Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin

Journal of Molecular Biology
S H ChouB R Reid

Abstract

The DNA undecamers GTACAAAGTAC (AAA 11-mer) and GTACGAGGTAC (GAG 11-mer) have been studied in solution by high-resolution NMR spectroscopy. Both duplexes form stable hairpins containing single deoxyadenosine loops and stems containing five base-pairs that are closed at the loop end by sheared AxA and GxC pairs, respectively. These molecules thus contain new AAA and GAG loop turn motifs. All protons, including the chiral H5'/H5" protons of the loop residues, were assigned using NOESY, DQF-COSY and heteronuclear 1H-31P COSY experiments. The backbone torsion angles were constrained using experimental data from NOE crosspeaks, three-bond 1H-1H coupling constants and four-bond 1H-31P coupling constants and four-bond 1H-31P coupling constants. The AAA and GAG 11-mers form similar structures in solution. The detailed structure of the AAA 11-mer was determined by the combined use of NMR, distance geometry and energy minimization methods. This structure exhibits good stacking of the loop adenosine base on the closing 5Ax7A sheared pair, with the 6A base stacking on the 5A base and the 6A deoxyribose stacking with the 7A base. All sugars in the AAA 11-mer hairpin adopt the typical DNA C2'-endo conformation and a sharp backbone turn occur...Continue Reading

Citations

Oct 16, 1999·Nucleic Acids Research·H M VuD R Kearns
Jun 13, 2002·Nucleic Acids Research·Friedrich A GollmickHartmut Fritzsche
May 9, 2003·Nucleic Acids Research·Shan-Ho ChouAndrew H-J Wang
Jan 13, 2004·Nucleic Acids Research·Fu-Ming ChenShan-Ho Chou
May 25, 2004·Nucleic Acids Research·N B Fredrik EdfeldtBrian R Reid
May 25, 2004·Nucleic Acids Research·N B Fredrik EdfeldtBrian R Reid
Jul 5, 2011·Nucleic Acids Research·Srinivasaraghavan Kannan, Martin Zacharias
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Shan-Ho ChouFu-Ming Chen
Mar 19, 1999·Journal of Molecular Biology·S H ChouS W Wang
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Apr 18, 1997·Journal of Molecular Biology·S H ChouB R Reid
Dec 13, 2006·Journal of Molecular Biology·Arthur F MonzingoJon D Robertus

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