BMRB Entry 36526

Name: Double methyl modification on guanosine promotes unusual structural distortion and conformational transition in Z-DNA
Published: 2025-10-27

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PDB ID: 8hmw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36526
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Double methyl modification on guanosine promotes unusual structural distortion and conformational transition in Z-DNA

Deposition date:

2022-12-06

Original release date:

2025-10-27

Authors:

Lee, J.-H., .; Oh, K.-I., .

Citation:

Citation: Oh, Kwang-Inn; Jin, Ho-Seong; Balasubramaniyam, Thananjeyan; Shin, Ji-Yeon; Choi, Seo-Ree; Seo, Young; Kim, Byeong-Seon; Seo, Yeo-Jin; Kwon, Seung-Ryong; Kim, Nak-Kyoon; Lee, Joon-Hwa. "Entropy-driven conformational transition of flexible Z-DNA to a novel non-B helix by double-methylated guanosine" J. Mol. Liq. ., .-. (2023).

Assembly members:

Assembly members:
DNA (5'-D(*CP*GP*CP*(SJO)P*CP*G)-3'), polymer, 12 residues, 1854.258 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 2853804 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*CP*(SJO)P*CP*G)-3'): CGCXCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	60

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1

Entities:

Entity 1, entity_1_1 12 residues - 1854.258 Da.

1

DC

DG

DC

SJO

DC

DG

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*(SJO)P*CP*G)-3') mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 100 mM; pH: 6; pressure: 1 atm; temperature: 283.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	isotropic	sample_conditions_1
2D NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VnmrJ, Agilent, Santa Clara, CA, USA - data analysis

NMRFAM-SPARKY, Woonghee Lee - chemical shift assignment

NMR spectrometers:

Agilent DD2 700 MHz
Bruker AVANCE III HD 800 MHz
Bruker AVANCE NEO 900 MHz