Affiliation: | 1. Department of Organic and Medicinal Chemistry, CSIR – Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB India
Academy of Scientific and Innovative Research (AcSIR) CSIR – Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002 India
These authors contributed equally to this work.;2. Department of Organic and Medicinal Chemistry, CSIR – Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB India
These authors contributed equally to this work.;3. Department of Organic and Medicinal Chemistry, CSIR – Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB India;4. Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054 India |
Abstract: | Transfer RNAs (tRNAs) are fundamental molecules in cellular translation. In this study we have highlighted a fluorescence-based perceptive approach for tRNAs by using a quinoxaline small molecule. We have synthesised a water-soluble fluorescent pyrimido-quinoxaline-fused heterocycle containing a mandatory piperazine tail ( DS1 ) with a large Stokes shift (∼160 nm). The interaction between DS1 and tRNA results in significant fluorescence enhancement of the molecule with Kd∼5 μM and multiple binding sites. Our work reveals that the DS1 binding site overlaps with the specific Mg2+ ion binding site in the D loop of tRNA. As a proof-of-concept, the molecule inhibited Pb2+-induced cleavage of yeast tRNAPhe in the D loop. In competitive binding assays, the fluorescence of DS1 -tRNA complex is quenched by a known tRNA-binder, tobramycin. This indicates the displacement of DS1 and, indeed, a substantiation of specific binding at the site of tertiary interaction in the central region of tRNA. The ability of compound DS1 to bind tRNA with a higher affinity compared to DNA and single-stranded RNA offers a promising approach to developing tRNA-based biomarker diagnostics in the future. |