BMRB Entry 34397

Name: Imidazole Polyamide-DNA complex NMR structure (5&#039;-CGATGTACATCG-3&#039;)
Published: 2019-10-21

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PDB ID: 6rio
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34397
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')

Deposition date:

2019-04-24

Original release date:

2019-10-21

Authors:

Padroni, G.; Withers, J.; Taladriz-Sender, A.; Reichenbach, L.; Parkinson, J.; Burley, G.

Citation:

Citation: Padroni, G.; Withers, J.; Taladriz-Sender, A.; Reichenbach, L.; Parkinson, J.; Burley, G.. "Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components." J. Am. Chem. Soc. 141, 9555-9563 (2019).
PubMed: 31117639

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 3582.424 Da.
entity_K4Z, non-polymer, 1237.334 Da.

Natural source:

Natural source: Common Name: Homo Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XGATGTACATCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	271

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1
3	entity_2	2

Entities:

Entity 1, entity_1, 1 12 residues - 3582.424 Da.

1

DCZ

DG

DA

DT

DG

DT

DA

DC

DA

DT

2

DC

DG

Entity 2, entity_2 - C58 H74 N22 O10 - 1237.334 Da.

1

K4Z

Samples:

sample_1: DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3') 1.3 mM; Polyamide 1.3 mM; sodium phosphate 100 mM

sample_2: DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3') 1.3 mM; Polyamide 1.3 mM; sodium phosphate 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.45; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_2	isotropic	sample_conditions_1
1D 31P	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

Sparky, Goddard - chemical shift assignment

MARDIGRAS, N. Ulyanov - structure calculation

TopSpin, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 600 MHz