1. Aristoteles. in Nichomachean Ethics.
2. Watson, J.D. & Crick, F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171, 737-8 (1953).
3. Yakovchuk, P., Protozanova, E. & Frank-Kamenetskii, M.D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix.
Nucleic Acids Res 34, 564-74 (2006).
4. Lodish, H. et al. Molecular Cell Biology, 4th edition (W. H. Freeman, New York, 2000).
5. Arnott, S., Chandrasekaran, R., Birdsall, D.L., Leslie, A.G. & Ratliff, R.L.
Left-handed DNA helices. Nature 283, 743-5 (1980).
6. Gosh, A. & Bansal, M. A glossary of DNA structures from A to Z. Acta Cryst. D59, 620-626 (2003).
7. Kornberg, A. & Baker, T.A. DNA Replication, 2nd edition (University Science Books, 2005).
8. Watson, J.D. & Crick, F.H. Genetical implications of the structure of deoxyribonucleic acid. Nature 171, 964-7 (1953).
9. Bebenek, K. & Kunkel, T.A. Functions of DNA polymerases. Adv Protein Chem 69, 137-65 (2004).
10. Bessman, M.J., Kornberg, A., Lehman, I.R. & Simms, E.S. Enzymic synthesis of deoxyribonucleic acid. Biochim Biophys Acta 21, 197-8 (1956).
11. Berdis, A.J. Mechanisms of DNA polymerases. Chem Rev 109, 2862-79 (2009).
12. Creighton, S., Bloom, L.B. & Goodman, M.F. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol 262, 232-56 (1995).
176
13. Boosalis, M.S., Petruska, J. & Goodman, M.F. DNA polymerase insertion fidelity. Gel assay for site-specific kinetics. J Biol Chem 262, 14689-96 (1987).
14. Johnson, K.A. Conformational coupling in DNA polymerase fidelity. Annu Rev Biochem 62, 685-713 (1993).
15. Steitz, T.A. A mechanism for all polymerases. Nature 391, 231-2 (1998).
16. Kohlstaedt, L.A., Wang, J., Friedman, J.M., Rice, P.A. & Steitz, T.A. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256, 1783-90 (1992).
17. Sousa, R., Chung, Y.J., Rose, J.P. & Wang, B.C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution. Nature 364, 593-9 (1993).
18. Hansen, J.L., Long, A.M. & Schultz, S.C. Structure of the RNA-dependent RNA polymerase of poliovirus. Structure 5, 1109-22 (1997).
19. Wang, J. et al. Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell 89, 1087-99 (1997).
20. Doublie, S., Tabor, S., Long, A.M., Richardson, C.C. & Ellenberger, T.
Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391, 251-8 (1998).
21. Kiefer, J.R., Mao, C., Braman, J.C. & Beese, L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391, 304-7 (1998).
22. Ito, J. & Braithwaite, D.K. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res 19, 4045-57 (1991).
23. Cann, I.K. & Ishino, Y. Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics 152, 1249-67 (1999).
24. Ohmori, H. et al. The Y-family of DNA polymerases. Mol Cell 8, 7-8 (2001).
25. Lipps, G., Rother, S., Hart, C. & Krauss, G. A novel type of replicative enzyme harbouring ATPase, primase and DNA polymerase activity. EMBO J 22, 2516-25 (2003).
_____________________________________________________________________
177
26. Huebscher, U., Maga, G. & Spadari, S. Eukaryotic DNA polymerases. Annu Rev Biochem 71, 133-63 (2002).
27. Steitz, T.A. DNA polymerases: structural diversity and common mechanisms.
J Biol Chem 274, 17395-8 (1999).
28. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102 (2001).
29. Galhardo, R.S., Hastings, P.J. & Rosenberg, S.M. Mutation as a stress response and the regulation of evolvability. Crit Rev Biochem Mol Biol 42, 399-435 (2007).
30. Loeb, L.A. Mutator phenotype in cancer: origin and consequences. Semin Cancer Biol 20, 279-80 (2010).
31. Du Pasquier, L. Origin and evolution of the vertebrate immune system.
APMIS 100, 383-92 (1992).
