BMRB: 30336

NMR and Restrained Molecular Dynamics Determination of the Structure of an Aza-Benzimidazole Derivative Complex with the DNA Minor Groove of an -AAGATA Sequence

Authors

Harika, N.K., Germann, M.W., Wilson, W.D.

Assembly

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

Entity

1. DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'), entity 1 (polymer, Thiol state: not present), 9 monomers, 2811.810 Da Detail

CCAAGATAG

2. DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'), entity 2 (polymer, Thiol state: not present), 9 monomers, 2784.768 Da Detail

CTATCTTGG

3. DNA (5'-D(*CP*CP*AP*AP*GP*AP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*TP*CP*TP*TP*GP*G)-3'), entity BVV (non-polymer), 387.438 Da

Total weight

5984.016 Da

Max. entity weight

2811.81 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 69.7 %, Completeness (bb): 71.4 % Detail

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Polymer type: polydeoxyribonucleotide

	Total	1H
All	69.7 % (122 of 175)	69.7 % (122 of 175)
Suger, PO4	71.4 % (90 of 126)	71.4 % (90 of 126)
Nucleobase	65.3 % (32 of 49)	65.3 % (32 of 49)
Aromatic	75.0 % (27 of 36)	75.0 % (27 of 36)
Methyl	100.0 % (5 of 5)	100.0 % (5 of 5)

1. entity 1

CCAAGATAG

2. entity 2

CTATCTTGG

Show sample condition

Sample

Solvent system 100% D2O, Pressure 1 atm, Temperature 285 K, pH 6.3, Details 0.8 mM DNA hairpin, 10 mM Tris-d11 buffer, 10 mM sodium chloride, 0.14 mM EDTA, 0.4 mM DSS, 0.8 mM DB2277 molecule, 100% D2O

#	Name	Isotope labeling	Type	Concentration
1	DB2277 molecule	natural abundance		0.8 mM
2	DNA hairpin	natural abundance		0.8 mM
3	DNA hairpin	natural abundance		0.8 mM
4	DSS	natural abundance		0.4 mM
5	EDTA	natural abundance		0.14 mM
6	Tris-d11 buffer	natural abundance		10 mM
7	sodium chloride	natural abundance		10 mM

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Release date

2017-08-28

Citation

First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences
Harika, N.K., Markus, M.W., Wilson, W.D.
Chemistry (2017), 23, 17612-17620, PubMed 29044822 , DOI 10.1002/chem.201704563 , Abstract

Experiments performed 11 experiments Detail