The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides. 1. Introduction Since the structure of DNA was determined [1, 2], biochemists have sought more detailed ways to study DNA and the proteins that interact with it [3, 4]. Solid phase nucleic acid synthesis of DNA molecules facilitates the site-specific incorporation of a wide range of chemically modified bases and sugar-phosphate backbones, allowing the roles of specific atoms in DNA function and recognition to be probed. Synthetic nonnatural nucleobases are useful for a variety of studies of DNA polymerase function, such as studies of DNA polymerase specificity, mutagenesis, and dynamics, as well as fluorescence resonance energy transfer (FRET) analysis of DNA polymerase interactions with DNA. The study of mutagenesis facilitated by DNA polymerases has attracted increasing interest because replication defects can lead to certain human diseases like the cancer-prone syndrome xeroderma pigmentosum variant (XPV) [5, 6] and other diseases [7–9], as well as potentially contribute to antibiotic resistance [10, 11]. Moreover, specialized damage-bypass DNA polymerases are implicated in conferring cellular tolerance to cancer chemotherapy agents that act via DNA damage, thereby decreasing their effectiveness [12–16]. This paper will focus on the ability of DNA polymerases to recognize and accept nonnatural bases either on the
References
[1]
R. E. Franklin and R. G. Gosling, “Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate,” Nature, vol. 172, no. 4369, pp. 156–157, 1953.
[2]
J. D. Watson and F. H. Crick, “Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid,” Nature, vol. 171, no. 4356, pp. 737–738, 1953.
[3]
A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid,” Harvey Lectures, vol. 53, pp. 83–112, 1957.
[4]
K. Kleppe, E. Ohtsuka, R. Kleppe, I. Molineux, and H. G. Khorana, “Studies on polynucleotides. XCVI. Repair replication of short synthetic DNA's as catalyzed by DNA polymerases,” Journal of Molecular Biology, vol. 56, no. 2, pp. 341–361, 1971.
[5]
A. M. Cordonnier and R. P. Fuchs, “Replication of damaged DNA: molecular defect in Xeroderma pigmentosum variant cells,” Mutation Research, vol. 435, no. 2, pp. 111–119, 1999.
[6]
A. Bresson and R. P. Fuchs, “Lesion bypass in yeast cells: pol eta participates in a multi-DNA polymerase process,” EMBO Journal, vol. 21, no. 14, pp. 3881–3887, 2002.
[7]
V. Pages and R. P. Fuchs, “How DNA lesions are turned into mutations within cells?” Oncogene, vol. 21, no. 58, pp. 8957–8966, 2002.
[8]
S. S. Lange, K. Takata, and R. D. Wood, “DNA polymerases and cancer,” Nature Reviews Cancer, vol. 11, no. 2, pp. 96–110, 2011.
[9]
L. A. Loeb and R. J. Monnat Jr., “DNA polymerases and human disease,” Nature Reviews Genetics, vol. 9, no. 8, pp. 594–604, 2008.
[10]
C. Miller, L. E. Thomsen, C. Gaggero, R. Mosseri, H. Ingmer, and S. N. Cohen, “SOS response induction by beta-lactams and bacterial defense against antibiotic lethality,” Science, vol. 305, no. 5690, pp. 1629–1631, 2004.
[11]
R. Napolitano, R. Janel-Bintz, J. Wagner, and R. P. Fuchs, “All three SOS-inducible DNA polymerases (pol II, pol IV and pol V) are involved in induced mutagenesis,” EMBO Journal, vol. 19, no. 22, pp. 6259–6265, 2000.
[12]
M. R. Albertella, C. M. Green, A. R. Lehmann, and M. J. O'Connor, “A role for polymerase eta in the cellular tolerance to cisplatin-induced damage,” Cancer Research, vol. 65, no. 21, pp. 9799–9806, 2005.
[13]
M. R. Albertella, A. Lau, and M. J. O'Connor, “The overexpression of specialized DNA polymerases in cancer,” DNA Repair, vol. 4, no. 5, pp. 583–593, 2005.
[14]
E. Bassett, N. M. King, M. F. Bryant et al., “The role of DNA polymerase eta in translesion synthesis past platinum-DNA adducts in human fibroblasts,” Cancer Research, vol. 64, no. 18, pp. 6469–6475, 2004.
[15]
Y. W. Chen, J. E. Cleaver, F. Hanaoka, C. F. Chang, and K. M. Chou, “A novel role of DNA polymerase eta in modulating cellular sensitivity to chemotherapeutic agents,” Molecular Cancer Research, vol. 4, no. 4, pp. 257–265, 2006.
[16]
T. V. Ho, A. Guainazzi, S. B. Derkunt, M. Enoiu, and O. D. Scharer, “Structure-dependent bypass of DNA interstrand crosslinks by translesion synthesis polymerases,” Nucleic Acids Research, vol. 39, pp. 7455–7464, 2011.
[17]
H. Ohmori, E. C. Friedberg, R. P. Fuchs et al., “The Y-family of DNA polymerases,” Molecular Cell, vol. 8, no. 1, pp. 7–8, 2001.
[18]
P. H. Patel, M. Suzuki, E. Adman, A. Shinkai, and L. A. Loeb, “Prokaryotic DNA polymerase I: evolution, structure, and “base flipping” mechanism for nucleotide selection,” Journal of Molecular Biology, vol. 308, no. 5, pp. 823–837, 2001.
[19]
R. G. Federley and L. J. Romano, “DNA polymerase: structural homology, conformational dynamics, and the effects of carcinogenic DNA adducts,” Journal of Nucleic Acids, vol. 2010, Article ID 457176, 15 pages, 2010.
[20]
P. M. Burgers and F. Eckstein, “A study of the mechanism of DNA polymerase I from Escherichia coli with diastereomeric phosphorothioate analogs of deoxyadenosine triphosphate,” The Journal of Biological Chemistry, vol. 254, no. 15, pp. 6889–6893, 1979.
[21]
J. Adler, I. R. Lehman, M. J. Bessman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. IV. linkage of single deoxynucleotides to the deoxynucleoside ends of deoxyribonucleic acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 44, pp. 641–647, 1958.
[22]
M. J. Bessman, I. R. Lehman, J. Adler, S. B. Zimmerman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. III. The incorporation of pyrimidine and purine analogues into deoxyribonucleic acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 44, pp. 633–640, 1958.
[23]
M. J. Bessman, I. R. Lehman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. II. General properties of the reaction,” The Journal of Biological Chemistry, vol. 233, no. 1, pp. 171–177, 1958.
[24]
S. R. Kornberg, I. R. Lehman, M. J. Bessman, E. S. Simms, and A. Kornberg, “Enzymatic cleavage of deoxyguanosine triphosphate to deoxyguanosine and tripolyphosphate,” The Journal of Biological Chemistry, vol. 233, no. 1, pp. 159–162, 1958.
[25]
I. R. Lehman, M. J. Bessman, E. S. Simms, and A. Kornberg, “Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from Escherichia coli,” The Journal of Biological Chemistry, vol. 233, no. 1, pp. 163–170, 1958.
[26]
A. J. Berdis, “Mechanisms of DNA polymerases,” Chemical Reviews, vol. 109, no. 7, pp. 2862–2879, 2009.
[27]
L. J. Reha-Krantz, “DNA polymerase proofreading: multiple roles maintain genome stability,” Biochimica et Biophysica Acta, vol. 1804, no. 5, pp. 1049–1063, 2010.
[28]
I. Lee and A. J. Berdis, “Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases,” Biochimica et Biophysica Acta, vol. 1804, no. 5, pp. 1064–1080, 2010.
[29]
E. Friedberg, G. C. Walker, W. W. Siede, R. D. Wood, R. Schultz, and T. Ellenberger, DNA Repair and Mutagenesis, ASM Press, 2nd edition, 2006.
