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Publication Abstract from PubMed

A structural and quantitative biophysical profile of the DNA binding affinity, kinetics and sequence-selectivity of minor-groove binding polyamides (PAs) incorporating N-terminal 5-alkyl thiazole (Nt) and 1-alkyl imidazole (Im) units is described. DNA duplexes containing either target binding sites or mismatch sequences for a suite of hairpin PAs are immobilized on a microelectrode surface. Quantitation of the binding kinetics (i.e., kon, koff), dissociation constant (KD) and melting temperatures show that PAs exhibit picomolar to low nanomolar binding affinities for their target dsDNA sequences. NMR structural analysis of the iPr-Im-containing PA reveals the steric bulk of the isopropyl substituent induces more extensive major groove compression than the corresponding methyl-Im hairpin PA*dsDNA complex. These results show that increasing steric bulk at distal locations to the DNA binding face of the PA plays an influential role in allosteric modulation of the DNA duplex.

Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues.,Burley G, Padroni G, Parkinson J, Welte T Chemistry. 2018 Nov 8. doi: 10.1002/chem.201805338. PMID:30407668^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.