Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS

Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5′GGGGTTGGGG3′) designated as d(T2G8), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T2G8) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T2G8)2 and d(T2G8)4 forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T2G8) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex

UV-Visible spectral titration results for binding of PBD1, PBD2, and TMPyP4 to d(T₂G₈) G-quadruplex.

<p>UV-Visible spectral titration results for binding of PBD1, PBD2, and TMPyP4 to d(T₂G₈) G-quadruplex.</p

IRa values of ligands (PBD1, PBD2, and TMPyP4) with the G-quadruplex DNA.

<p>IRa values of ligands (PBD1, PBD2, and TMPyP4) with the G-quadruplex DNA.</p

Fluorescence emission titration results for binding of PBD1, PBD2, and TMPyP4 to d(T₂G₈) G-quadruplex.

<p>Fluorescence emission titration results for binding of PBD1, PBD2, and TMPyP4 to d(T₂G₈) G-quadruplex.</p

Fluorescence emission spectra of A G-quadruplex on interaction with PBD1 ligand and B G-quadruplex on interaction with PBD2 ligand.

<p>Fluorescence emission spectra of A G-quadruplex on interaction with PBD1 ligand and B G-quadruplex on interaction with PBD2 ligand.</p

Melting of (1) G-quadruplex using SYBR Green alone, (2) with PBD1, and (3) with PBD2.

<p>Melting of (1) G-quadruplex using SYBR Green alone, (2) with PBD1, and (3) with PBD2.</p

UV-Visible spectra of A G-quadruplex (5 µM) on interaction with PBD1 ligand and B G-quadruplex (5 µM) on interaction with PBD2 ligand.

<p>UV-Visible spectra of A G-quadruplex (5 µM) on interaction with PBD1 ligand and B G-quadruplex (5 µM) on interaction with PBD2 ligand.</p

Structure of G-quadruplex, TMPyP4, PBD1 and PBD2.

<p>Structure of G-quadruplex, TMPyP4, PBD1 and PBD2.</p

ITC binding isotherms for titration of PBD ligands (PBD1 and PBD2) with G- quadruplex DNA in 100 mM KBPES (pH 7.0) buffer.

<p>ITC binding isotherms for titration of PBD ligands (PBD1 and PBD2) with G- quadruplex DNA in 100 mM KBPES (pH 7.0) buffer.</p

ESI-MS spectra of PBDs (PBD1 and PBD2) and TMPyP4 with G-quadruplex DNA with <i>m/z</i> (Relative abundances) and stoichiometry.

<p>ESI-MS spectra of PBDs (PBD1 and PBD2) and TMPyP4 with G-quadruplex DNA with <i>m/z</i> (Relative abundances) and stoichiometry.</p