[30]
S. J. Johnson, J. S. Taylor, and L. S. Beese, “Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 7, pp. 3895–3900, 2003.
[31]
H. Ling, F. Boudsocq, R. Woodgate, and W. Yang, “Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication,” Cell, vol. 107, no. 1, pp. 91–102, 2001.
[32]
J. R. Kiefer, C. Mao, C. J. Hansen et al., “Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1？？ resolution,” Structure, vol. 5, no. 1, pp. 95–108, 1997.
[33]
P. J. Rothwell and G. Waksman, “Structure and mechanism of DNA polymerases,” Advances in Protein Chemistry, vol. 71, pp. 401–440, 2005.
[34]
R. P. Fuchs and S. Fujii, “Translesion synthesis in Escherichia coli: lessons from the NarI mutation hot spot,” DNA Repair, vol. 6, no. 7, pp. 1032–1041, 2007.
[35]
S. Fujii and R. P. Fuchs, “Defining the position of the switches between replicative and bypass DNA polymerases,” EMBO Journal, vol. 23, no. 21, pp. 4342–4352, 2004.
[36]
D. F. Jarosz, S. E. Cohen, J. C. Delaney, J. M. Essigmann, and G. C. Walker, “A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 50, pp. 21137–21142, 2009.
[37]
V. Pages, R. Janel-Bintz, and R. P. Fuchs, “Pol III proofreading activity prevents lesion bypass as evidenced by its molecular signature within E. coli cells,” Journal of Molecular Biology, vol. 352, no. 3, pp. 501–509, 2005.
[38]
E. T. Kool, “Replacing the nucleobases in DNA with designer molecules,” Accounts of Chemical Research, vol. 35, no. 11, pp. 936–943, 2002.
[39]
M. Takeshita, C. N. Chang, F. Johnson, S. Will, and A. P. Grollman, “Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases,” The Journal of Biological Chemistry, vol. 262, no. 21, pp. 10171–10179, 1987.
[40]
B. S. Strauss, “The “A rule” of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions?” BioEssays, vol. 13, no. 2, pp. 79–84, 1991.
[41]
S. Obeid, N. Blatter, R. Kranaster et al., “Replication through an abasic DNA lesion: structural basis for adenine selectivity,” EMBO Journal, vol. 29, no. 10, pp. 1738–1747, 2010.
[42]
I. Bruck, M. F. Goodman, and M. O'Donnell, “The essential C family DnaE polymerase is error-prone and efficient at lesion bypass,” The Journal of Biological Chemistry, vol. 278, no. 45, pp. 44361–44368, 2003.
[43]
E. Le Chatelier, O. J. Bécherel, E. d'Alen？on et al., “Involvement of DnaE, the second replicative DNA polymerase from Bacillus subtilis, in DNA mutagenesis,” The Journal of Biological Chemistry, vol. 279, no. 3, pp. 1757–1767, 2004.
[44]
C. S. McHenry, “Breaking the rules: bacteria that use several DNA polymerase IIIs,” EMBO Reports, vol. 12, no. 5, pp. 408–414, 2011.
[45]
J. E. Stone, D. Kumar, S. K. Binz et al., “Lesion bypass by S. cerevisiae Pol zeta alone,” DNA Repair, vol. 10, no. 8, pp. 826–834, 2011.
[46]
S. Kumar, B. J. Lamarche, and M. D. Tsai, “Use of damaged DNA and dNTP substrates by the error-prone DNA polymerase X from African swine fever virus,” Biochemistry, vol. 46, no. 12, pp. 3814–3825, 2007.
[47]
K. A. Fiala, C. D. Hypes, and Z. Suo, “Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase,” The Journal of Biological Chemistry, vol. 282, no. 11, pp. 8188–8198, 2007.
[48]
A. Maor-Shoshani, K. Hayashi, H. Ohmori, and Z. Livneh, “Analysis of translesion replication across an abasic site by DNA polymerase IV of Escherichia coli,” DNA Repair, vol. 2, no. 11, pp. 1227–1238, 2003.
