Polypurine/polypyrimidine hairpins form a triple helix structure at low pH

Abstract

1D and 2D NMR investigations of the 15 residue deoxynucleotide sequence d(TCTCTC-TTT-GAGAGA) show that above pH = 6.5 the molecule adopts a B-form hairpin conformation. As the pH is lowered below 6.5 molecules progressively associate in pairs to form a partially triple helical, partially single stranded structure in which the bases of the oligopyrimidine d(TC)3 tract from one molecule form Hoogsteen pairs with the d(G-A)3 tract of the other. Imino protons of protonated cytosines can be observed at very low field (approximately 15 ppm). The enthalpy of triplex formation was estimated by NMR techniques to be -16 kcal mol-1. Intense H6 to H3' cross peaks from residues in all three strands suggest the presence of N-type sugars at some but not at all possible sites. Surprisingly strong cross peaks between H5' or H5" and non-exchangeable base protons are also observed. These suggest that certain of the O5'-C5'-C4'-C3' phosphate backbone torsion angles (gamma) are unusual.

The Transition from a Neutral-pH Double Helix to a Low-pH Triple Helix Induces a Conformational Switch in the CCCG Tetraloop Closing a Watson-Crick Stem

“…For example, in addition to NOEs demonstrating six Watson-Crick interactions, distinct cross-peaks were observed between thymine imino proton and adenine H8 resonances, as well as between the resonances belonging to the amino groups of protonated and unprotonated cytosine residues, respectively (see e.g. Mooren et al, 1991b;Radhakrishnan et al, 1991;Macaya et al, 1992). NMR spectra were also recorded for a H 2 Osample of the 16-mer (shown in Figure 2b) at pH 4.5.…”

The Hairpin Elements of Nucleic Acid Structure: DNA and RNA Folding

“…This sequence forms a' hairpin with three loop residues at neutral pH (Mooren et al 1990). The three-dimensional structure was determined from the distance and torsion angle constraints determined by NMR, using a variable target function approach (DIANA) followed by unconstrained energy minimization (Mooren et al 1993a).…”

DNA structure at low pH values, in the presence of Mn2+ ions: a Raman study

“…3,4 In supercoiled plasmids, protonated nuclease sensitive states persist under neutral pH conditions, suggesting that protonated structures may play a role in the transcriptional activity of the living cell. 3,4 The S 1 nuclease sensitivity was attributed to alterations in sugar phosphate backbone torsion angles necessary to accommodate protonated GÐCH C Hoogsteen pairs in a double helix 5 that also contains AT Watson-Crick pairs; low pH stabilizes such a conformation. 6 Hence, Hoogsteen syn dG : dCH C base pairs might be implied in the mechanism of S 1 recognition in eukaryotic cells.…”