32. Hughes, A.L. & Yeager, M. Molecular evolution of the vertebrate immune system. Bioessays 19, 777-86 (1997).
33. Seki, M., Gearhart, P.J. & Wood, R.D. DNA polymerases and somatic hypermutation of immunoglobulin genes. EMBO Rep 6, 1143-8 (2005).
34. Strachan, T. & Read, A.P. (1999).
35. Holland, J.F. & Frei, E. Cancer Medicine, 6th edition (Decker Publishing Inc, Hamilton (ON), 2003).
36. McCulloch, S.D. & Kunkel, T.A. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res 18, 148-61 (2008).
37. Kunkel, T.A. & Bebenek, K. DNA replication fidelity. Annu Rev Biochem 69, 497-529 (2000).
38. Goodman, M.F., Creighton, S., Bloom, L.B. & Petruska, J. Biochemical basis of DNA replication fidelity. Crit Rev Biochem Mol Biol 28, 83-126 (1993).
39. Echols, H. & Goodman, M.F. Fidelity mechanisms in DNA replication. Annu Rev Biochem 60, 477-511 (1991).
178
40. Goodman, M.F. Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replication fidelity. Proc Natl Acad Sci U S A 94, 10493-5 (1997).
41. Kool, E.T. Active site tightness and substrate fit in DNA replication. Annu Rev Biochem 71, 191-219 (2002).
42. Kunkel, T.A. DNA replication fidelity. J Biol Chem 267, 18251-4 (1992).
43. Beard, W.A. & Wilson, S.H. Structural insights into DNA polymerase beta fidelity: hold tight if you want it right. Chem Biol 5, R7-13 (1998).
44. Li, Y. & Waksman, G. Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: insights into nucleotide incorporation and selectivity. Protein Sci 10, 1225-33 (2001).
45. Strerath, M., Cramer, J., Restle, T. & Marx, A. Implications of active site constraints on varied DNA polymerase selectivity. J Am Chem Soc 124, 11230-1 (2002).
46. Lee, I. & Berdis, A.J. Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases. Biochim Biophys Acta 1804, 1064-80 (2010).
47. Summerer, D., Rudinger, N.Z., Detmer, I. & Marx, A. Enhanced fidelity in mismatch extension by DNA polymerase through directed combinatorial enzyme design. Angew Chem Int Ed Engl 44, 4712-5 (2005).
48. Rudinger, N.Z. New insights into selectivity of DNA polymerases: A combinatorial approach, Dissertation. (2007).
49. Yao, N.Y. & O'Donnell, M. Replisome structure and conformational dynamics underlie fork progression past obstacles. Curr Opin Cell Biol 21, 336-43 (2009).
50. Huebscher, U., Spadari, S., Villani, G. & Maga, G. DNA Polymerases:
Discovery, Characterization and Functions in Cellular DNA Transactions (World Scientific Publishing Co. Pte. Ltd, Singapur, 2010).
_____________________________________________________________________
179
51. Kamtekar, S. et al. Insights into strand displacement and processivity from the crystal structure of the protein-primed DNA polymerase of bacteriophage phi29. Mol Cell 16, 609-18 (2004).
52. Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. & Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol Cell 30, 137-44 (2008).
53. Burgers, P.M. Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284, 4041-5 (2009).
54. Kaguni, L.S. DNA polymerase gamma, the mitochondrial replicase. Annu Rev Biochem 73, 293-320 (2004).
55. Lee, Y.S., Kennedy, W.D. & Yin, Y.W. Structural insight into processive human mitochondrial DNA synthesis and disease-related polymerase mutations. Cell 139, 312-24 (2009).
56. Barry, E.R. & Bell, S.D. DNA replication in the archaea. Microbiol Mol Biol Rev 70, 876-87 (2006).
57. Ling, H., Boudsocq, F., Plosky, B.S., Woodgate, R. & Yang, W. Replication of a cis-syn thymine dimer at atomic resolution. Nature 424, 1083-7 (2003).
58. Wang, J., Jiang, P.X., Feng, H., Feng, Y. & He, Z.G. Three eukaryote-like Orc1/Cdc6 proteins functionally interact and mutually regulate their activities of binding to the replication origin in the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun 363, 63-70 (2007).