[49]
N. B. Reuven, G. Arad, A. Maor-Shoshani, and Z. Livneh, “The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication,” The Journal of Biological Chemistry, vol. 274, no. 45, pp. 31763–31766, 1999.
[50]
M. Tang, P. Pham, X. Shen et al., “Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis,” Nature, vol. 404, no. 6781, pp. 1014–1018, 2000.
[51]
K. Bebenek, A. Tissier, E. G. Frank et al., “ -deoxyribose phosphate lyase activity of human DNA polymerase iota in vitro,” Science, vol. 291, no. 5511, pp. 2156–2159, 2001.
[52]
Y. Zhang, F. Yuan, X. Wu, J. S. Taylor, and Z. Wang, “Response of human DNA polymerase iota to DNA lesions,” Nucleic Acids Research, vol. 29, no. 4, pp. 928–935, 2001.
[53]
C. Masutani, R. Kusumoto, S. Iwai, and F. Hanaoka, “Mechanisms of accurate translesion synthesis by human DNA polymerase eta,” EMBO Journal, vol. 19, no. 12, pp. 3100–3109, 2000.
[54]
R. J. Kokoska, S. D. McCulloch, and T. A. Kunkel, “The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase eta and Sulfolobus solfataricus Dpo4,” The Journal of Biological Chemistry, vol. 278, no. 50, pp. 50537–50545, 2003.
[55]
S. M. Sherrer, K. A. Fiala, J. D. Fowler, S. A. Newmister, J. M. Pryor, and Z. Suo, “Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases,” Nucleic Acids Research, vol. 39, no. 2, pp. 609–622, 2011.
[56]
Y. Zhang, F. Yuan, X. Wu et al., “Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro,” Nucleic Acids Research, vol. 28, no. 21, pp. 4138–4146, 2000.
[57]
N. Kim, S. V. Mudrak, and S. Jinks-Robertson, “The dCMP transferase activity of yeast Rev1 is biologically relevant during the bypass of endogenously generated AP sites,” DNA Repair, vol. 10, pp. 1262–1271, 2011.
[58]
J. M. Pryor and M. T. Washington, “Pre-steady state kinetic studies show that an abasic site is a cognate lesion for the yeast Rev1 protein,” DNA Repair, vol. 10, pp. 1138–1144, 2011.
[59]
C. Otsuka, D. Loakes, and K. Negishi, “The role of deoxycytidyl transferase activity of yeast Rev1 protein in the bypass of abasic sites,” Nucleic Acids Research, no. 2, pp. 87–88, 2002.
[60]
N. Sabouri and E. Johansson, “Translesion synthesis of abasic sites by yeast DNA polymerase epsilon,” The Journal of Biological Chemistry, vol. 284, no. 46, pp. 31555–31563, 2009.
[61]
B. Zhao, Z. Xie, H. Shen, and Z. Wang, “Role of DNA polymerase eta in the bypass of abasic sites in yeast cells,” Nucleic Acids Research, vol. 32, no. 13, pp. 3984–3994, 2004.
[62]
T. J. Matray and E. T. Kool, “A specific partner for abasic damage in DNA,” Nature, vol. 399, no. 6737, pp. 704–708, 1999.
[63]
L. Sun, K. Zhang, L. Zhou et al., “Yeast pol eta holds a Cis-Syn thymine dimer loosely in the active site during elongation opposite the -T of the dimer, but tightly opposite the -T,” Biochemistry, vol. 42, no. 31, pp. 9431–9437, 2003.
[64]
X. Zhang, I. Lee, X. Zhou, and A. J. Berdis, “Hydrophobicity, shape, and pi-electron contributions during translesion DNA synthesis,” Journal of the American Chemical Society, vol. 128, no. 1, pp. 143–149, 2006.
[65]
E. Z. Reineks and A. J. Berdis, “Evaluating the contribution of base stacking during translesion DNA replication,” Biochemistry, vol. 43, no. 2, pp. 393–404, 2004.
