Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs.

Tetrahedron
Seergazhi G Srivatsan, Yitzhak Tor

Abstract

Emissive nucleoside analogues that are sensitive to their microenvironment can serve as probes for exploring RNA folding and recognition. We have previously described the synthesis of an environmentally sensitive furan-containing uridine and its triphosphate, and have demonstrated that T7 RNA polymerase recognizes this modified ribonucleoside triphosphate as a substrate in in vitro transcription reactions. Here we report the enzymatic preparation of fluorescently tagged HIV-1 TAR constructs and study their interactions with a Tat peptide. Two extreme labeling protocols are examined, where either all native uridine residues are replaced with the corresponding modified fluorescent analogue, or only key residues are site-specifically modified. For the HIV-1 Tat-TAR system, labeling all native uridine residues resulted in relatively small changes in emission upon increasing concentrations of the Tat peptide. In contrast, when the two bulge U residues were site-specifically labeled, a reasonable fluorescence response was observed upon Tat titration. The scope and limitations of such fluorescently tagged RNA systems are discussed.

References

Oct 27, 1992·Biochemistry·K M Weeks, D M Crothers
Jul 3, 1992·Science·J D PuglisiJ R Williamson
May 24, 1991·Science·B J CalnanA D Frankel
Sep 14, 1990·Science·K M WeeksD M Crothers
Oct 20, 1989·Cell·P A Sharp, R A Marciniak
Apr 15, 1997·Proceedings of the National Academy of Sciences of the United States of America·F HamyT Klimkait
Oct 6, 1998·Annual Review of Biochemistry·A D Frankel, J A Young
Jan 8, 1999·Journal of Molecular Biology·B G Turner, M F Summers
May 18, 1999·Archives of Biochemistry and Biophysics·T M Rana, K T Jeang
Nov 5, 1999·Journal of Molecular Biology·J Karn
Nov 11, 1999·Proceedings of the National Academy of Sciences of the United States of America·S HwangT M Rana
Sep 21, 2001·Nucleosides, Nucleotides & Nucleic Acids·A ArzumanovM J Gait
Mar 20, 2002·Cell Biochemistry and Biophysics·M E Hawkins
Sep 23, 2003·Nucleic Acids Research·Kenneth F Blount, Yitzhak Tor
Oct 3, 2003·Chembiochem : a European Journal of Chemical Biology·Andreas KrebsMichael W Göbel
Aug 4, 2005·Journal of the American Chemical Society·Nicholas J Greco, Yitzhak Tor
Dec 17, 2005·Chemical Communications : Chem Comm·Rohan T Ranasinghe, Tom Brown
Sep 14, 2006·Chemical Reviews·Adam P Silverman, Eric T Kool
Jan 30, 2007·Journal of the American Chemical Society·Seergazhi G Srivatsan, Yitzhak Tor

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Citations

Apr 4, 2008·Organic & Biomolecular Chemistry·Seergazhi G SrivatsanYitzhak Tor
Feb 20, 2009·Organic & Biomolecular Chemistry·Hyun Seok JeongByeang Hyean Kim
May 7, 2011·Analytical and Bioanalytical Chemistry·Mayurbhai PatelHaidong Huang
May 19, 2010·Quarterly Reviews of Biophysics·L Marcus Wilhelmsson
Feb 11, 2012·Bioconjugate Chemistry·Lena Wicke, Joachim W Engels
Dec 31, 2008·Journal of the American Chemical Society·Roslyn S ButlerRonald K Castellano
Jan 6, 2009·Journal of the American Chemical Society·Matthew J BelousoffBim Graham
Sep 1, 2012·The Journal of Organic Chemistry·Jan RiedlMichal Hocek
Jun 16, 2007·Nature Protocols·Seergazhi G Srivatsan, Yitzhak Tor
Jan 21, 2016·Journal of Inorganic Biochemistry·Bopha KongLeone Spiccia
Dec 17, 2008·Chemistry, an Asian Journal·Seergazhi G Srivatsan, Yitzhak Tor
Oct 17, 2012·Chembiochem : a European Journal of Chemical Biology·Arun A Tanpure, Seergazhi G Srivatsan
Sep 3, 2011·Chembiochem : a European Journal of Chemical Biology·Kousuke SatoAkira Matsuda
May 28, 2014·Chembiochem : a European Journal of Chemical Biology·Arun A Tanpure, Seergazhi G Srivatsan
Dec 17, 2016·Organic & Biomolecular Chemistry·Patrycja A HopkinsYitzhak Tor
Mar 20, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yong Liang, Stanislaw F Wnuk
Jan 19, 2018·Physical Chemistry Chemical Physics : PCCP·Mohit ChawlaLuigi Cavallo
Jun 23, 2009·The Journal of Physical Chemistry. B·Masahiro MizutaMitsuo Sekine
Mar 9, 2010·Chemical Reviews·Renatus W SinkeldamYitzhak Tor
Feb 7, 2009·Organic Letters·Nicholas J GrecoYitzhak Tor
Feb 27, 2019·The Journal of Organic Chemistry·Zhiwei WenStanislaw F Wnuk

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