5OGA image
Deposition Date 2017-07-12
Release Date 2017-11-29
Last Version Date 2024-06-19
Entry Detail
PDB ID:
5OGA
Keywords:
DNA
Title:
Structure of minimal i-motif domain
Biological Source:
Source Organism(s):
synthetic construct (Taxon ID: 32630)
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
10
Conformers Submitted:
10
Selection Criteria:
all calculated structures submitted
5OGA validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3')
Chain IDs:A
Chain Length:21
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH.
J. Am. Chem. Soc. 139 13985 13988 (2017)
PMID: 28933543 DOI: 10.1021/jacs.7b07383

Abstact

We report here the solution structure of several repetitive DNA sequences containing d(TCGTTCCGT) and related repeats. At physiological pH, these sequences fold into i-motif like quadruplexes in which every two repeats a globular structure is stabilized by two hemiprotonated C:C+ base pairs, flanked by two minor groove tetrads resulting from the association of G:C or G:T base pairs. The interaction between the minor groove tetrads and the nearby C:C+ base pairs affords a strong stabilization, which results in effective pHT values above 7.5. Longer sequences with more than two repeats are able to fold in tandem, forming a rosary bead-like structure. Bioinformatics analysis shows that these sequences are prevalent in the human genome, and are present in development-related genes.

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Primary Citation of related structures
5OGA
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