BMRB Entry 34594

Title:
Solution structure of DNA duplex 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, 6 residues, 1845.198 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: CGTAXG

Data sets:
Data typeCount
1H chemical shifts120

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_21

Entities:

Entity 1, unit_1 6 residues - 1845.198 Da.

1   DCDGDTDAU7BDG

Samples:

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

sample_2: DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3') 0.5 mM; 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:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_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