Synthesis and Substrate Evaluation of (E)-5-[(3-Selenophene-2-Carboxamido)Prop-1-en-1-yl]-Uridine-5′-O-Triphosphate for RNA Polymerase

REFERENCES

• Hermann, T.; Patel, D.J. RNA bulges as architectural and recognition motifs. Structure 2000, 8, R47–R54. Leulliot, N.; Varani, G. Current topics in RNA−protein recognition:  control of specificity and biological function through induced fit and conformational capture. Biochemistry 2001, 40, 7947–7956. . (c) Al-Hasani, H.M.; Walter, N.G. RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 2008, 18, 321–329. . (d) Aitken, C.E.; Petrov, A.; Puglisi, J.D. Single ribosome dynamics and the mechanism of translation. Ann. Rev. Biophys. 2010, 39, 491–513.
   PubMed Web of Science ®Google Scholar
• Ranasinghe, R.T.; Brown, T. Fluorescence based strategies for genetic analysis. Chem. Commun. 2005, 5487–5502. (b) Asseline, U. Development and applications of fluorescent oligonucleotides. Curr. Org. Chem. 2006, 10, 491–518.
   Web of Science ®Google Scholar
• Marti, A.A.; Jockusch, S.; Stevens, N.; Ju, J.; Turro, N.J. Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc. Chem. Res. 2007, 40, 402–409. (d) Bardaro, M.F. Jr.; Varani, G. Examining the relationship between RNA function and motion using nuclear magnetic resonance. WIREs RNA, 2012, 3, 122–132. . (e) Nguyen, P.; Qin, P.Z. RNA dynamics: perspectives from spin labels. WIREs RNA, 2012, 3, 62–72.
   PubMed Web of Science ®Google Scholar
• Holbrook, S.R. Structural principals from large RNAs. Ann. Rev. Biophys. 2008, 37, 445–464. (b) Serganov, A.; Patel, D.J. Molecular recognition and function of riboswitches. Curr. Opin. Struct. Biol. 2012, 22, 279–286.
   PubMed Web of Science ®Google Scholar
• Ennifar, E.; Carpentier, P.; Ferrer, J.-L.; Walter, P.; Dumas, P. X-ray-induced debromination of nucleic acids at the Br K absorption edge and implications for MAD phasing. Acta Crystallogr. 2002, D58, 1262–1268. (b) Dibrov, S.; Mclean, J.; Hermann, T. Structure of an RNA dimer of a regulatory element from human thymidylate synthase mRNA. Acta Crystallogr. 2011, D67, 97–104.
   Google Scholar
• Egli, M.; Pallan, P.S. Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides. Ann. Rev. Biophys. Biomol. Struct. 2007, 36, 281–305. (b) Sheng, J.; Huang, Z. Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Chem. Biodivers. 2010, 7, 753–785.
   PubMedGoogle Scholar
• Du, Q.; Carrasco, N.; Teplova, M.; Wilds, C.J.; Egli, M.; Huang, Z. Internal derivatization of oligonucleotides with selenium for X-ray crystallography using MAD. J. Am. Chem. Soc. 2002, 124, 24–25. (b) Wilds, C.J.; Pattenayek, R.; Pan, C.; Wawrzak, Z.; Egli, M. Selenium-assisted nucleic acid crystallography:  use of phosphoroselenoates for MAD phasing of a DNA structure. J. Am. Chem. Soc. 2002, 124, 14910–14916. . (c) Teplova, M.; Wilds, C.J.; Wawrzak, Z.; Tereshko, V.; Du, Q.; Carrasco, N.; Huang, Z.; Egli, M. Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: Proof of principle. Biochimie 2002, 84, 849–858.
   PubMed Web of Science ®Google Scholar
• Salon, J.; Gan, J.; Abdur, R.; Liu, H.; Huang, Z. Synthesis of 6-Se-guanosine RNAs for structural study. Org. Lett. 2013, 15, 3934–3937. (b) Hassan, A.E.A.; Sheng, J.; Jiang, J.; Zhang, W.; Huang, Z. Synthesis and crystallographic analysis of 5-Se-thymidine DNAs. Org. Lett. 2009, 11, 2503–2506. . (c) Sheng, J.; Jiang, J.; Salon, J.; Huang, Z. Synthesis of a 2′-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Org. Lett. 2007, 9, 749–752. . (d) Salon, J.; Chen, G.; Portilla, Y.; Germann, M.W.; Huang, Z. Synthesis of a 2’-Se-uridine phosphoramidite and its incorporation into oligonucleotides for structural study. Org. Lett. 2005, 7, 5645–5648. . (e) Buzin, Y.; Carrasco, N.; Huang, Z. Synthesis of selenium-derivatized cytidine and oligonucleotides for X-ray crystallography using MAD. Org. Lett. 2004, 6, 1099–1102.
