6IJW

SOLUTION NMR STRUCTURE OF A DODECAMERIC dsDNA COMPLEXED WITH A NIR FLUORESCENT PROBE QCy-DT


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA Minor Groove-Induced cis - trans Isomerization of a Near-Infrared Fluorescent Probe.

Ganguly, S.Murugan, N.A.Ghosh, D.Narayanaswamy, N.Govindaraju, T.Basu, G.

(2021) Biochemistry 

  • DOI: https://doi.org/10.1021/acs.biochem.1c00281
  • Primary Citation of Related Structures:  
    5ZLD, 6IJV, 6IJW

  • PubMed Abstract: 

    The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis - trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis / trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis - trans isomerization and that the minor groove preferentially selects an otherwise unstable cis / trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis / trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.


  • Organizational Affiliation

    Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A, B
12Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QCY (Subject of Investigation/LOI)
Query on QCY

Download Ideal Coordinates CCD File 
C [auth B]2,2'-{(4-hydroxy-1,3-phenylene)di[(E)ethene-2,1-diyl]}bis(3-methyl-1,3-benzothiazol-3-ium)
C26 H22 N2 O S2
ZYZHFHLUSJZEIK-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other