Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe.
Comprehensive understanding of the structure-function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation-sensitive fluorophore and an anomalous X-ray diffraction label (5-selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand-induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.
Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
Ashok
A
Nuthanakanti
Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
Mark A
MA
Boerneke
Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
Thomas
T
Hermann
Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
Seergazhi G
SG
Srivatsan
D001419:Bacteria / Q000737:chemistry; D018360:Crystallography, X-Ray; D005453:Fluorescence; D005456:Fluorescent Dyes / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D012335:RNA, Ribosomal / Q000737:chemistry*; D012263:Ribonucleosides / Q000737:chemistry*; D012643:Selenium / Q000737:chemistry*
D005456:Fluorescent Dyes; D012335:RNA, Ribosomal; D012263:Ribonucleosides; D012643:Selenium
X-ray diffraction; antibiotics; fluorescent nucleosides; ribosomal RNA; selenium