5ODM

NtiPr polyamide in complex with 5'CGATGTACTACG3

Summary for 5ODM

• Entry DOI: 10.2210/pdb5odm/pdb
• NMR Information: BMRB: 34158
• Descriptor: DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 5-propan-2-yl-1,3-thiazole-4-carbaldehyde, 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID, ... (6 entities in total)
• Functional Keywords: minor groove binders- hairpin polyamides, dna
• Biological source: Homo sapiens
• Total number of polymer chains: 2
• Total formula weight: 8580.43

Authors

Padroni, G.,Parkinson, J.,Burley, G.A. (deposition date: 2017-07-06, release date: 2017-12-06, Last modification date: 2023-11-15)

Primary citation

Padroni, G.,Parkinson, J.A.,Fox, K.R.,Burley, G.A.
Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides.
Nucleic Acids Res., 46:42-53, 2018

PubMed 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.

PubMed: 29194552
DOI: 10.1093/nar/gkx1211

Experimental method

SOLUTION NMR