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Sequence‐dependent properties of DNA. Optimization of empirical parameterizations
Author(s) -
Pysh Eugene S.
Publication year - 1975
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.1975.360140707
Subject(s) - polynucleotide , chemistry , k nearest neighbors algorithm , truncation (statistics) , sequence (biology) , dna , base pair , selection (genetic algorithm) , set (abstract data type) , base (topology) , statistical physics , algorithm , physics , mathematics , computer science , statistics , mathematical analysis , artificial intelligence , biochemistry , programming language
Some physical properties of DNA can be expressed reasonably as an expansion of the interaction among base pairs. For strictly random sequences, the terms of the expansion can be rearranged in such a way that an empirical parameterization of the nearest neighbor truncation is in fact correct to all orders. A parameterization obtained from data on real native DNA's is shown to be more accurate than the term “nearest neighbor approximation” implies. When synthetic polynucleotide duplexes are used in the parameterization, the degree of its accuracy depends on the selection of duplexes. It is shown here how to optimize such a parameterization for a given set of available duplexes.