[66]
R. E. Johnson, M. T. Washington, L. Haracska, S. Prakash, and L. Prakash, “Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions,” Nature, vol. 406, no. 6799, pp. 1015–1019, 2000.
[67]
S. Shachar, O. Ziv, S. Avkin et al., “Two-polymerase mechanisms dictate error-free and error-prone translesion DNA synthesis in mammals,” EMBO Journal, vol. 28, no. 4, pp. 383–393, 2009.
[68]
D. Jarosz, P. Beuning, S. Cohen, and G. C. Walker, “Y-family DNA polymerases in Escherichia coli,” Trends in Microbiology, vol. 15, no. 2, pp. 70–77, 2007.
[69]
J. M. Walsh, L. A. Hawver, and P. J. Beuning, “Escherichia coli Y family DNA polymerases,” Frontiers in Bioscience, vol. 16, no. 7, pp. 3164–3182, 2011.
[70]
L. S. Waters, B. K. Minesinger, M. E. Wiltrout, S. D'Souza, R. V. Woodruff, and G. C. Walker, “Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance,” Microbiology and Molecular Biology Reviews, vol. 73, no. 1, pp. 134–154, 2009.
[71]
M. T. Washington, K. D. Carlson, B. D. Freudenthal, and J. M. Pryor, “Variations on a theme: Eukaryotic Y-family DNA polymerases,” Biochimica et Biophysica Acta, vol. 1804, no. 5, pp. 1113–1123, 2010.
[72]
W. Yang, “Damage repair DNA polymerases Y,” Current Opinion in Structural Biology, vol. 13, no. 1, pp. 23–30, 2003.
[73]
W. Yang and R. Woodgate, “What a difference a decade makes: insights into translesion DNA synthesis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 40, pp. 15591–15598, 2007.
[74]
A. Maor-Shoshani, V. Ben-Ari, and Z. Livneh, “Lesion bypass DNA polymerases replicate across non-DNA segments,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 25, pp. 14760–14765, 2003.
[75]
S. Adar and Z. Livneh, “Translesion DNA synthesis across non-DNA segments in cultured human cells,” DNA Repair, vol. 5, no. 4, pp. 479–490, 2006.
[76]
J. Y. Choi, K. C. Angel, and F. P. Guengerich, “Translesion synthesis across bulky N2-alkyl guanine DNA adducts by human DNA polymerase kappa,” The Journal of Biological Chemistry, vol. 281, no. 30, pp. 21062–21072, 2006.
[77]
J. Y. Choi and F. P. Guengerich, “Adduct size limits efficient and error-free bypass across bulky N2-guanine DNA lesions by human DNA polymerase eta,” Journal of Molecular Biology, vol. 352, no. 1, pp. 72–90, 2005.
[78]
J. Y. Choi and F. P. Guengerich, “Kinetic evidence for inefficient and error-prone bypass across bulky N2-guanine DNA adducts by human DNA polymerase,” The Journal of Biological Chemistry, vol. 281, no. 18, pp. 12315–12324, 2006.
[79]
J. Y. Choi and F. P. Guengerich, “Kinetic analysis of translesion synthesis opposite bulky N2- and O6-alkylguanine DNA adducts by human DNA polymerase REV1,” The Journal of Biological Chemistry, vol. 283, no. 35, pp. 23645–23655, 2008.
[80]
J. Y. Choi and F. P. Guengerich, “Analysis of the effect of bulk at N2-alkylguanine DNA adducts on catalytic efficiency and fidelity of the Processive DNA polymerases bacteriophage T7 exonuclease- and HIV-1 reverse transcriptase,” The Journal of Biological Chemistry, vol. 279, no. 18, pp. 19217–19229, 2004.
[81]
J. Y. Choi, G. Chowdhury, H. Zang et al., “Translesion synthesis across O6-alkylguanine DNA adducts by recombinant human DNA polymerases,” The Journal of Biological Chemistry, vol. 281, no. 50, pp. 38244–38256, 2006.
