8WU5 | pdb_00008wu5

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

(2024) JACS Au 4: 1801-1810

PubMed Abstract:
Triplet repeat diseases are caused by the abnormal elongation of repeated sequences comprising three bases. In particular, the elongation of CAG/CTG repeat sequences is thought to result in conditions such as Huntington's disease and myotonic dystrophy type 1. Although the causes of these diseases are known, fundamental treatments have not been established, and specific drugs are expected to be developed. Pyrrole imidazole polyamide (PIP) is a class of molecules that binds to the minor groove of the DNA duplex in a sequence-specific manner; because of this property, it shows promise in drug discovery applications. Earlier, it was reported that PIP designed to bind CAG/CTG repeat sequences suppresses the genes that cause triplet repeat diseases. In this study, we performed an X-ray crystal structure analysis of a complex of double-stranded DNA containing A-A mismatched base pairs and a cyclic-PIP that binds specifically to CAG/CTG sequences. Furthermore, the validity and characteristics of this structure were analyzed using in silico molecular modeling, ab initio energy calculations, gel electrophoresis, and surface plasmon resonance. With our direct observation using atomic force microscopy and DNA origami, we revealed that the PIP caused structural changes in the DNA strands carrying the expanded CAG/CTG repeat. Overall, our study provides new insight into PIP from a structural perspective.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.

Macromolecule Content

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(GPCP(CBR)PGPAPGPCPAPGPCPAPCPGPGP*C)-3')	A, B, C, D	15	synthetic construct
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Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1LYO Query on A1LYO Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain F [auth C]	E [auth B], F [auth C]	(1^2Z,4^2Z,11^2Z,14^2Z,22^2Z,25^2Z,32^2Z,35^2Z,19R,40R)-1^1,4^1,11^1,14^1,22^1,25^1,32^1,35^1-octamethyl-2,5,9,12,15,20,23,26,30,33,36,41-dodecaoxo-1^1H,4^1H,11^1H,14^1H,22^1H,25^1H,32^1H,35^1H-3,6,10,13,16,21,24,27,31,34,37,42-dodecaaza-1(2,4),11,22,32(4,2)-tetraimidazola-4,14,25,35(4,2)-tetrapyrrolacyclodotetracontaphane-19,40-diaminium C₅₈ H₇₀ N₂₆ O₁₂ QKAIZNHPQCMMDA-KKLWWLSJSA-N		Interactions Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth C]