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 5134

Title: Solution Structure of dAAUAA DNA Bulge   PubMed: 12060684

Authors: Gollmick, F.; Lorenz, M.; Dornberger, U.; von Langen, J.; Diekmann, S.; Fritzsche, H.

Citation: Gollmick, F.; Lorenz, M.; Dornberger, U.; von Langen, J.; Diekmann, S.; Fritzsche, H.. "Solution Structure of dAATAA and dAAUAA DNA Bulges"  Nucleic Acids Res. 30, 2669-2677 (2002).

Assembly members:
5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3', polymer, 17 residues, Formula weight is not available
5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3', polymer, 12 residues, Formula weight is not available

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):
5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3': GCATCGAAUAAGCTACG
5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3': CGTAGCCGATGC

Data sets:
Data typeCount
1H chemical shifts248
31P chemical shifts27

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
15'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3'1
25'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'2

Entities:

Entity 1, 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3' 17 residues - Formula weight is not available

1   DGDCDADTDCDGDADADUDA
2   DADGDCDTDADCDG

Entity 2, 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3' 12 residues - Formula weight is not available

1   DCDGDTDADGDCDCDGDADT
2   DGDC

Samples:

sample_1: 5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*UP*AP*AP*GP*CP*TP*AP*CP*G)-3' 3.8 mM; 5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3' 3.8 mM; phosphate buffer 10 mM; NaCl 100 mM; EDTA 0.05 mM; D2O 100%

sample_cond_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D NOESYsample_1not availablesample_cond_1
E-COSYsample_1not availablesample_cond_1
31P-1H heteronuclear correlatedsample_1not availablesample_cond_1

Software:

NMRPipe v3 - processing

MARDIGRAS v3.2 - iterative matrix relaxation

DYANA v1.5 - structure solution

AMBER v5.0 - data analysis, refinement

NMR spectrometers:

  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 750 MHz

Related Database Links: