BMRB: 34594

Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Authors

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

Assembly

DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')

Entity

1. DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3') (polymer, Thiol state: not present), 6 monomers, 1564.993 × 2 Da Detail

CGTAXG

Total weight

3129.986 Da

Max. entity weight

1564.993 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 83.3 %, Completeness: 95.8 %, Completeness (bb): 97.1 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	95.8 % (46 of 48)	95.8 % (46 of 48)
Suger, PO4	97.1 % (34 of 35)	97.1 % (34 of 35)
Nucleobase	92.3 % (12 of 13)	92.3 % (12 of 13)
Aromatic	90.0 % (9 of 10)	90.0 % (9 of 10)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

CGTAXG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 0.5 M DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')	natural abundance		0.5 M
2	sodium phosphate	natural abundance		25 mM
3	sodium chloride	natural abundance		100 mM
4	DSS	natural abundance		0.5 % v/v

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 100% D2O

#	Name	Isotope labeling	Type	Concentration
5	DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3')	natural abundance		0.5 mM
6	sodium phosphate	natural abundance		25 mM
7	sodium chloride	natural abundance		100 mM
8	DSS	natural abundance		0.5 % v/v

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Release date

2021-03-18

Citation

Structural Effects of Incorporation of 2'-Deoxy-2'2'-Difluorodeoxycytidine (Gemcitabine) in A- and B-Form Duplexes
Cabrero, C., Martin-Pintado, N., Mazzini, S., Gargallo, R., Eritja, R., Avino, A., Gonzalez, C.
Chemistry (2021), 27, 7351-7355, PubMed 33772916 , DOI 10.1002/chem.202100503 , Abstract

Experiments performed 5 experiments Detail

Chemical shift validation 3 contents Detail