Nucleic Acids Research, Vol 25, Issue 8 1537-1547, Copyright © 1997 by Oxford University Press
MJ van Dongen, MM Mooren, EF Willems, GA van der Marel, JH van Boom, SS Wijmenga and CW Hilbers
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.
ARTICLES
Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop
NSR Centre for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Nijmegen, The Netherlands.
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