BMRB Entry 34740

Title:
Solution structure of Phen-DC3 intercalating into a quadruplex-duplex hybrid
Deposition date:
2022-07-04
Original release date:
2022-10-27
Authors:
Vianney, Y.; Weisz, K.
Citation:

Citation: Vianney, Y.; Weisz, K.. "High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception"  Nucleic Acids Res. 50, 11948-11964 (2022).
PubMed: 36416262

Assembly members:

Assembly members:
entity_1, polymer, 36 residues, 11210.249 Da.
entity_PQ3, non-polymer, 550.609 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: synthetic construct

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XTAGGTGGGTAGGGTGGGCT AGTCATTTTGACTAGG

Data sets:
Data typeCount
13C chemical shifts41
1H chemical shifts249

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 36 residues - 11210.249 Da.

1   THMDTDADGDGDTDGDGDGDT
2   DADGDGDGDTDGDGDGDCDT
3   DADGDTDCDADTDTDTDTDG
4   DADCDTDADGDG

Entity 2, unit_2 - C34 H26 N6 O2 - 550.609 Da.

1   PQ3

Samples:

sample_1: DNA (36-MER) 0.5 mM

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

X-PLOR NIH v3.0.3, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

TopSpin v4.0.7, Bruker Biospin - data analysis

NMR spectrometers:

  • Bruker AVANCE NEO 600 MHz