59. Bae, B. et al. Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog. Structure 17, 211-22 (2009).
60. Berg, J.M., Tymoczko, J.L. & Stryer, L. Biochemistry, 5th edition (W. H.
Freeman, New York, 2002).
61. Price, S.R., Ito, N., Oubridge, C., Avis, J.M. & Nagai, K. Crystallization of RNA-protein complexes. I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J Mol Biol 249, 398-408 (1995).
180
62. Kuzmine, I., Gottlieb, P.A. & Martin, C.T. Binding of the priming nucleotide in the initiation of transcription by T7 RNA polymerase. J Biol Chem 278, 2819-23 (2003).
63. Jia, Y. & Patel, S.S. Kinetic mechanism of GTP binding and RNA synthesis during transcription initiation by bacteriophage T7 RNA polymerase. J Biol Chem 272, 30147-53 (1997).
64. Steitz, T.A. The structural changes of T7 RNA polymerase from transcription initiation to elongation. Curr Opin Struct Biol 19, 683-90 (2009).
65. Lubkowska, L., Maharjan, A.S. & Komissarova, N. RNA folding in transcription elongation complex: implication for transcription termination. J Biol Chem (2011).
66. The Basics: In Vitro Transcription.
http://www.ambion.com/techlib/basics/transcription/index.html. (2010).
67. Schärer, O.D. Chemistry and biology of DNA repair. Angew Chem Int Ed Engl 42, 2946-74 (2003).
68. Friedberg, E.C., Walker, G.C. & Siede, W. DNA repair and mutagenesis (American Society for Microbiology, Washington, DC, 1995).
69. Rich, T., Allen, R.L. & Wyllie, A.H. Defying death after DNA damage.
Nature 407, 777-83 (2000).
70. Fiala, K.A. & Suo, Z. Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase. J Biol Chem 282, 8199-206 (2007).
71. Goodman, M.F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu Rev Biochem 71, 17-50 (2002).
72. Lindahl, T. & Nyberg, B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 11, 3610-8 (1972).
73. Lindahl, T. Instability and decay of the primary structure of DNA. Nature 362, 709-15 (1993).
74. Randall, S.K., Eritja, R., Kaplan, B.E., Petruska, J. & Goodman, M.F.
Nucleotide insertion kinetics opposite abasic lesions in DNA. J Biol Chem 262, 6864-70 (1987).
_____________________________________________________________________
181
75. Biertümpfel, C. et al. Structure and mechanism of human DNA polymerase eta. Nature 465, 1044-8 (2010).
76. Boudsocq, F., Iwai, S., Hanaoka, F. & Woodgate, R. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta. Nucleic Acids Res 29, 4607-16 (2001).
77. Brown, J.A., Newmister, S.A., Fiala, K.A. & Suo, Z. Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase. Nucleic Acids Res 36, 3867-78 (2008).
78. Fiala, K.A., Hypes, C.D. & Suo, Z. Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase. J Biol Chem 282, 8188-98 (2007).
79. Strauss, B.S. The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions? Bioessays 13, 79-84 (1991).
80. Goodman, M.F., Cai, H., Bloom, L.B. & Eritja, R. Nucleotide insertion and primer extension at abasic template sites in different sequence contexts. Ann N Y Acad Sci 726, 132-42; discussion 142-3 (1994).
81. Taylor, J.S. New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions. Mutat Res 510, 55-70 (2002).
82. Obeid, S. et al. Replication through an abasic DNA lesion: structural basis for adenine selectivity. EMBO J 29, 1738-47 (2010).
83. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol Cell 13, 751-62 (2004).
84. Mullis, K.B. & Faloona, F.A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155, 335-50 (1987).
85. Morrison, T.B., Weis, J.J. & Wittwer, C.T. Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification.
Biotechniques 24, 954-8, 960, 962 (1998).
182
86. Kranaster, R. & Marx, A. Engineered DNA polymerases in biotechnology.
Chembiochem 11, 2077-84 (2010).
87. U.S. Department of Energy Genome Programs,
http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml.
(2010).
88. Martin, E.R. et al. SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. Am J Hum Genet 67, 383-94 (2000).
89. Bertina, R.M. et al. Mutation in blood coagulation factor V associated with resistance to activated protein C. Nature 369, 64-7 (1994).
90. Syvanen, A.C. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet 2, 930-42 (2001).
91. McCarthy, J.J. & Hilfiker, R. The use of single-nucleotide polymorphism maps in pharmacogenomics. Nat Biotechnol 18, 505-8 (2000).
92. Giacomini, K.M. et al. The pharmacogenetics research network: from SNP discovery to clinical drug response. Clin Pharmacol Ther 81, 328-45 (2007).
93. Germer, S. & Higuchi, R. Single-tube genotyping without oligonucleotide probes. Genome Res 9, 72-8 (1999).
94. Livak, K.J. Allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet Anal 14, 143-9 (1999).
95. Mein, C.A. et al. Evaluation of single nucleotide polymorphism typing with invader on PCR amplicons and its automation. Genome Res 10, 330-43 (2000).
96. Strerath, M., Gaster, J., Summerer, D. & Marx, A. Increased single-nucleotide discrimination of PCR by primer probes bearing hydrophobic 4'C modifications. Chembiochem 5, 333-9 (2004).
97. Mardis, E.R. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9, 387-402 (2008).
98. Morozova, O. & Marra, M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 92, 255-64 (2008).
_____________________________________________________________________
183
99. Huber, J.A. et al. Microbial population structures in the deep marine biosphere. Science 318, 97-100 (2007).
100. Simon, C. & Daniel, R. Metagenomic analyses: past and future trends. Appl Environ Microbiol 77, 1153-61 (2011).
101. Jung, K.H. & Marx, A. Nucleotide analogues as probes for DNA polymerases. Cell Mol Life Sci 62, 2080-91 (2005).
102. Jung, K.H. & Marx, A. in Modified Nucleosides: in Biochemistry, Biotechnology and Medicine (ed. Herdewijn, P.) (WILEY-VCH, Weinheim, 2008).
103. Obika, S. et al. Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3, -endo sugar puckering. Tetrahedron Letters 38, 8735-8738 (1997).
104. Singh, S.K., Nielsen, P., Koshkin, A.A. & Wengel, J. LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem. Commun., 455-456 (1998).
105. Veedu, R.N. & Wengel, J. Locked nucleic acid nucleoside triphosphates and polymerases: on the way towards evolution of LNA aptamers. Mol Biosyst 5, 787-92 (2009).
106. Chaput, J.C. & Szostak, J.W. TNA synthesis by DNA polymerases. J Am Chem Soc 125, 9274-5 (2003).
107. Kempeneers, V., Vastmans, K., Rozenski, J. & Herdewijn, P. Recognition of threosyl nucleotides by DNA and RNA polymerases. Nucleic Acids Res 31, 6221-6 (2003).
108. Horhota, A.T., Szostak, J.W. & McLaughlin, L.W. Glycerol nucleoside triphosphates: synthesis and polymerase substrate activities. Org Lett 8, 5345-7 (2006).
109. Fa, M., Radeghieri, A., Henry, A.A. & Romesberg, F.E. Expanding the substrate repertoire of a DNA polymerase by directed evolution. J Am Chem Soc 126, 1748-54 (2004).
184
110. Ghadessy, F.J. et al. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nat Biotechnol 22, 755-9 (2004).
111. Henry, A.A. & Romesberg, F.E. The evolution of DNA polymerases with novel activities. Curr Opin Biotechnol 16, 370-7 (2005).
112. Leconte, A.M., Chen, L. & Romesberg, F.E. Polymerase evolution: efforts toward expansion of the genetic code. J Am Chem Soc 127, 12470-1 (2005).
113. Ong, J.L., Loakes, D., Jaroslawski, S., Too, K. & Holliger, P. Directed evolution of DNA polymerase, RNA polymerase and reverse transcriptase activity in a single polypeptide. J Mol Biol 361, 537-50 (2006).
114. Loakes, D. & Holliger, P. Polymerase engineering: towards the encoded synthesis of unnatural biopolymers. Chem Commun (Camb), 4619-31 (2009).
115. Ramsay, N. et al. CyDNA: synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase. J Am Chem Soc 132, 5096-104 (2010).
116. Holmberg, R.C., Henry, A.A. & Romesberg, F.E. Directed evolution of novel polymerases. Biomol Eng 22, 39-49 (2005).
117. Astatke, M., Ng, K., Grindley, N.D. & Joyce, C.M. A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc Natl Acad Sci U S A 95, 3402-7 (1998).
118. Gao, G., Orlova, M., Georgiadis, M.M., Hendrickson, W.A. & Goff, S.P.
Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc Natl Acad Sci U S A 94, 407-11 (1997).
119. Bonnin, A., Lazaro, J.M., Blanco, L. & Salas, M. A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase. J Mol Biol 290, 241-51 (1999).
120. Li, Y., Mitaxov, V. & Waksman, G. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
Proc Natl Acad Sci U S A 96, 9491-6 (1999).
_____________________________________________________________________
185
121. Padilla, R. & Sousa, R. A Y639F/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs.
Nucleic Acids Res 30, e138 (2002).
122. Rudinger, N.Z., Kranaster, R. & Marx, A. Hydrophobic amino acid and single-atom substitutions increase DNA polymerase selectivity. Chem Biol 14, 185-94 (2007).
123. Patel, P.H. & Loeb, L.A. Multiple amino acid substitutions allow DNA polymerases to synthesize RNA. J Biol Chem 275, 40266-72 (2000).
124. Xia, G. et al. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc Natl Acad Sci U S A 99, 6597-602 (2002).
125. Staiger, N. & Marx, A. A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides. Chembiochem 11, 1963-6 (2010).
126. Ghadessy, F.J. & Holliger, P. Compartmentalized self-replication: a novel method for the directed evolution of polymerases and other enzymes.
Methods Mol Biol 352, 237-48 (2007).
127. Strerath, M., Gloeckner, C., Liu, D., Schnur, A. & Marx, A. Directed DNA polymerase evolution: effects of mutations in motif C on the mismatch-extension selectivity of thermus aquaticus DNA polymerase. Chembiochem 8, 395-401 (2007).
128. Arnold, F.H. & Georgiou, G. (eds.) Directed evolution library creation:
methods and protocols (Humana Press, Totowa (NJ), 2003).
129. Cadwell, R.C. & Joyce, G.F. Randomization of genes by PCR mutagenesis.
PCR Methods Appl 2, 28-33 (1992).
130. Biles, B.D. & Connolly, B.A. Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR. Nucleic Acids Res 32, e176 (2004).
131. GeneMorph® II Random Mutagenesis kit, Agilent Technologies.
186
132. Ghadessy, F.J., Ong, J.L. & Holliger, P. Directed evolution of polymerase function by compartmentalized self-replication. Proc Natl Acad Sci U S A 98, 4552-7 (2001).
133. Sauter, K.B. & Marx, A. Evolving thermostable reverse transcriptase activity in a DNA polymerase scaffold. Angew Chem Int Ed Engl 45, 7633-5 (2006).
134. Gloeckner, C., Sauter, K.B. & Marx, A. Evolving a thermostable DNA polymerase that amplifies from highly damaged templates. Angew Chem Int Ed Engl 46, 3115-7 (2007).
135. Gieseking, S. et al. Human DNA polymerase beta mutations allowing efficient abasic site bypass. J Biol Chem 286, 4011-20 (2011).
136. Kurtzman, A.L. et al. Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins. Curr Opin Biotechnol 12, 361-70 (2001).
137. Giver, L. & Arnold, F.H. Combinatorial protein design by in vitro recombination. Curr Opin Chem Biol 2, 335-8 (1998).
138. Zhao, H., Giver, L., Shao, Z., Affholter, J.A. & Arnold, F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16, 258-61 (1998).
139. Henke, E. & Bornscheuer, U.T. Directed evolution of an esterase from Pseudomonas fluorescens. Random mutagenesis by error-prone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay. Biol Chem 380, 1029-33 (1999).
140. Wong, T.S., Tee, K.L., Hauer, B. & Schwaneberg, U. Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution. Nucleic Acids Res 32, e26 (2004).
141. Tawfik, D.S. & Griffiths, A.D. Man-made cell-like compartments for molecular evolution. Nat Biotechnol 16, 652-6 (1998).
