8PWR | pdb_00008pwr

TINA-conjugated antiparallel DNA triplex

• PDB DOI: https://doi.org/10.2210/pdb8PWR/pdb
• Entry: 8PWR supersedes: 6QHI
• BMRB: 34836
• NAKB: 8PWR

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2023-07-21 Released: 2024-01-17 
• Deposition Author(s): Garavis, M., Edwards, P.J.B., Serrano-Chacon, I., Doluca, O., Filichev, V.V., Gonzalez, C.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 15 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.

Garavis, M., Edwards, P.J.B., Serrano-Chacon, I., Doluca, O., Filichev, V.V., Gonzalez, C.

(2024) Nucleic Acids Res 52: 2686-2697

• PubMed: 38281138 
• DOI: https://doi.org/10.1093/nar/gkae028
• Primary Citation Related Structures: 
  8PWR


• PubMed Abstract: 
  

  We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.

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Organizational Affiliation: 
• Instituto de Química Física 'Blas Cabrera', (IQF-CSIC), Madrid 28006, Spain.
School of Natural Sciences, Massey University, Palmerston North 4412, New Zealand.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 6.87 kDa 
• Atom Count: 460 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3')	A	7	Homo sapiens

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3')	B	7	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3')	C	8	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 15 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Garavis, M., Edwards, P.J.B., Serrano-Chacon, I., Doluca, O., Filichev, V.V., Gonzalez, C.
• This entry supersedes: 6QHI

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2017-89707-P
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-116620GB-I00

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Database references