Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study

Sannikova, Natalya E.; Kolokolov, Mikhail I.; Khlynova, Tamara A.; Chubarov, Alexey S.; Polienko, Yuliya F.; Fedin, Matvey V.; Krumkacheva, Olesya A.

doi:10.1039/d3cp01775c

Phys. Chem. Chem. Phys.

2023

DOI: 10.1039/d3cp01775c

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Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study

Natalya E. Sannikova,

Mikhail I. Kolokolov,

Tamara A. Khlynova

et al.

Abstract: The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable interest in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience...

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Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Chubarov,

Endeward,

Kanarskaya

et al. 2024

Biomolecules

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Pulsed electron–electron double resonance (PELDOR) spectroscopy is a powerful method for determining nucleic acid (NA) structure and conformational dynamics. PELDOR with molecular dynamics (MD) simulations opens up unique possibilities for defining the conformational ensembles of flexible, three-dimensional, self-assembled complexes of NA. Understanding the diversity and structure of these complexes is vital for uncovering matrix and regulative biological processes in the human body and artificially influencing them for therapeutic purposes. To explore the reliability of PELDOR and MD simulations, we site-specifically attached nitroxide spin labels to oligonucleotides, which form self-assembled complexes between NA chains and exhibit significant conformational flexibility. The DNA complexes assembled from a pair of oligonucleotides with different linker sizes showed excellent agreement between the distance distributions obtained from PELDOR and calculated from MD simulations, both for the mean inter-spin distance and the distance distribution width. These results prove that PELDOR with MD simulations has significant potential for studying the structure and dynamics of conformational flexible complexes of NA.

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Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Chubarov,

Endeward,

Kanarskaya

et al. 2024

Biomolecules

View full text Add to dashboard Cite

show abstract

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Revealing light-induced structural shifts in G-quadruplex-porphyrin complexes: a pulsed dipolar EPR study

Abstract: The binding of G-quadruplex structures (G4s) with photosensitizers is of considerable interest in medicinal chemistry and drug discovery due to their promising potential in photodynamic therapy applications. G4s can experience...

Cited by 1 publication

References 98 publications

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

Pulsed Dipolar EPR for Self-Limited Complexes of Oligonucleotides Studies

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