Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Selective G-Quadruplex Recognition by a Novel Cyanine Dye

G-rich sequences have been the focus of intense investigations into their widespread occurrence in the human genome. The primary motivation behind these investigations is the ability of G-rich sequences to fold into G-quadruplexes. Putative G-quadruplex forming sequences are implicated in genome regulation and stability. Further, their presence in oncogene promoters has spurred research from the perspective of cancer detection and therapeutics (Siddiqui-Jain, A., etal, 2002). In this context, small molecules that are able to selectively interact with quadruplexes are attractive for their therapeutic or diagnostic applications (Schultze, P., et al 1999; Datta, SG. et al 2014). Relatively small number of quadruplex-specific ligands have been developed so far, primarily owing to the challenge in distinguishing quadruplexes from canonical duplex DNA. (Ihmels, H. & Thomas, L. , 2013). In this work we describe the use of a dimeric benzothiazole-based cyanine dye to selectively bind G-quadruplexes formed by specific G-rich sequences. Fluorimetric titrations of a variety of G-rich sequences into the novel dimeric cyanine dye reveals a nearly 50-fold enhancement in fluorescence of the dye, compared to the emission of the dye in presence of duplex DNA. This enhancement is all the more notable for the fact that the dye fluorescence in presence of duplex DNA is similar to emission of the free dye in solution. The lower background emission of the novel cyanine dye is based on its propensity to self-assemble into fluorescence quenched H-dimers and H-aggregates in a controlled fashion. The fluorescence turn-on observed in presence of specific G-rich sequences is attributable to the de-aggregation of the dyes due to selective interaction with quadruplex secondary structures. UV-visible, fluorescence, CD spectroscopy and foot printing reveal a distinctive binding interaction of the dimeric cyanine dye with quadruplex DNA. We also investigate the ability of the ligand to affect the stability of the quadruplex target. Our results emphasize the potential of a novel dimeric cyanine dye for sensing specific quadruplex secondary structures and opens the possibility of using the dye as a diagnostic and therapeutic agent.

This research has been supported by IIT Gandhinagar.

    Siddiqui-Jain, A., Grand, C. L., Bearss, D. J. & Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. U. S. A. 99, 11593-8 (2002).

    Schultze, P., Hud, N. V., Smith, F. W. & Feigon, J. The effect of sodium, potassium and ammonium ions on the conformation of the dimeric quadruplex formed by the Oxytricha nova telomere repeat oligonucleotide d(G4T4G4). Nucleic Acids Res. 27, 3018-3028 (1999).

    Datta, S. G., Reynolds, C., Goud, Y. K. & Datta, B. Interaction of YOYO-1 with guanine-rich DNA. J. Biomol. Struct. Dyn. 32, 1155-63 (2014).

    Ihmels, H. & Thomas, L. Light up G-Quadruplex DNA with a [2.2.2]-heptamethine cyanine dye. Org. Biomol. Chem. 11, 480 - 487 (2013)

Pallavi Chilka
Prathap Reddy Patlolla
Bhaskar Datta*

Department of Chemistry & Biological Engineering
IIT Gandhinagar
VGEC Campus, Chandkheda
Ahmedabad 382424 Gujarat, India