Review
Chemistry on Nucleic Acid Templates
Jennifer Berger,
Michael Oberhuber,
Jennifer Berger
Laimburg Research Centre for Agriculture and Forestry, Pfatten 6, I-39040 Auer/Ora, (phone: +39 0471969510)
Search for more papers by this authorMichael Oberhuber
Laimburg Research Centre for Agriculture and Forestry, Pfatten 6, I-39040 Auer/Ora, (phone: +39 0471969510)
Search for more papers by this authorJennifer Berger,
Michael Oberhuber,
Jennifer Berger
Laimburg Research Centre for Agriculture and Forestry, Pfatten 6, I-39040 Auer/Ora, (phone: +39 0471969510)
Search for more papers by this authorMichael Oberhuber
Laimburg Research Centre for Agriculture and Forestry, Pfatten 6, I-39040 Auer/Ora, (phone: +39 0471969510)
Search for more papers by this authorGraphical Abstract
References
- 1 S. Anderson, H. L. Anderson, in ‘Templated Organic Synthesis’, Eds. P. Stang, F. Diederich, Wiley-VCH, Weinheim, 1999, p. 1.
- 2 J. D. Watson, F. H. C. Crick, Nature 1953, 171, 737.
- 3 A. Kornberg, T. Baker, in ‘DNA Replication’, Ed. W. H. Freeman, New York, 1992.
- 4 R. Kornberg, Angew. Chem., Int. Ed. 2007, 46, 6956.
- 5 M. M. Yusupov, G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. D. Cate, H. F. Noller, Science 2001, 292, 883.
- 6 S. McKnight, K. Yamamoto, in ‘Transciptional Regulation’, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1992.
- 7 C. C. Mello, D. Conte Jr., Nature 2004, 431, 338.
- 8 M. Mandal, B. Boese, J. E. Barrick, W. C. Winkler, R. R. Breaker, Cell 2003, 113, 577.
- 9 Y. Gat, D. Lynn, in ‘Templated Organic Synthesis’, Eds. P. Stang, F. Diederich, Wiley-VCH, Weinheim, 1999, p. 133.
- 10 X. Li, D. R. Liu, Angew. Chem., Int. Ed. 2004, 43, 4848.
- 11 S. J. Wrenn, P. B. Harbury, Annu. Rev. Biochem. 2007, 76, 331.
- 12 M. M. Rozenman, B. R. McNaughton, D. R. Liu, Curr. Opin. Chem. Biol. 2007, 11, 259.
- 13 G. Quinkert, H. Wallmeier, N. Windhab, D. Reichert, in ‘Chemical Biology’, Eds. S. L. Schreiber, T. M. Kapoor, G. Wess, Wiley-VCH, Weinheim, 2007, p. 3.
- 14 L. E. Orgel, R. Lohrmann, Acc. Chem. Res. 1974, 7, 368.
- 15 L. E. Orgel, Acc. Chem. Res. 1995, 28, 109.
- 16 R. Naylor, P. T. Gilham, Biochemistry 1966, 5, 2722.
- 17 J. Sulston, R. Lohrmann, L. E. Orgel, H. T. Miles, Proc. Natl. Acad. Sci. U.S.A. 1968, 59, 726.
- 18 J. Sulston, R. Lohrmann, L. E. Orgel, H. T. Miles, Proc. Natl. Acad. Sci. U.S.A. 1968, 60, 409.
- 19 G. von Kiedrowski, Angew. Chem., Int. Ed. 1986, 25, 932.
- 20 Z. A. Shabarova, I. N. Merenkova, T. S. Oretskaya, N. I. Sokolova, E. A. Skripkin, E. V. Alexeyeva, A. G. Balakin, A. A. Bogdanov, Nucleic Acids Res. 1991, 19, 4247.
- 21
J. Ye, Y. Gat, D. G. Lynn, Angew. Chem., Int. Ed. 2000, 39, 3641.
10.1002/1521-3773(20001016)39:20<3641::AID-ANIE3641>3.0.CO;2-J CAS PubMed Web of Science® Google Scholar
- 22 K. J. Luebke, P. B. Dervan, J. Am. Chem. Soc. 1989, 111, 8733.
- 23 T. Li, K. C. Nicolaou, Nature 1994, 369, 218.
- 24 K. J. Luebke, P. B. Dervan, J. Am. Chem. Soc. 1991, 113, 7447.
- 25 E. Rubin, S. Rumney IV, S. Wang, E. T. Kool, Nucleic Acids Res. 1995, 23, 3547.
- 26 R. Rohatgi, D. P. Bartel, J. W. Szostak, J. Am. Chem. Soc. 1996, 118, 3332.
- 27 R. Rohatgi, D. P. Bartel, J. W. Szostak, J. Am. Chem. Soc. 1996, 118, 3340.
- 28 S. Pitsch, R. Krishnamurthy, M. Bolli, S. Wendeborn, A. Holzner, M. Minton, C. Lesueur, I. Schlönvogt, B. Jaun, A. Eschenmoser, Helv. Chim. Acta 1995, 78, 1621.
- 29 A. P. Silverman, E. T. Kool, Chem. Rev. 2006, 106, 3775.
- 30 S. Gryaznov, R. Letsinger, J. Am. Chem. Soc. 1993, 115, 3808.
- 31 S. Gryaznov, R. Schultz, S. Chaturvedi, R. L. Letsinger, Nucleic Acids Res. 1994, 22, 2366.
- 32 R. Letsinger, T. Wu, R. Elghanian, Nucleosides, Nucleotides Nucleic Acids 1997, 16, 643.
- 33 Y. Xu, E. T. Kool, Tetrahedron Lett. 1997, 38, 5595.
- 34 Y. Xu, N. B. Karalkar, E. T. Kool, Nat. Biotechnol. 2001, 19, 148.
- 35 S. Sando, H. Abe, E. T. Kool, J. Am. Chem. Soc. 2004, 126, 1081.
- 36 B. J. Weimann, R. Lohrmann, L. E. Orgel, H. Schneider-Bernloehr, J. E. Sulston, Science 1968, 161, 387.
- 37 T. Inoue, L. E. Orgel, J. Mol. Biol. 1982, 162, 201.
- 38 T. Inoue, L. E. Orgel, Science 1983, 219, 859.
- 39 O. L. Acevedo, L. E. Orgel, J. Mol. Biol. 1987, 197, 187.
- 40 G. F. Joyce, G. M. Visser, C. A. A. Van Boeckel, J. H. Van Boom, L. E. Orgel, J. van Westrenen, Nature 1984, 310, 602.
- 41 C. B. Chen, T. Inoue, L. E. Orgel, J. Mol. Biol. 1985, 181, 271.
- 42 I. A. Kozlov, B. De Bouvere, A. Van Aerschot, P. Herdewijn, L. E. Orgel, J. Am. Chem. Soc. 1999, 121, 5856.
- 43 B. D. Heuberger, C. Switzer, Org. Lett. 2006, 8, 5809.
- 44 A. Luther, R. Brandsch, G. von Kiedrowski, Nature 1998, 396, 245.
- 45 R. K. Bruick, P. E. Dawson, S. B. H. Kent, N. Usman, G. F. Joyce, Chem. Biol. 1996, 3, 49.
- 46 C. Böhler, P. E. Nielsen, L. E. Orgel, Nature 1995, 376, 578.
- 47 A. Mattes, O. Seitz, Chem. Commun. 2001, 20, 2050.
- 48
A. Mattes, O. Seitz, Angew. Chem., Int. Ed. 2001, 40, 3178.
10.1002/1521-3773(20010903)40:17<3178::AID-ANIE3178>3.0.CO;2-M CAS PubMed Web of Science® Google Scholar
- 49 S. Ficht, A. Mattes, O. Seitz, J. Am. Chem. Soc. 2004, 126, 9970.
- 50 C. Dose, O. Seitz, Bioorg. Med. Chem. 2008, 16, 65.
- 51 Z.-Y. J. Zhan, D. G. Lynn, J. Am. Chem. Soc. 1997, 119, 12420.
- 52 K. Fujimoto, S. Matsuda, N. Takahashi, I. Saito, J. Am. Chem. Soc. 2000, 122, 5646.
- 53 I. Saito, Y. Miyauchi, Y. Saito, K. Fujimoto, Tetrahedron Lett. 2005, 46, 97.
- 54 Y. Yoshimura, Y. Noguchi, H. Sato, K. Fujimoto, ChemBioChem 2006, 7, 598.
- 55 R. J. Lewis, P. C. Hanawalt, Nature 1982, 298, 393.
- 56 J. Liu, J.-S. Taylor, Nucleic Acids Res. 1998, 26, 3300.
- 57 T. Ihara, T. Fujii, M. Mukae, Y. Kitamura, A. Jyo, J. Am. Chem. Soc. 2004, 126, 8880.
- 58 M. I. Dobrikov, S. A. Gaidamakov, T. I. Gainutdinov, A. A. Koshkin, V. V. Vlassov, Antisense Nucleic Acid Drug Dev. 1997, 7, 309.
- 59 M. I. Dobrikov, T. I. Gainutdinov, V. V. Vlassov, Nucleosides, Nucleotides Nucleic Acids 1999, 18, 1517.
- 60 M. H. Caruthers, G. Beaton, J. V. Wu, W. Wiesler, Methods Enzymol. 1992, 211, 3.
- 61 K.-U. Schöning, P. Scholz, S. Guntha, X. Wu, R. Krishnamurthy, A. Eschenmoser, Science 2000, 290, 1347.
- 62 R. L. Letsinger, T. Wu, J. Am. Chem. Soc. 1994, 116, 811.
- 63 J. Woo, P. B. Hopkins, J. Am. Chem. Soc 1991, 113, 5457.
- 64 Z. J. Gartner, D. R. Liu, J. Am. Chem. Soc. 2001, 123, 6961.
- 65 X. Li, D. R. Liu, J. Am. Chem. Soc. 2003, 125, 10188.
- 66
C. T. Calderone, J. W. Puckett, Z. J. Gartner, D. R. Liu, Angew. Chem., Int. Ed. 2002, 41, 4104.
10.1002/1521-3773(20021104)41:21<4104::AID-ANIE4104>3.0.CO;2-O CAS PubMed Web of Science® Google Scholar
- 67
Z. J. Gartner, M. W. Kanan, D. R. Liu, Angew. Chem., Int. Ed. 2002, 41, 1796.
10.1002/1521-3773(20020517)41:10<1796::AID-ANIE1796>3.0.CO;2-Z CAS PubMed Web of Science® Google Scholar
- 68 Z. J. Gartner, B. N. Tse, R. Grubina, J. B. Doyon, T. M. Snyder, D. R. Liu, Science 2004, 305, 1601.
- 69 M. M. Rozenman, D. R. Liu, ChemBioChem 2006, 7, 253.
- 70 Y. Chen, C. Mao, J. Am. Chem. Soc. 2004, 126, 13240.
- 71 D. M. Rosenbaum, D. R. Liu, J. Am. Chem. Soc. 2003, 125, 13924.
- 72 K. V. Gothelf, A. Thomsen, M. Nielsen, E. Cló, R. S. Brown, J. Am. Chem. Soc. 2004, 126, 1044.
- 73 L. H. Eckardt, K. Naumann, W. M. Pankau, M. Rein, M. Schweitzer, N. Windhab, G. von Kiedrowski, Nature 2002, 420, 286.
- 74 X. Li, Z. J. Gartner, B. N. Tse, D. R. Liu, J. Am. Chem. Soc. 2004, 126, 5090.
- 75 T. M. Snyder, D. R. Liu, Angew. Chem., Int. Ed. 2005, 44, 7379.
- 76 Z. J. Gartner, R. Grubina, C. T. Calderone, D. R. Liu, Angew. Chem., Int. Ed. 2003, 42, 1370.
- 77 A. T. Poulin-Kerstien, P. B. Dervan, J. Am. Chem. Soc. 2003, 125, 15811.
- 78 M. W. Kanan, M. M. Rozenman, K. Sakurai, T. M. Snyder, D. R. Liu, Nature 2004, 431, 545.
- 79 M. Oberhuber, G. F. Joyce, Angew. Chem., Int. Ed. 2005, 44, 7580.
- 80 Z. Tang, A. Marx, Angew. Chem., Int. Ed. 2007, 46, 7297.
- 81 J. L. Czlapinski, T. L. Sheppard, J. Am. Chem. Soc. 2001, 123, 8618.
- 82 K. Tanaka, G. H. Clever, Y. Takezawa, Y. Yamada, C. Kaul, M. Shionoya, T. Carell, Nat. Nanotechnol. 2006, 1, 190.
- 83 M. M. Rozenman, M. W. Kanan, D. R. Liu, J. Am. Chem. Soc. 2007, 129, 14933.
