A direct and nondestructive approach to determine the folding structure of the I-motif DNA secondary structure by NMR

Jixun Dai, A. Ambrus, Laurence H. Hurley, Danzhou Yang

Research output: Article

32 Citations (Scopus)

Abstract

I-motifs are four-stranded DNA secondary structures formed in C-rich DNA sequences and consist of parallel-stranded DNA duplexes zipped together in an antiparallel orientation by intercalated, hemiprotonated cytosine +-cytosine base pairs. I-motif structures have been indicated to form in various regions of the human genome as well as in nanotechnological applications. While NMR is a major tool for structural studies of I-motifs, the determination of the folding topologies of unimolecular I-motifs has been a challenging and arduous task using conventional NMR spectral assignment strategies, due to the inherent sequence redundancy of the C-rich strands in the formation of unimolecular I-motif structures. We report here a direct and nondestructive method that can be utilized to unambiguously determine the hemiprotonated C +-C base pairs and thus the folding topology of unimolecular I-motif structures formed from native C-rich DNA sequences. The reported approach uses affordable low-enrichment site-specific labeling. More significantly, the reported method can directly and unambiguously determine the equilibrating multiple conformations coexisting in a single DNA sequence, which would be a very difficult task using conventional assignment strategies. Additionally, this method can be applied to the direct detection of the base-paired thymines that are involved in the capping structures.

Original languageEnglish
Pages (from-to)6102-6104
Number of pages3
JournalJournal of the American Chemical Society
Volume131
Issue number17
DOIs
Publication statusPublished - máj. 6 2009

Fingerprint

Nucleotide Motifs
DNA sequences
DNA
Cytosine
Nuclear magnetic resonance
Base Pairing
Topology
Thymine
Human Genome
Labeling
Redundancy
Conformations
Genes

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

A direct and nondestructive approach to determine the folding structure of the I-motif DNA secondary structure by NMR. / Dai, Jixun; Ambrus, A.; Hurley, Laurence H.; Yang, Danzhou.

In: Journal of the American Chemical Society, Vol. 131, No. 17, 06.05.2009, p. 6102-6104.

Research output: Article

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