DSSR-PyMOL cartoon-block schematics: PDB entry 5odm

PDB-id

5odm; DSSR-derived features in text and JSON formats

Class

DNA

Method

NMR

Summary

Ntipr polyamide in complex with 5'cgatgtactacg3

Reference

Padroni G, Parkinson JA, Fox KR, Burley GA (2018): "Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides." Nucleic Acids Res., 46, 42-53. doi: 10.1093/nar/gkx1211.

Abstract

This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.