- 84 J. Brunner, A. Mokhir, R. Krämer, J. Am. Chem. Soc. 2003, 125, 12410.
- 85 Z. Ma, J.-S. Taylor, Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11159.
- 86 K. Sakurai, T. M. Snyder, D. R. Liu, J. Am. Chem. Soc. 2005, 127, 1660.
- 87 J. Cai, X. Li, X. Yue, J. S. Taylor, J. Am. Chem. Soc. 2004, 126, 16324.
- 88 G. F. Joyce, Annu. Rev. Biochem. 2004, 73, 791.
- 89 R. K. O. Sigel, A. M. Pyle, Chem. Rev. 2007, 107, 97.
- 90 C. Drayton, K. du Plooy, K. Greenfield, R. Purchase, E. Smeaton, in ‘Science of Synthesis – Houben-Weyl Methods of chemical transformations’, Thieme, Stuttgart, 2001.
- 91
R. Breslow, Tetrahedron Lett. 1959, 21, 22.
10.1016/S0040-4039(01)99487-0 Google Scholar
- 92 M. Rueping, Angew. Chem., Int. Ed. 2006, 45, 1838.
- 93 G. Illuminati, L. Mandolini, Acc. Chem. Res. 1981, 14, 95.
- 94 T. M. Snyder, B. N. Tse, D. R. Liu, J. Am. Chem. Soc. 2008, 130, 1392.
- 95 S. Narayan, J. Muldoon, M. G. Finn, V. V. Fokin, H. C. Kolb, K. B. Sharpless, Angew. Chem., Int. Ed. 2005, 44, 3275.
- 96 G. Roelfes, Mol. Biosyst. 2007, 3, 126.
- 97 A. Jäschke, Curr. Opin. Struct. Biol. 2001, 11, 321.
- 98 M. Bolli, R. Micura, A. Eschenmoser, Chem. Biol. 1997, 4, 309.
- 99 I. A. Kozlov, L. E. Orgel, P. E. Nielsen, Angew. Chem., Int. Ed. 2000, 39, 4292.
- 100
H. C. Kolb, M. G. Finn, K. B. Sharpless, Angew. Chem., Int. Ed. 2001, 40, 2004.
10.1002/1521-3773(20010601)40:11<2004::AID-ANIE2004>3.0.CO;2-5 CAS PubMed Web of Science® Google Scholar
- 101 W. M. Shih, J. D. Quispe, G. F. Joyce, Nature 2004, 427, 618.
- 102 U. Feldkamp, C. M. Niemeyer, Angew. Chem., Int. Ed. 2006, 45, 1856.
- 103 N. C. Seeman, Nature 2003, 421, 427.
- 104 S. Liao, N. C. Seeman, Science 2004, 306, 2072.
- 105 N. M. Green, Adv. Protein Chem. 1975, 29, 85.
- 106 Z. J. Gartner, M. W. Kanan, D. R. Liu, J. Am. Chem. Soc. 2002, 124, 10304.
- 107 P. Brown, D. Botstein, Nat. Genet. 1999, 21, 33.
- 108 K. Mullis, Angew. Chem., Int. Ed. 1994, 33, 1209.
- 109 M. Kramer, D. Coen, in ‘Current Protocols in Molecular Biology’, Vol. 3, Ed. F. M. Ausubel, Wiley, New York, 2000, p. 15.11.
- 110 A. R. Katritzky, G. Musumarra, Chem. Soc. Rev. 1984, 13, 47.
- 111 M. Simon, K. Shokat, in ‘Chemical Biology’, Eds. S. L. Schreiber, T. M. Kapoor, G. Wess, Wiley-VCH, Weinheim, 2007, p. 115.
- 112 D. S. Tan, in ‘Chemical Biology’, Eds. S. L. Schreiber, T. M. Kapoor, G. Wess, Wiley-VCH, Weinheim, 2007, p. 483.
- 113 S. Brenner, R. A. Lerner, Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5381.
- 114 J. Nielsen, S. Brenner, K. D. Janda, J. Am. Chem. Soc. 1993, 115, 9812.
- 115 L. M. Smith, J. Z. Sanders, R. J. Kaiser, P. Hughes, C. Dodd, C. R. Connell, C. Heiner, S. B. H. Kent, L. E. Hood, Nature 1986, 321, 674.
- 116 A. Jain, G. M. Whitesides, R. S. Alexander, D. W. Christianson, J. Med. Chem. 1994, 37, 2100.
- 117 B. N. Tse, T. M. Snyder, Y. Shen, D. R. Liu, J. Am. Chem. Soc. 2008, 130, 15611.
- 118 D. R. Halpin, P. B. Harbury, PLoS Biol. 2004, 2, E174.
- 119 S. Melkko, J. Scheuermann, C. E. Dumelin, D. Neri, Nat. Biotechnol. 2004, 22, 568.
- 120 J. B. Doyon, T. M. Snyder, D. R. Liu, J. Am. Chem. Soc. 2003, 125, 12372.
- 121 S. Klussman, ‘The Aptamer Handbook’, Wiley-VCH, Weinheim, 2006.
- 122 M. Kaiser, S. Wetzel, K. Kumar, H. Waldmann, Cell. Mol. Life Sci. 2008, 65, 1186.
- 123 G. P. Smith, V. A. Petrenko, Chem. Rev. 1997, 97, 391.
- 124 D. R. Halpin, P. B. Harbury, PLoS Biol. 2004, 2, E173.
- 125 D. R. Halpin, J. A. Lee, S. J. Wrenn, P. B. Harbury, PLoS Biol. 2004, 2, E175.
- 126 T. Meo, C. Gramsch, R. Inan, V. Höllt, E. Weber, A. Herz, G. Riethmüller, Proc. Natl. Acad. Sci. U.S.A. 1983, 80, 4084.
- 127 S. J. Wrenn, R. M. Weisinger, D. R. Halpin, P. B. Harbury, J. Am. Chem. Soc. 2007, 129, 13137.
- 128 M. Matsuda, S. Tanaka, S. Nagata, A. Kojima, T. Kurata, M. Shibuya, Mol. Cell. Biol. 1992, 12, 3482.
- 129 W. P. C. Stemmer, Nature 1994, 370, 389.
- 130 C. Lipinski, F. Lombardo, B. Dominy, P. J. Feeney, Adv. Drug Delivery Rev. 1997, 23, 3.
- 131 S. Melkko, C. Dumelin, J. Scheuermann, D. Neri, Drug Discovery Today 2007, 12, 465.
- 132 C. B. Carlson, P. Mowery, R. M. Owen, E. C. Dykhuizen, L. L. Kiessling, ACS Chem. Biol. 2007, 2, 119.
- 133 A. B. Beeler, S. Su, C. A. Singleton, J. A. Porco Jr., J. Am. Chem. Soc. 2007, 129, 1413.
- 134 B. L. Horecker, O. Tsolas, C. Y. Lai, Enzymes 1972, 7, 213.
- 135 J. Kofoed, J.-L. Reymond, T. Darbre, Org. Biomol. Chem. 2005, 3, 1850.
- 136 J. Seayad, B. List, Org. Biomol. Chem. 2005, 3, 719.
- 137 W. Tan, K. Wang, T. J. Drake, Curr. Opin. Chem. Biol. 2004, 8, 547.
- 138 J. Levsky, R. Singer, J. Cell. Sci. 2003, 116, 2833.
- 139 C. A. Heid, J. Stevens, K. J. Livak, P. M. Williams, Genome Res. 1996, 6, 986.
- 140 R. R. Breaker, Nature 2004, 432, 838.
- 141 F. Barany, Proc. Natl. Acad. Sci. U.S.A. 1991, 88, 189.
- 142 V. V. Demidov, M. D. Frank-Kamenetskii, Trends Biochem. Sci. 2004, 29, 62.
- 143 P. E. Dawson, T. W. Muir, I. Clark-Lewis, S. B. Kent, Science 1994, 266, 776.
- 144 J. A. Prescher, C. R. Bertozzi, Nat. Chem. Biol. 2005, 1, 13.
- 145 C. Ziegler, W. Göpel, Curr. Opin. Chem. Biol. 1998, 2, 585.
- 146 N. L. Rosi, C. A. Mirkin, Chem. Rev. 2005, 105, 1547.
- 147 S. L. Schreiber, Nat. Chem. Biol. 2005, 1, 64.
- 148 M. Oberhuber, in ‘The Chemical Biology of Nucleic Acids’, Ed. G. Mayer, Wiley-VCH, Weinheim, 2010, p. 73.
