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BMRB: 34157

5ODF

NtMe polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies

Authors

Padroni, G., Parkinson, J., Burley, G.A.

Assembly

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

Entity

1. DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3') (polymer, Thiol state: not present), 12 monomers, 3645.396 × 2 Da Detail

XGATGTACAT CG

2. 5-methyl-1,3-thiazole-4-carboxylic acid (non-polymer), 143.164 Da
3. 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID (non-polymer), 140.140 × 6 Da
4. GAMMA-AMINO-BUTANOIC ACID (non-polymer), 103.120 Da
5. 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID (non-polymer), 141.128 Da
6. 3-(3-azaniumylpropanoylamino)propyl-dimethyl-azanium (non-polymer), 175.272 Da

Total weight

8694.316 Da

Max. entity weight

3645.396 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 91.7 %, Completeness: 87.2 %, Completeness (bb): 84.1 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	87.2 % (102 of 117)	96.2 % (102 of 106)	0.0 % (0 of 11)
Suger, PO4	84.1 % (74 of 88)	96.1 % (74 of 77)	0.0 % (0 of 11)
Nucleobase	96.6 % (28 of 29)	96.6 % (28 of 29)
Aromatic	95.5 % (21 of 22)	95.5 % (21 of 22)
Methyl	100.0 % (3 of 3)	100.0 % (3 of 3)

1. DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')

XGATGTACAT CG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 1.3 nM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPGPAPTPGPTPAPCPAPTPCPG)-3')	natural abundance	1.3 nM
2	PA6	natural abundance	1.3 mM
3	Phosphate	natural abundance	100 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 100% D2O

#	Name	Isotope labeling	Concentration
4	DNA (5'-D(CPGPAPTPGPTPAPCPAPTPCPG)-3')	natural abundance	1.3 mM
5	PA6	natural abundance	1.3 mM
6	Phosphate	natural abundance	100 mM

Chem. Shift Complete2

Sequence coverage: 91.7 %, Completeness: 70.1 %, Completeness (bb): 66.5 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H	³¹P
All	70.1 % (164 of 234)	72.2 % (153 of 212)	50.0 % (11 of 22)
Suger, PO4	66.5 % (117 of 176)	68.8 % (106 of 154)	50.0 % (11 of 22)
Nucleobase	81.0 % (47 of 58)	81.0 % (47 of 58)
Aromatic	84.1 % (37 of 44)	84.1 % (37 of 44)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3')

XGATGTACAT CG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 1.3 nM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DNA (5'-D(CPGPAPTPGPTPAPCPAPTPCPG)-3')	natural abundance	1.3 nM
2	PA6	natural abundance	1.3 mM
3	Phosphate	natural abundance	100 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4, Details 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA6, 100% D2O

#	Name	Isotope labeling	Concentration
4	DNA (5'-D(CPGPAPTPGPTPAPCPAPTPCPG)-3')	natural abundance	1.3 mM
5	PA6	natural abundance	1.3 mM
6	Phosphate	natural abundance	100 mM

Release date

2017-08-01

Citation

Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides
Padroni, G., Parkinson, J.A., Fox, K.R., Burley, G.A.
Nucleic Acids Res. (2018), 46, 42-53, PubMed 29194552 , DOI 10.1093/nar/gkx1211 , Abstract

Experiments performed 6 experiments Detail

1 2D DQF-COSY