Hairpin versus Extended DNA Binding of a Substituted β-Alanine Linked Polyamide
作者:Craig R. Woods、Takahiro Ishii、Bing Wu、Kenneth W. Bair、Dale L. Boger
DOI:10.1021/ja0122039
日期:2002.3.1
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).