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Theoretical solvation potential of thymine CH₃ groups in double-stranded DNA: application to exon-intron architecture

Authors: Ivan Zucconelli;

Theoretical solvation potential of thymine CH₃ groups in double-stranded DNA: application to exon-intron architecture

Abstract

This work proposes a theoretical sequence-based descriptor of the solvation potential associated with thymine CH₃ groups in double-stranded DNA, with application to exon-intron architecture. The model shifts the reference from the annotated FASTA strand to the DNA duplex and estimates the number of thymine CH₃ groups from the A + T content of the annotated sequence, since each A:T pair contains one thymine on one of the two strands. The duplex density of thymine CH₃ groups is linked to the relative free energy of solvation reported by Plaxco and Goddard for the thymine methyl group in helical DNA. This allows the definition of P_CH₃, a mean theoretical solvation potential that can be calculated for exons, introns and consecutive gene segments. The proposed descriptor is intended as a simple, reproducible and comparative index. It does not represent a direct experimental measure of DNA-protein binding energy and should not be interpreted as a prediction of protein specificity, regulatory activity or splicing. Its main purpose is to provide a derived biophysical map of exon-intron architecture based on nucleotide composition and the chemical specificity of thymine in double-stranded DNA.

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