BMRB Entry 34599

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34599
MolProbity Validation Chart

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Title:
Solution structure of DNA:RNA hybrid duplex
Deposition date:
2021-02-04
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, 2411.606 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: CTACACGG
entity_2: CCGUGUAG

Data sets:
Data typeCount
1H chemical shifts121

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 8 residues - 2411.606 Da.

1   DCDTDADCDADCDGDG

Entity 2, unit_2 8 residues - 2542.561 Da.

1   CCGUGUAG

Samples:

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

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