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BMRB: 34397

Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')
Authors
Padroni, G., Withers, J.M., Taladriz-Sender, A., Reichenbach, L.F., Parkinson, J.A., Burley, G.A.
Assembly
DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')
Entity
1. DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), entity 1 (polymer, Thiol state: not present), 12 monomers, 3645.396 × 2 Da Detail

XGATGTACAT CG


2. DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), entity K4Z (non-polymer), 1239.350 Da
Total weight
8530.142 Da
Max. entity weight
3645.396 Da
Source organism
Homo sapiens
Exptl. method
solution NMR
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 91.7 %, Completeness: 89.6 %, Completeness (bb): 87.0 % Detail
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Polymer type: polydeoxyribonucleotide

Total1H
All89.6 % (95 of 106)89.6 % (95 of 106)
Suger, PO487.0 % (67 of 77)87.0 % (67 of 77)
Nucleobase96.6 % (28 of 29)96.6 % (28 of 29)
Aromatic95.5 % (21 of 22)95.5 % (21 of 22)
Methyl100.0 % (3 of 3)100.0 % (3 of 3)

1. entity 1

XGATGTACAT CG

Show sample condition
Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.45, Details 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate, 90% H2O/10% D2O


#NameIsotope labelingTypeConcentration
1DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')natural abundance1.3 mM
2Polyamidenatural abundance1.3 mM
3sodium phosphatenatural abundance100 mM
Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.45, Details 1.3 mM DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3'), 1.3 mM Polyamide, 100 mM sodium phosphate, 100% D2O


#NameIsotope labelingTypeConcentration
4DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')natural abundance1.3 mM
5Polyamidenatural abundance1.3 mM
6sodium phosphatenatural abundance100 mM

Release date
2019-10-10
Citation
Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components
Padroni, G., Withers, J.M., Taladriz-Sender, A., Reichenbach, L.F., Parkinson, J.A., Burley, G.A.
J. Am. Chem. Soc. (2019), 141, 9555-9563, PubMed 31117639 , DOI 10.1021/jacs.8b12444 ,
Experiments performed 7 experiments Detail
Chemical shift validation 4 contents Detail
Keywords DNA, Minor groove binder, Polyamide