PDBsum entry 1ac7

DNA

PDB id: 1ac7

Contents

DNA/RNA

PDB id:

1ac7

Name:

DNA

Title:

Structural features of the DNA hairpin d(atcctagttataggat): the formation of a g-a base pair in the loop, nmr, 10 structures

Structure:

DNA (5'-d( Ap Tp Cp Cp Tp Ap Gp Tp Tp Ap Tp Ap Gp Gp Ap T)- 3'). Chain: a. Synonym: DNA (atcctagttataggat). Engineered: yes

Source:

Synthetic: yes

NMR struc:

10 models

Authors:

M.J.P.Van Dongen,M.M.W.Mooren,E.F.A.Willems,G.A.Van Der Marel,J.H.Van Boom,S.S.Wijmenga,C.W.Hilbers

Key ref:

M.J.van Dongen et al. (1997). Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop. Nucleic Acids Res, 25, 1537-1547. PubMed id: 9092659

Date:

14-Feb-97 Release date: 07-Jul-97

DNA/RNA chain

A-T-C-C-T-A-G-T-T-A-T-A-G-G-A-T 16 bases

Nucleic Acids Res 25:1537-1547 (1997)

PubMed id: 9092659

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

M.J.van Dongen, M.M.Mooren, E.F.Willems, G.A.van der Marel, J.H.van Boom, S.S.Wijmenga, C.W.Hilbers.

ABSTRACT

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair.