Synthesis of HIV-1 Psi-site RNA sequences with site specific incorporation of the fluorescent base analog 2-aminopurine.

Tetrahedron
Chang Zhao, John P Marino

Abstract

Fluorescent nucleotide base analogs can serve as sensitive probes of the local structure and chemical environment of the base within a nucleic acid sequence. A significant strength of these base analogs is their similarity in molecular constitution and chemical properties to natural bases. While chemical synthesis has afforded the ability to generate oligonucleotides in good yield with sequence-specific incorporation of fluorescent base analogs, this method is limited in practice to the synthesis of relatively small RNAs of less than ~ 80 nucleotides. Since most RNAs of biological interest are greater than 80 nucleotides in length, methods for synthesizing these larger RNAs in good yield, while maintaining the ability to site-specifically incorporate base analogs that allow for fluorescence measurements, could be of broad interest. Here we describe an approach for synthesis of large RNA molecules (>100 nt) that uses T4 RNA ligase to segmentally join a sequence fragment of an RNA, chemically synthesized with a fluorescent base analog, with the remaining unmodified portion of the RNA oligonucleotide, synthesized through in vitro transcription with T7 polymerase. This method is demonstrated through synthesis of packaging sequences...Continue Reading

References

Jan 1, 1989·Methods in Enzymology·J F Milligan, O C Uhlenbeck
Oct 1, 1986·Analytical Biochemistry·D C TessierT Vernet
Jan 1, 1983·Methods in Enzymology·P J Romaniuk, O C Uhlenbeck
May 24, 1994·Proceedings of the National Academy of Sciences of the United States of America·E SkripkinC Ehresmann
May 31, 1996·Journal of Molecular Biology·M HaddrickS Heaphy
Oct 1, 1996·Journal of Virology·B Berkhout, J L van Wamel
Jun 1, 1996·Current Opinion in Structural Biology·D P Millar
Nov 15, 1996·The Journal of Biological Chemistry·E SkripkinC Ehresmann
Nov 26, 1996·Biochemistry·M MengerD Porschke
Feb 24, 2001·RNA·H Huthoff, B Berkhout
Mar 13, 2001·Methods : a Companion to Methods in Enzymology·J E BarrickR W Roberts
May 29, 2001·Nucleic Acids Research·M Rist, J Marino
Aug 9, 2002·Journal of the American Chemical Society·Insil KimJoseph D Puglisi
Aug 14, 2002·Biochemistry·Hendrik Huthoff, Ben Berkhout
Dec 17, 2003·Biochemistry·Ryan J AustinRichard W Roberts
Jan 22, 2004·Proceedings of the National Academy of Sciences of the United States of America·Mihaela-Rita Mihailescu, John P Marino
Oct 27, 2004·Bioorganic & Medicinal Chemistry Letters·Zhaohui Yan, Anne M Baranger

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Citations

Jan 1, 2013·Nucleic Acids Research·Sumangala ShettyMihaela Rita Mihailescu
May 23, 2009·Methods : a Companion to Methods in Enzymology·Hui-Wen LeeJohn P Marino
Jul 26, 2007·ACS Chemical Biology·Philip C Bevilacqua, John SantaLucia
Mar 9, 2010·Chemical Reviews·Renatus W SinkeldamYitzhak Tor
Dec 5, 2018·Biochemistry·Christopher S Eubanks, Amanda E Hargrove

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