0 ± 0.9; d(G)=18.0 ± 0.6; d(C)=25.1 ± 0.8 deg. Our results indicate that the bases in synthetic and natural DNAs are not perpendicular to the helix axis, even in the B form. The mathematical bases and numerical analyses are presented in detail since both are the keys for successful spectral decompositions in this study, and could be applied to nonlinear optimization problems encountered in other types of biochemistry and biophysics measurements. The interplay between computer programming and scientific measurements can not be overemphasized for modern research.
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