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A comparative NMR study of a LNA substituted DNA hairpin and the unmodified analog
Author(s) -
Ormond Thomas Keith,
Kerwood Deborah J.,
Borer Philip N,
St. John Pamela M
Publication year - 2006
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.20.5.a946
Subject(s) - nuclear overhauser effect , oligonucleotide , dihedral angle , chemistry , locked nucleic acid , nucleic acid , two dimensional nuclear magnetic resonance spectroscopy , dna , stereochemistry , nuclear magnetic resonance spectroscopy , proton nmr , crystallography , biochemistry , organic chemistry , molecule , hydrogen bond
Locked nucleic acids (LNA) are bicyclic alternative nucleic acids wherein a 2′ – O, 4′ – C methyl ether linker has been shown to restrict the sugar pucker to a 3′ – endo conformation. It has been shown previously that LNA:DNA hybrids exhibit unprecedented thermal stability relative to the unmodified DNA:DNA counterparts. In this study, a 20‐mer single stranded DNA hairpin containing the GAAA tetraloop with 5 G‐C complements in the stem and LNA substituted tetraloop have been studied via 2‐dimensional double quantum filter correlation (DQF‐COSY) and nuclear Overhauser effect NMR spectroscopy (NOESY). The motivation for this study is based on previous experiments involving kinetic and thermodynamic investigations, which suggest that the LNA substituted hairpin conformation is unstable relative to the unmodified hairpin conformation. Rate constant determinations have shown that the modified strand exhibits a second order hybridization rate constant of at least one order of magnitude greater than the unmodified analog. Attempts to account for this instability in solution will be shown including structural elucidations following extraction of distance and dihedral restraints from the above mentioned 2‐dimensional spectra en route to structural stereo views generated from restrained molecular dynamics simulations.