   PubMed Web of Science ®Google Scholar
• Serganov, A.; Keiper, S.; Malinina, L.; Tereshko, V.; Skripkin, E.; Hobartner, C.; Polonskaia, A.; Phan, A.T.; Wombacher, R.; Micura, R.; Dauter, Z.; Jaschke, A.; Patel, D.J. Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat. Struct. Mol. Biol. 2005, 12, 218–224. (b) Freisz, S.; Lang, K.; Micura, R.; Dumas, P.; Ennifar, E. Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site. Angew. Chem. Int. Ed. 2008, 47, 4110–4113. . (c) Salon, J.; Jiang, J.; Sheng, J.; Gerlits, O.O.; Haung, Z. Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies. Nucleic Acids Res. 2008, 36, 7009–7018. . (d) Olieric, V.; Rieder, U.; Lang, K.; Serganov, A.; Schulze-Briese, C.; Micura, R.; Dumas, P.; Ennifar, E. A fast selenium derivatization strategy for crystallization and phasing of RNA structures. RNA 2009, 15, 707–715. . (e) Sun, H.; Sheng, J.; Hassan, A.E.A.; Jiang, S.; Gan, J.; Huang, Z. Novel RNA base pair with higher specificity using single selenium atom. Nucleic Acids Res. 2012, 40, 5171–5179.
   PubMed Web of Science ®Google Scholar
• Pawar, M.G.; Nuthanakanti, A.; Srivatsan, S.G. Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjugate Chem. 2013, 24, 1367–1377.
   PubMed Web of Science ®Google Scholar
• Vaghefi, M. Nucleoside Triphosphates and their Analogues; CRC Press, Taylor and Francis Droup, Boca Raton, 2005.
   Google Scholar
• Brown, P.O.; Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet. 1999, 21, 33–37. (b) Lockhart, D.J.; Winzeler, E.A. Genomics, gene expression and DNA arrays. Nature 2000, 405, 827–836.
   PubMed Web of Science ®Google Scholar
• Srivatsan, S.G.; Tor, Y. Fluorescent pyrimidine ribonucleotide:  synthesis, enzymatic incorporation, and utilization. J. Am. Chem. Soc. 2007, 129, 2044–2053. (b) Greco, N.J.; Tor, Y. Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites. J. Am. Chem. Soc. 2007, 127, 10784–10785.
   PubMed Web of Science ®Google Scholar
• Zhang, W.; Huang, Z. Synthesis of the 5′-Se-thymidine phosphoramidite and convenient labeling of DNA oligonucleotide. Org. Lett. 2011, 13, 2000–2003. (b) Sun, H.; Jiang, S.; Caton-Williams, J.; Liu, H.; Huang, Z. 2-Selenouridine triphosphate synthesis and Se-RNA transcription. RNA 2013, 19, 1309–1314.
   PubMed Web of Science ®Google Scholar
• Kore, A.R.; Yang, B.; Srinivasan, B. Ionic-tag-assisted synthesis of nucleoside triphosphates. Tetrahedron Lett. 2014, 55, 5088–5091. (b) Kore, A.R.; Yang, B.; Srinivasan, B. Efficient synthesis of terminal 4-methylumbelliferyl labeled 5-fluoro-2′-deoxyuridine-5′-O-tetraphosphate (Um-PPPP-FdU): a potential probe for homogenous fluorescent assay. Tetrahedron Lett. 2014, 55, 4822–4825. . (c) Kore, A.R.; Yang, B.; Srinivasan, B. Concise and efficient synthesis of 3′-O-triphosphates of 2′-deoxyadenosine and 2′-deoxycytidine. Tetrahedron Lett. 2014, 55, 1573–1576. . (d) Kore, A.R.; Yang, B.; Srinivasan, B. Concise synthesis of 5-methyl-, 5-formyl, and 5-carboxy analogues of 2′-deoxycytidine-5′-triphosphate. Tetrahedron Lett. 2013, 54, 5325–5327. . (e) Kore, A.R.; Yang, B.; Srinivasan, B. Fluorous-assisted synthesis of (E)-5-[3-Aminoallyl]-uridine-5′-triphosphate. Tetrahedron Lett. 2013, 54, 6264–6266. . (f) Kore, A.R.; Senthilvelan, A.; Srinivasan, B.; Shanmugasundaram, M. Facile protection-free one-pot synthesis of 7-deaza-2′-deoxyguanosine-5′-triphosphate – a versatile molecular biology probe. Can. J. Chem. 2013, 91, 718–720. . (g) Kore, A.R.; Srinivasan, B. Recent advances in the syntheses of nucleoside triphosphates. Curr. Org. Synth. 2013, 10, 903–934. . (h) Kore, A.R.; Senthilvelan, A.; Srinivasan, B.; Shanmugasundaram, M. Facile protection-free one-pot chemical synthesis of nucleoside-5’-tetraphosphates. Nucleosides Nucleotides Nucleic Acids 2013, 32, 411–420. . (i) Kore, A.R.; Srinivasan, B. Efficient synthesis of 3-cyanovinylcarbazole-1′-β-deoxyriboside-5′-triphosphate: a reversible photo-cross-linking probe. Tetrahedron Lett., 2012, 53, 4012–4014. . (j) Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M. Highly chemoselective palladium-catalyzed Sonogashira coupling of 5-iodouridine-5′-triphosphates with propargylamine: a new efficient method for the synthesis of 5-aminopropargyl-uridine-5′-triphosphates. Tetrahedron Lett., 2012, 53, 3070–3072. . (k) Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M. A new, facile, and protection-free one-pot chemical synthesis of 2′-deoxynucleoside-5′-tetraphosphates. Tetrahedron Lett., 2012, 53, 5868–5870.
   Web of Science ®Google Scholar
• Noguchi, T.; Hasegawa, M.; Tomisawa, K.; Mitsukuchi, M. Synthesis and structure–activity relationships of 5-phenylthiophenecarboxylic acid derivatives as antirheumatic agents. Bioorg. Med. Chem. 2003, 11, 4729–4742.
   PubMed Web of Science ®Google Scholar
• Langer, P.R.; Waldrop, A.A.; Ward, D.C. Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 6633–6637. (b) Schoetzau, T.; Langner, J.; Moyroud, E.; Roehl, I.; Vonhoff, S.; Klussmann, S. Aminomodified nucleobases:  functionalized nucleoside triphosphates applicable for SELEX. Bioconjug. Chem. 2003, 14, 919–926.
   PubMed Web of Science ®Google Scholar
• Kore, A.R.; Shanmugasundaram, M. Highly stereoselective palladium-catalyzed Heck coupling of 5-iodouridine-5′-triphosphates with allylamine: a new efficient method for the synthesis of (E)-5-aminoallyl-uridine-5′-triphosphates. Tetrahedron Lett., 2012, 53, 2530–2532.
   Web of Science ®Google Scholar
• Kore, A.R.; Senthilvelan, A.; Shanmugasundaram, M.; Sandoval, D.; and Pardo, A. A new efficient stereoselective method for the synthesis of (E)-5-aminoallyl-pyrimidine-5-triphosphates using palladium-catalyzed Heck reaction. Nucleosides, Nucleotides and Nucleic Acids 2015, 34, 221–228.
   PubMed Web of Science ®Google Scholar
• Dadova, J.; Vidlakova, P.; Pohl, R.; Havran, L.; Fojta, M.; and Hocek, M. Aqueous Heck cross-coupling preparation of acrylate-modified nucleotides and nucleoside triphosphates for polymerase synthesis of acrylate-labeled DNA. J. Org. Chem. 2013, 78, 9627–9637.
   PubMed Web of Science ®Google Scholar
• Vaish, N.K.; Fraley, A.W.; Szostak, J.W.; McLaughlin, L.W. Expanding the structural and functional diversity of RNA: analog uridine triphosphates as candidates for in vitro selection of nucleic acids. Nucleic Acid Res. 2000, 28, 3316–3322.
   PubMed Web of Science ®Google Scholar
• Pawar, M.G.; Srivatsan, S.G. Photophysical Characterization, and Enzymatic Incorporation of a Microenvironment-Sensitive Fluorescent Uridine Analog. Org. Lett. 2011, 13, 1114–1117.
   PubMed Web of Science ®Google Scholar
• Analysis of Cy5-labeled cRNAs and cDNAs using the Agilent 2100 Bioanalyzer and the RNA 6000 LabChip® kit.
   Google Scholar
• Sakamoto, T.; Kondo, Y.; Uchiyama, M.; Yamanaka, H. Concise synthesis of CC-1065/duocarmycin pharmacophore using the intramolecular Heck reaction. J. Chem. Soc., Perkin Trans. 1993, 1941–1942.
   Google Scholar