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Structural models for non‐helical DNA.
Author(s) -
Yagil G.,
Sussman J.L.
Publication year - 1986
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1002/j.1460-2075.1986.tb04416.x
Subject(s) - dna , dihedral angle , biology , base pair , combinatorics , crystallography , genetics , physics , mathematics , molecule , quantum mechanics , hydrogen bond , chemistry
Structural modelling techniques are employed to explore the energetic requirements for the transformation of classical B DNA into unwound yet double‐stranded DNA structures. Structural idealization using CORELS computer program of Sussman et al. followed by energy minimization using the EREF program of Levitt, leads to two regular non‐helical models. In both models, the bases are conventionally paired and stacked, yet there is no net rotation between successive base pairs. One model, N1, has a 1‐bp repeating unit; the second, N2, has a 2‐bp repeating unit. The dihedral angles of the backbone all have values found either in the B or the Z form of DNA, except for the P‐O5′‐C5′‐C4′ angle, which is in the unprecedented g+ or g‐ domains. The energy difference found between the two N form models and B form DNA are 6.6 and 3.4 kcal/mol/nucleotide for N1 and N2 respectively. These relatively low energy differences encourage the idea that non‐helical forms of DNA may contribute to the alternate DNA structures found in S1 nuclease sensitive and other regulatory regions of active genes.