BMRB Entry 34595

Name: Solution structure of DNA:RNA hybrid containing a 2&#039;-deoxy-2&#039;2&#039;-difluorodeoxycytidine (gemcitabine) modification
Published: 2021-04-05

Click here to enlarge.

PDB ID: 7nbl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34595
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

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

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Deposition date:

2021-01-27

Original release date:

2021-04-05

Authors:

Cabrero, C.; Martin-Pintado, N.; Mazzini, S.; Gargallo, R.; Eritja, R.; Avino, A.; Gonzalez, C.

Citation:

Citation: Cabrero, C.; Martin-Pintado, N.; Mazzini, S.; Gargallo, R.; Eritja, R.; Avino, A.; Gonzalez, C.. "Structural Effects of Incorporation of 2'-Deoxy-2'2'-Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes" Chemistry 27, 7351-7355 (2021).
PubMed: 33772916

Assembly members:

Assembly members:
entity_1, polymer, 8 residues, 2447.587 Da.
entity_2, polymer, 8 residues, 2542.561 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CTAXACGG
entity_2: CCGUGUAG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	113

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 8 residues - 2447.587 Da.

1

DC

DT

DA

U7B

DA

DC

DG

Entity 2, unit_2 8 residues - 2542.561 Da.

1

C

G

U

G

U

A

G

Samples:

sample_1: DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3') 0.5 M; RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3') 0.5 M; sodium phosphate 25 mM; sodium chloride 100 mM; DSS 0.5 % v/v

sample_2: DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3') 0.5 M; RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3') 0.5 M; sodium phosphate 25 mM; sodium chloride 100 mM; DSS 0.5 % v/v

sample_conditions_1: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2

Software:

TopSpin, Bruker Biospin - collection, processing

NMRFAM-SPARKY, Goddard & Kneller - chemical shift assignment

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

3DNA, Lu & Olson - data analysis

NMR spectrometers:

Bruker AVANCE 600 MHz