1. Hairpin versus Extended DNA Binding of a Substituted β-Alanine Linked Polyamide
- Author
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Kenneth W. Bair, Woods Craig R, Takahiro Ishii, Bing Wu, and Dale L. Boger
- Subjects
Models, Molecular ,Alanine ,Stereochemistry ,Chemistry ,Intercalation (chemistry) ,DNA ,General Chemistry ,Biochemistry ,Fluorescence ,Molecular biology ,Intercalating Agents ,Catalysis ,Nylons ,chemistry.chemical_compound ,Cross-Linking Reagents ,Colloid and Surface Chemistry ,Polyamide ,Nucleic Acid Conformation ,Pyrroles ,Binding site ,Linker ,Strong binding - Abstract
A series of alpha-substituted beta-alanine (beta) linked polyamides (DbaPyPyPy-beta*-PyPyPy) were prepared and examined. This resulted in the observation that while most substituents disrupt DNA binding, (R)-alpha-methoxy-beta-alanine (beta((R)-OMe)) maintains strong binding affinity and preferentially adopts a hairpin versus extended binding mode, providing an alternative hairpin linker to gamma-aminobutyric acid (gamma). A generalized variant of a fluorescent intercalator displacement assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding site size was developed to distinguish between the extended binding of the parent beta-alanine 1 (DbaPyPyPy-beta-PyPyPy) and the hairpin binding of 3 (DbaPyPyPy-beta((R)-OMe)-PyPyPy).
- Published
- 2002
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