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A Pyrimido‐Quinoxaline Fused Heterocycle Lights Up Transfer RNA upon Binding at the Mg 2+ Binding Site
Author(s) -
Patra Dipendu,
Banerjee Sayanika,
Sova Mandi Chandra,
Haseena K. S.,
Basu Gautam,
Dutta Sanjay
Publication year - 2021
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.202000584
Subject(s) - quinoxaline , chemistry , binding site , stereochemistry , combinatorial chemistry , biochemistry , organic chemistry
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 K d ∼5 μM and multiple binding sites. Our work reveals that the DS1 binding site overlaps with the specific Mg 2+ ion binding site in the D loop of tRNA. As a proof‐of‐concept, the molecule inhibited Pb 2+ ‐induced cleavage of yeast tRNA Phe 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.