BMRB: 34595

Solution structure of DNA:RNA hybrid 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*TP*AP*(FFC)P*AP*CP*GP*G)-3'), RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')

Entity

1. DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), entity 1 (polymer, Thiol state: not present), 8 monomers, 2167.381 Da Detail

CTAXACGG

2. DNA (5'-D(*CP*TP*AP*(FFC)P*AP*CP*GP*G)-3'), RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), entity 2 (polymer, Thiol state: not present), 8 monomers, 2605.533 Da Detail

CCGUGUAG

Total weight

4772.914 Da

Max. entity weight

2605.533 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 67.4 %, Completeness (bb): 53.6 % Detail

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Polymer type: polydeoxyribonucleotide polyribonucleotide

	Total	1H
All	67.4 % (93 of 138)	67.4 % (93 of 138)
Suger, PO4	53.6 % (52 of 97)	53.6 % (52 of 97)
Nucleobase	100.0 % (41 of 41)	100.0 % (41 of 41)
Aromatic	100.0 % (32 of 32)	100.0 % (32 of 32)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

CTAXACGG

2. entity 2

CCGUGUAG

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*TP*AP*(FFC)P*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*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*TP*AP*(FFC)P*AP*CP*GP*G)-3')	natural abundance		0.5 M
2	RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3')	natural abundance		0.5 M
3	sodium phosphate	natural abundance		25 mM
4	sodium chloride	natural abundance		100 mM
5	DSS	natural abundance		0.5 % v/v

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 278 K, pH 7, Details 0.5 M 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'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 100% D2O

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

Hide sample codition

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 4 contents Detail