Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG·C+ triplets

Juan Luis Asensio, Tom Brown, Andrew N. Lane

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAG-GAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR. 1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the 13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1J(CH)) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with > 19 restraints per residue are very similar (RMSD = 0.96 Å). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG·C+ triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between γ ≃ 60°and γ ≃= 180°. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.

Original languageEnglish
Pages (from-to)3677-3686
Number of pages10
JournalNucleic Acids Research
Issue number16
StatePublished - Aug 15 1998

Bibliographical note

Funding Information:
This work was supported by the Medical Research Council of the UK and Oswel Research Products Ltd. J.L.A. gratefully acknowledges a Fellowship from the Spanish Ministry of Education. Accession nos: 1bcb and 1bce.

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG·C+ triplets'. Together they form a unique fingerprint.

Cite this