The ATT strand of AAT.ATT trinucleotide repeats adopts stable hairpin structures induced by minor groove binding ligands

AAT.ATT is the most abundant and also the most frequently polymorphic class of trinucleotide repeats in the human genome. To characterize its structural properties and conformational changes induced by minor groove ligands, (AAT)(6) and (ATT)(6) oligomers as well as their complexes with DAPI were in...

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Bibliographic Details
Published in:Biochemistry (Easton) 2000-06, Vol.39 (23), p.6799-6808
Main Authors: Trotta, E, Del Grosso, N, Erba, M, Paci, M
Format: Article
Language:English
Subjects:
Base Pairing
Electrophoresis, Polyacrylamide Gel
Humans
Hydrogen Bonding
Indoles - chemistry
Magnetic Resonance Spectroscopy
Models, Molecular
Nucleic Acid Conformation
Nucleic Acid Denaturation
Oligodeoxyribonucleotides - chemistry
Spectrometry, Fluorescence
Static Electricity
Temperature
Trinucleotide Repeats - genetics
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Summary:AAT.ATT is the most abundant and also the most frequently polymorphic class of trinucleotide repeats in the human genome. To characterize its structural properties and conformational changes induced by minor groove ligands, (AAT)(6) and (ATT)(6) oligomers as well as their complexes with DAPI were investigated by electrophoretic mobility and UV thermal stability as well as fluorescence and NMR spectroscopy. The results show that individual (AAT)(6) and (ATT)(6) strands exist principally as monomeric non-hydrogen-bonded structures. Their individual interaction with DAPI induces the formation of base-paired structures with different thermal stabilities by quite spectroscopically distinct binding mechanisms. In the presence of DAPI, (ATT)(6) forms a monomeric hairpin structure stabilized by two ligands located in the minor groove with a strong apparent binding constant of 3.4 x 10(6) M(-)(1). The DAPI-induced (ATT)(6) hairpin is characterized by well-stacked A.T Watson-Crick and T.T wobble base pairs, a high electrophoretic mobility, and a melting temperature of 41 degrees C. Interaction of DAPI with the complementary (AAT)(6) strand favors less stable base-paired structures, and the results are consistent with electrostatic and hydrogen-bond interactions of the ligand with the phosphodiester backbone of (AAT)(6) by minor involvement of DNA bases.
ISSN:0006-2960