BMRB Entry 34836

Title:
TINA-conjugated antiparallel DNA triplex
Deposition date:
2023-07-21
Original release date:
2024-01-11
Authors:
Garavis, M.; Edwards, P.; Serrano-Chacon, I.; Doluca, O.; Filichev, V.; Gonzalez, C.
Citation:

Citation: Garavis, M.; Edwards, P.; Serrano-Cachon, I.; Doluca, O.; Filichev, V.; Gonzalez, C.. "Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex"  Nucleic Acids Res. 52, 2686-2697 (2024).
PubMed: 38281138

Assembly members:

Assembly members:
entity_1, polymer, 7 residues, 2024.348 Da.
entity_2, polymer, 7 residues, 2211.486 Da.
entity_3, polymer, 8 residues, 2636.882 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TCCTCCT
entity_2: AGGAGGA
entity_3: TGGTGXGT

Data sets:
Data typeCount
1H chemical shifts213

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33

Entities:

Entity 1, unit_1 7 residues - 2024.348 Da.

1   DTDCDCDTDCDCDT

Entity 2, unit_2 7 residues - 2211.486 Da.

1   DADGDGDADGDGDA

Entity 3, unit_3 8 residues - 2636.882 Da.

1   DTDGDGDTDGX0KDGDT

Samples:

sample_1: Triplex-TINA 0.5 mM

sample_2: Triplex-TINA 0.5 mM

sample_conditions_1: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 279.6 K

sample_conditions_2: ionic strength: 125 mM; pH: 7; pressure: 1 atm; temperature: 300.4 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_2

Software:

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL - chemical shift assignment, peak picking

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

TopSpin, Bruker Biospin - collection

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE 800 MHz