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Nucleic Acids Research, 2000, Vol. 28, No. 15 E74-e74
© 2000 Oxford University Press

Discriminating duplex and hairpin oligonucleotides using chemical shifts: application to the anticodon stem–loop of Escherichia coli tRNAPhe

J. Cabello-Villegas and E. P. Nikonowicz*

Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA

A sensitive NMR spectroscopic method for detection of duplex forms of self-complementary nucleic acid sequences has been implemented. The G·U wobble base pair formed between a 15N-labeled strand and an unlabeled probe strand is used to identify the duplex. The guanine imino resonance, with its characteristic chemical shift, is detected using a 2D 15N–1H heteronuclear multiple quantum coherence (HMQC) spectrum and provides a sensitive and unambiguous route to hairpin–duplex discrimination. The method has been used to identify the duplex and hairpin forms of an RNA oligonucleotide at concentrations of ~20 µM. This method has also been used to rule out possible duplex formation of an RNA oligonucleotide corresponding to the unmodified anticodon stem–loop of Escherichia coli tRNAPhe and suggests that this hairpin has a 3 nt loop.

* To whom correspondence should be addressed. Tel: +1 713 348 4912; Fax: +1 713 348 5154; Email: edn@bioc.rice.edu


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