[82]
S. Matsuda, A. A. Henry, and F. E. Romesberg, “Optimization of unnatural base pair packing for polymerase recognition,” Journal of the American Chemical Society, vol. 128, no. 19, pp. 6369–6375, 2006.
[83]
S. Matsuda, A. M. Leconte, and F. E. Romesberg, “Minor groove hydrogen bonds and the replication of unnatural base pairs,” Journal of the American Chemical Society, vol. 129, no. 17, pp. 5551–5557, 2007.
[84]
D. L. McMinn, A. K. Ogawa, Y. Wu, J. Liu, P. G. Schultz, and F. E. Romesberg, “Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base,” Journal of the American Chemical Society, vol. 121, no. 49, pp. 11585–11586, 1999.
[85]
G. T. Hwang and F. E. Romesberg, “Substituent effects on the pairing and polymerase recognition of simple unnatural base pairs,” Nucleic Acids Research, vol. 34, no. 7, pp. 2037–2045, 2006.
[86]
A. A. Henry, C. Yu, and F. E. Romesberg, “Determinants of unnatural nucleobase stability and polymerase recognition,” Journal of the American Chemical Society, vol. 125, no. 32, pp. 9638–9646, 2003.
[87]
M. J. Guo, S. Hildbrand, C. J. Leumann, L. W. McLaughlin, and M. J. Waring, “Inhibition of DNA polymerase reactions by pyrimidine nucleotide analogues lacking the 2-keto group,” Nucleic Acids Research, vol. 26, no. 8, pp. 1863–1869, 1998.
[88]
J. A. Piccirilli, S. E. Moroney, and S. A. Benner, “A C-nucleotide base pair: methylpseudouridine-directed incorporation of formycin triphosphate into RNA catalyzed by T7 RNA polymerase,” Biochemistry, vol. 30, no. 42, pp. 10350–10356, 1991.
[89]
M. Trostler, A. Delier, J. Beckman et al., “Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus,” Biochemistry, vol. 48, no. 21, pp. 4633–4641, 2009.
[90]
H. Zhang, U. Bren, I. D. Kozekov, C. J. Rizzo, D. F. Stec, and F. P. Guengerich, “Steric and electrostatic effects at the C2 atom substituent influence replication and miscoding of the DNA deamination product deoxyxanthosine and analogs by DNA polymerases,” Journal of Molecular Biology, vol. 392, no. 2, pp. 251–269, 2009.
[91]
N. Paul, V. C. Nashine, G. Hoops et al., “DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs,” Chemistry and Biology, vol. 10, no. 9, pp. 815–825, 2003.
[92]
A. A. Henry, A. G. Olsen, S. Matsuda, C. Yu, B. H. Geierstanger, and F. E. Romesberg, “Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair,” Journal of the American Chemical Society, vol. 126, no. 22, pp. 6923–6931, 2004.
[93]
K. Eng, S. K. Scouten-Ponticelli, M. Sutton, and A. Berdis, “Selective inhibition of DNA replicase assembly by a non-natural nucleotide: exploiting the structural diversity of ATP-binding sites,” ACS Chemical Biology, vol. 5, no. 2, pp. 183–194, 2010.
[94]
F. J. Ghadessy, N. Ramsay, F. Boudsocq et al., “Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution,” Nature Biotechnology, vol. 22, no. 6, pp. 755–759, 2004.
[95]
X. Zhang, I. Lee, and A. J. Berdis, “The use of nonnatural nucleotides to probe the contributions of shape complementarity and pi-electron surface area during DNA polymerization,” Biochemistry, vol. 44, no. 39, pp. 13101–13110, 2005.
[96]
X. Zhang, I. Lee, and A. J. Berdis, “A potential chemotherapeutic strategy for the selective inhibition of promutagenic DNA synthesis by nonnatural nucleotides,” Biochemistry, vol. 44, no. 39, pp. 13111–13121, 2005.