142. Matsuura, T. & Yomo, T. In vitro evolution of proteins. J Biosci Bioeng 101, 449-56 (2006).
_____________________________________________________________________
187
143. Washington, S.L. et al. A genetic system to identify DNA polymerase beta mutator mutants. Proc Natl Acad Sci U S A 94, 1321-6 (1997).
144. Summerer, D. Die Selektivität der DNA-Replikation: Neue Einblicke durch synthetische Sonden und kombinatorisches Protein-Design, Dissertation.
(2004).
145. Obeid, S., Yulikov, M., Jeschke, G. & Marx, A. Enzymatic synthesis of multiple spin-labeled DNA. Angew Chem Int Ed Engl 47, 6782-5 (2008).
146. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-9 (2008).
147. Wilson, D.S. & Szostak, J.W. In vitro selection of functional nucleic acids.
Annu Rev Biochem 68, 611-47 (1999).
148. Klug, S.J. & Famulok, M. All you wanted to know about SELEX. Mol Biol Rep 20, 97-107 (1994).
149. Famulok, M., Hartig, J.S. & Mayer, G. Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy. Chem Rev 107, 3715-43 (2007).
150. Shih, W.M., Quispe, J.D. & Joyce, G.F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618-21 (2004).
151. Lin, C., Wang, X., Liu, Y., Seeman, N.C. & Yan, H. Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure. J Am Chem Soc 129, 14475-81 (2007).
152. Keller, S., Wang, J., Chandra, M., Berger, R. & Marx, A. DNA polymerase-catalyzed DNA network growth. J Am Chem Soc 130, 13188-9 (2008).
153. Gardner, A.F. & Jack, W.E. Determinants of nucleotide sugar recognition in an archaeon DNA polymerase. Nucleic Acids Res 27, 2545-53 (1999).
154. Obeid, S., Baccaro, A., Welte, W., Diederichs, K. & Marx, A. Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 107, 21327-31 (2010).
155. Egli, M. & Gryaznov, S.M. Synthetic oligonucleotides as RNA mimetics: 2'-modified Rnas and N3'-->P5' phosphoramidates. Cell Mol Life Sci 57, 1440-56 (2000).
188
156. Czauderna, F. et al. Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res 31, 2705-16 (2003).
157. Allerson, C.R. et al. Fully 2'-modified oligonucleotide duplexes with improved in vitro potency and stability compared to unmodified small interfering RNA. J Med Chem 48, 901-4 (2005).
158. Gardner, A.F. & Jack, W.E. Acyclic and dideoxy terminator preferences denote divergent sugar recognition by archaeon and Taq DNA polymerases.
Nucleic Acids Res 30, 605-13 (2002).
159. Southworth, M.W. et al. Cloning of thermostable DNA polymerases from hyperthermophilic marine Archaea with emphasis on Thermococcus sp. 9 degrees N-7 and mutations affecting 3'-5' exonuclease activity. Proc Natl Acad Sci U S A 93, 5281-5 (1996).
160. McCullum, E.O. & Chaput, J.C. Transcription of an RNA aptamer by a DNA polymerase. Chem Commun (Camb), 2938-40 (2009).
161. Horhota, A. et al. Kinetic analysis of an efficient DNA-dependent TNA polymerase. J Am Chem Soc 127, 7427-34 (2005).
162. Ichida, J.K., Horhota, A., Zou, K., McLaughlin, L.W. & Szostak, J.W. High fidelity TNA synthesis by Therminator polymerase. Nucleic Acids Res 33, 5219-25 (2005).
163. Chen, J.J. et al. Enzymatic primer-extension with glycerol-nucleoside triphosphates on DNA templates. PLoS One 4, e4949 (2009).
164. Welch, M. et al. Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 4, e7002 (2009).
165. Peist, R. et al. Characterization of the aes gene of Escherichia coli encoding an enzyme with esterase activity. J Bacteriol 179, 7679-86 (1997).
166. Kranaster, R. & Marx, A. Taking fingerprints of DNA polymerases: multiplex enzyme profiling on DNA arrays. Angew Chem Int Ed Engl 48, 4625-8 (2009).
167. Barbas, C.F., Burton, D.R., Scott, J.K. & Silverman, G.J. Phage Display: A Laboratory Manual (Cold Spring Harbor Laboratory Press, New York, 2001).