BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25723

Title: Universal Base oligonucleotide structure   PubMed: 27566150

Authors: Spring-Connell, Alexander; Evich, Marina; Seela, Frank; Germann, Markus

Citation: Spring-Connell, Alexander; Evich, Marina; Debelak, Harald; Seela, Frank; Germann, Markus. "Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog"  Nucleic Acids Res. 44, 8576-8587 (2016).

Assembly members:
DNA_(5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3'), polymer, 9 residues, 2423.621 Da.
DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'), polymer, 9 residues, 2715.821 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_(5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3'): ATGGXGCTC
DNA_(5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3'): GAGCTCCAT

Data sets:
Data typeCount
1H chemical shifts136
31P chemical shifts16

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3')1
2DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')2

Entities:

Entity 1, DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 9 residues - 2423.621 Da.

1   DADTDGDG4ENDGDCDTDC

Entity 2, DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 9 residues - 2715.821 Da.

1   DGDADGDCDTDCDCDADT

Samples:

D2O_sample: DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 1 mM; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; D2O, 100% deuterium, 100%; sodium chloride 100 mM; sodium phosphate 10 mM

H2O_sample: DNA (5'-D(*AP*TP*GP*GP*(UB)P*GP*CP*TP*C)-3') 1 mM; DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3') 1 mM; sodium chloride 100 mM; sodium phosphate 10 mM; D2O, 100% deuterium, 10%; H2O 90%

D2O_conditions: ionic strength: 100 mM; pH*: 6.36; pressure: 1 atm; temperature: 294 K

H2O_conditions: pH: 6.79

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESY 75 msD2O_sampleisotropicD2O_conditions
2D 1H-1H NOESY 150 msD2O_sampleisotropicD2O_conditions
2D 1H-1H NOESY 250 msD2O_sampleisotropicD2O_conditions
2D Low Flip COSYD2O_sampleisotropicD2O_conditions
2D 1H-13C HSQCD2O_sampleisotropicD2O_conditions
2D 1H-1H constant time NOESYD2O_sampleisotropicD2O_conditions
2D 1H-1H TOCSYD2O_sampleisotropicD2O_conditions
2D 1H-31P CORRD2O_sampleisotropicD2O_conditions
1D 1HD2O_sampleisotropicD2O_conditions
1D 1H 1-1 jump and returnH2O_sampleisotropicH2O_conditions
1D 31PD2O_sampleisotropicD2O_conditions
2D 1H-1H NOESY 1-1 jump and returnH2O_sampleisotropicH2O_conditions

Software:

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

SPARKY, Goddard - chemical shift assignment, peak picking

xwinnmr, Bruker Biospin - collection

CORMA, Thomas James - data analysis, refinement

MARDIGRAS, Thomas James - data analysis, refinement

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 500 MHz

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