[97]
J. C. Morales and E. T. Kool, “Importance of terminal base pair hydrogen-bonding in 3'-end proofreading by the Klenow fragment of DNA polymerase I,” Biochemistry, vol. 39, no. 10, pp. 2626–2632, 2000.
[98]
F. Hill, D. M. Williams, D. Loakes, and D. M. Brown, “Comparative mutagenicities of N6-methoxy-2,6-diaminopurine and N6-methoxyaminopurine -deoxyribonucleosides and their -triphosphates,” Nucleic Acids Research, vol. 26, no. 5, pp. 1144–1149, 1998.
[99]
F. Hill, D. Loakes, and D. M. Brown, “Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 8, pp. 4258–4263, 1998.
[100]
M. Zaccolo, D. M. Williams, D. M. Brown, and E. Gherardi, “An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues,” Journal of Molecular Biology, vol. 255, no. 4, pp. 589–603, 1996.
[101]
C. Y. Switzer, S. E. Moroney, and S. A. Benner, “Enzymatic recognition of the base pair between isocytidine and isoguanosine,” Biochemistry, vol. 32, no. 39, pp. 10489–10496, 1993.
[102]
J. A. Piccirilli, T. Krauch, S. E. Moroney, and S. A. Benner, “Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet,” Nature, vol. 343, no. 6253, pp. 33–37, 1990.
[103]
M. J. Moser, D. J. Marshall, J. K. Grenier et al., “Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system,” Clinical Chemistry, vol. 49, no. 3, pp. 407–414, 2003.
[104]
K. P. Rice, J. C. Chaput, M. M. Cox, and C. Switzer, “RecA protein promotes strand exchange with DNA substrates containing isoguanine and 5-methyl isocytosine,” Biochemistry, vol. 39, no. 33, pp. 10177–10188, 2000.
[105]
S. C. Johnson, C. B. Sherrill, D. J. Marshall, M. J. Moser, and J. R. Prudent, “A third base pair for the polymerase chain reaction: inserting isoC and isoG,” Nucleic Acids Research, vol. 32, no. 6, pp. 1937–1941, 2004.
[106]
A. M. Maciejewska, K. D. Lichota, and J. T. Ku？mierek, “Neighbouring bases in template influence base-pairing of isoguanine,” The Biochemical Journal, vol. 369, no. 3, pp. 611–618, 2003.
[107]
S. Moran, R. X. Ren, S. Rumney, and E. T. Kool, “Difluorotoluene, a nonpolar isostere for thymine, codes specifically and efficiently for adenine in DNA replication,” Journal of the American Chemical Society, vol. 119, no. 8, pp. 2056–2057, 1997.
[108]
S. Xia, S. H. Eom, W. H. Konigsberg, and J. Wang, “Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue,” Biochemistry, vol. 51, pp. 1476–1485, 2012.
[109]
S. Xia, W. H. Konigsberg, and J. Wang, “Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex,” Journal of the American Chemical Society, vol. 133, no. 26, pp. 10003–10005, 2011.
[110]
H. R. Lee, S. A. Helquist, E. T. Kool, and K. A. Johnson, “Base pair hydrogen bonds are essential for proofreading selectivity by the human mitochondrial DNA polymerase,” The Journal of Biological Chemistry, vol. 283, no. 21, pp. 14411–14416, 2008.
[111]
T. W. Kim, J. C. Delaney, J. M. Essigmann, and E. T. Kool, “Probing the active site tightness of DNA polymerase in subangstrom increments,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 44, pp. 15803–15808, 2005.
[112]
W. T. Wolfle, M. T. Washington, E. T. Kool et al., “Evidence for a Watson-Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa,” Molecular and Cellular Biology, vol. 25, no. 16, pp. 7137–7143, 2005.
[113]
M. T. Washington, S. A. Helquist, E. T. Kool, L. Prakash, and S. Prakash, “Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta,” Molecular and Cellular Biology, vol. 23, no. 14, pp. 5107–5112, 2003.
