7PNE | pdb_00007pne

Parallel Q-D hybrid with 3' duplex stem-loop as a lateral snapback loop

PDB DOI: https://doi.org/10.2210/pdb7PNE/pdb
BMRB: 34664
NAKB: 7PNE

Classification: DNA
Organism(s): synthetic construct
Expression System: synthetic construct
Mutation(s): No

Deposited: 2021-09-06 Released: 2021-12-29
Deposition Author(s): Vianney, Y.M., Weisz, K.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces.

Vianney, Y.M., Weisz, K.

(2022) Chemistry 28: e202103718-e202103718

PubMed: 34905232 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/chem.202103718
Primary Citation Related Structures:
7PNE, 7PNG

PubMed Abstract:
Quadruplex-duplex (Q-D) junctions are increasingly considered promising targets for medicinal and technological applications. Here, a Q-D hybrid with a hairpin-type snapback loop coaxially stacked onto the quadruplex 3'-outer tetrad was designed and employed as a target structure for the indoloquinoline ligand SYUIQ-5. NMR spectral analysis demonstrated high-affinity binding of the ligand at the quadruplex-duplex interface with association constants determined by isothermal titration calorimetry of about 10 ⁷ M ^-1 and large exothermicities ΔH° of -14 kcal/mol in a 120 mM K ⁺ buffer at 40 °C. Determination of the ligand-bound hybrid structure revealed intercalation of SYUIQ-5 between 3'-outer tetrad and the neighboring CG base pair, maximizing π-π stacking as well as electrostatic interactions with guanine carbonyl groups in close vicinity to the positively charged protonated quinoline nitrogen of the tetracyclic indoloquinoline. Exhibiting considerable flexibility, the SYUIQ-5 sidechain resides in the duplex minor groove. Based on comparative binding studies with the non-substituted N5-methylated indoloquinoline cryptolepine, the sidechain is suggested to confer additional affinity and to fix the alignment of the intercalated indoloquinoline aromatic core. However, selectivity for the Q-D junction mostly relies on the geometry and charge distribution of the indoloquinoline ring system. The presented results are expected to provide valuable guidelines for the design of ligands specifically targeting Q-D interfaces.