1AC7

STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT): THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10 STRUCTURES

Summary for 1AC7

• Entry DOI: 10.2210/pdb1ac7/pdb
• Descriptor: DNA (5'-D(*AP*TP*CP*CP*TP*AP*GP*TP*TP*AP*TP*AP*GP*GP*AP*T)-3') (1 entity in total)
• Functional Keywords: deoxyribonucleic acid, dna
• Total number of polymer chains: 1
• Total formula weight: 4912.22

Authors

Van Dongen, M.J.P.,Mooren, M.M.W.,Willems, E.F.A.,Van Der Marel, G.A.,Van Boom, J.H.,Wijmenga, S.S.,Hilbers, C.W. (deposition date: 1997-02-14, release date: 1997-07-07, Last modification date: 2024-05-22)

Primary citation

van Dongen, M.J.,Mooren, M.M.,Willems, E.F.,van der Marel, G.A.,van Boom, J.H.,Wijmenga, S.S.,Hilbers, C.W.
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, 1997

PubMed 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.

PubMed: 9092659
DOI: 10.1093/nar/25.8.1537

Experimental method

SOLUTION NMR