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'''STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT): THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10 STRUCTURES''' | '''STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT): THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10 STRUCTURES''' | ||
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==About this Structure== | ==About this Structure== | ||
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AC7 OCA]. | |||
==Reference== | ==Reference== | ||
Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop., van Dongen MJ, Mooren MM, Willems EF, van der Marel GA, van Boom JH, Wijmenga SS, Hilbers CW, Nucleic Acids Res. 1997 Apr 15;25(8):1537-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9092659 9092659] | Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop., van Dongen MJ, Mooren MM, Willems EF, van der Marel GA, van Boom JH, Wijmenga SS, Hilbers CW, Nucleic Acids Res. 1997 Apr 15;25(8):1537-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9092659 9092659] | ||
[[Category: Boom, J H.Van.]] | [[Category: Boom, J H.Van.]] | ||
[[Category: Dongen, M J.P Van.]] | [[Category: Dongen, M J.P Van.]] | ||
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[[Category: Wijmenga, S S.]] | [[Category: Wijmenga, S S.]] | ||
[[Category: Willems, E F.A.]] | [[Category: Willems, E F.A.]] | ||
[[Category: | [[Category: Deoxyribonucleic acid]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:05:34 2008'' | |||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | |||
Revision as of 10:05, 2 May 2008
STRUCTURAL FEATURES OF THE DNA HAIRPIN D(ATCCTAGTTATAGGAT): THE FORMATION OF A G-A BASE PAIR IN THE LOOP, NMR, 10 STRUCTURES
OverviewOverview
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.
About this StructureAbout this Structure
Full crystallographic information is available from OCA.
ReferenceReference
Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop., van Dongen MJ, Mooren MM, Willems EF, van der Marel GA, van Boom JH, Wijmenga SS, Hilbers CW, Nucleic Acids Res. 1997 Apr 15;25(8):1537-47. PMID:9092659 Page seeded by OCA on Fri May 2 10:05:34 2008