BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34397

Title: Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')   PubMed: 31117639

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

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).

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

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: XGATGTACATCG

Data sets:
Data typeCount
1H chemical shifts271

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_1, 11
2entity_1, 21
3entity_22

Entities:

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

1   DCZDGDADTDGDTDADCDADT
2   DCDG

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:

NameSampleSample stateSample conditions
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-31P COSYsample_2isotropicsample_conditions_1
1D 31Psample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_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

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