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1XUE

STRUCTURE OF GTGGAATGCAATGGAAC HAIRPIN, NMR, 10 STRUCTURES

Summary for 1XUE
Entry DOI10.2210/pdb1xue/pdb
DescriptorDNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*CP*AP*AP*TP*GP*GP*AP*AP*C)-3') (1 entity in total)
Functional Keywordsdeoxyribonucleic acid, mutation, folding, centromere, satellite iii, dna
Total number of polymer chains1
Total formula weight5300.46
Authors
Zhu, L.,Chou, S.-H.,Reid, B.R. (deposition date: 1996-08-26, release date: 1997-03-12, Last modification date: 2024-05-22)
Primary citationZhu, L.,Chou, S.H.,Reid, B.R.
A single G-to-C change causes human centromere TGGAA repeats to fold back into hairpins.
Proc.Natl.Acad.Sci.USA, 93:12159-12164, 1996
Cited by
PubMed Abstract: Recently, we established that satellite III (TGGAA)n tandem repeats, which occur at the centromeres of human chromosomes, pair with themselves to form an unusual "self-complementary" antiparallel duplex containing (GGA)2 motifs in which two unpaired guanines from opposite strands intercalate between sheared G.A base pairs. In separate studies, we have also established that the GCA triplet does not form bimolecular (GCA)2 motifs but instead promotes the formation of hairpins containing a GCA-turn motif in which the loop contains a single cytidine closed by a sheared G.A pair. Since TGCAA is the most frequent variant of TGGAA found in satellite III repeats, we reasoned that the potential of this variant to form GCA-turn miniloop fold-back structures might be an important factor in modulating the local structure in natural (TGGAA)n repeats. We report here the NMR-derived solution structure of the heptadecadeoxynucleotide (G)TGGAATGCAATGGAA(C) in which a central TGCAA pentamer is flanked by two TGGAA pentamers. This 17-mer forms a rather unusual and very stable hairpin structure containing eight base pairs in the stem, only four of which are Watson-Crick pairs, and a loop consisting of a single cytidine residue. The stem contains a (GGA)2 motif with intercalative 14G/4G stacking between two sheared G.A base pairs; the loop end of the stem consists of a sheared 8G.10A closing pair with the cytosine base of the 9C loop stacked on 8G. The remarkable stability of this unusual hairpin structure (Tm = 63 degrees C) suggests that it probably plays an important role in modulating the folding of satellite III (TGGAA)n repeats at the centromere.
PubMed: 8901550
DOI: 10.1073/pnas.93.22.12159
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

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