Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides

Molecular electrostatic potentials and steric accessibilities are calculated for Dickerson's dodecanucleotide CGCGAATTCGCG and compared with those for the 'inverted' sequence TATAGGCCTATA. The results are used to distinguish between properties due to base sequence (the location of the deepest potential minimum in the minor groove of A-T sequences and in the major groove of G-C sequences) and those due to the finite length of the oligonucleotide (location of the deepest potential in the central part of the oligonucleotide).