title: Structural models for non-helical DNA.
abstract: 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.
mesh_terms: D001482:Base Composition; D004247:DNA; D004720:Endonucleases; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D015719:Single-Strand Specific DNA and RNA Endonucleases; D012984:Software
chemical_list: D004247:DNA; D004720:Endonucleases; D015719:Single-Strand Specific DNA and RNA Endonucleases