[114]
A. Irimia, R. L. Eoff, P. S. Pallan, F. P. Guengerich, and M. Egli, “Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene,” The Journal of Biological Chemistry, vol. 282, no. 50, pp. 36421–36433, 2007.
[115]
A. M. Sismour and S. A. Benner, “The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system,” Nucleic Acids Research, vol. 33, no. 17, pp. 5640–5646, 2005.
[116]
A. M. Sismour, S. Lutz, J. H. Park et al., “PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1,” Nucleic Acids Research, vol. 32, no. 2, pp. 728–735, 2004.
[117]
J. Caton-Williams and Z. Huang, “Synthesis and DNA-polymerase incorporation of colored 4-selenothymidine triphosphate for polymerase recognition and DNA visualization,” Angewandte Chemie, vol. 47, no. 9, pp. 1723–1725, 2008.
[118]
T. W. Kim, L. G. Brieba, T. Ellenberger, and E. T. Kool, “Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs,” The Journal of Biological Chemistry, vol. 281, no. 4, pp. 2289–2295, 2006.
[119]
H. O. Sintim and E. T. Kool, “Remarkable sensitivity to DNA base shape in the DNA polymerase active site,” Angewandte Chemie, vol. 45, no. 12, pp. 1974–1979, 2006.
[120]
M. Strerath, J. Cramer, T. Restle, and A. Marx, “Implications of active site constraints on varied DNA polymerase selectivity,” Journal of the American Chemical Society, vol. 124, no. 38, pp. 11230–11231, 2002.
[121]
M. Strerath, D. Summerer, and A. Marx, “Varied DNA polymerase-substrate interactions in the nucleotide binding pocket,” ChemBioChem, vol. 3, pp. 578–580, 2002.
[122]
J. Cramer, G. Rangam, A. Marx, and T. Restle, “Varied active-site constraints in the Klenow fragment of E. coli DNA polymerase I and the lesion-bypass Dbh DNA polymerase,” ChemBioChem, vol. 9, no. 8, pp. 1243–1250, 2008.
[123]
S. Mizukami, T. W. Kim, S. A. Helquist, and E. T. Kool, “Varying DNA base-pair size in subangstrom increments: evidence for a loose, not large, active site in low-fidelity Dpo4 polymerase,” Biochemistry, vol. 45, no. 9, pp. 2772–2778, 2006.
[124]
L. M. Wilhelmsson, “Fluorescent nucleic acid base analogues,” Quarterly Reviews of Biophysics, vol. 43, no. 2, pp. 159–183, 2010.
[125]
L. J. Reha-Krantz, C. Hariharan, U. Subuddhi et al., “Structure of the 2-aminopurine-cytosine base pair formed in the polymerase active site of the RB69 Y567A-DNA polymerase,” Biochemistry, vol. 50, pp. 10136–10149, 2011.
[126]
L. B. Bloom, M. R. Otto, J. M. Beechem, and M. F. Goodman, “Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment,” Biochemistry, vol. 32, no. 41, pp. 11247–11258, 1993.
[127]
B. W. Allan and N. O. Reich, “Targeted base stacking disruption by the EcoRI DNA methyltransferase,” Biochemistry, vol. 35, no. 47, pp. 14757–14762, 1996.
[128]
P. O. Lycksell, A. Graslund, F. Claesens, L. W. McLaughlin, U. Larsson, and R. Rigler, “Base pair opening dynamics of a 2-aminopurine substituted EcoRI restriction sequence and its unsubstituted counterpart in oligonucleotides,” Nucleic Acids Research, vol. 15, pp. 9011–9025, 1987.
[129]
T. M. Nordlund, S. Andersson, L. Nilsson, R. Rigler, A. Graslund, and L. W. McLaughlin, “Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies,” Biochemistry, vol. 28, no. 23, pp. 9095–9103, 1989.
[130]
J. T. Stivers, K. W. Pankiewicz, and K. A. Watanabe, “Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase,” Biochemistry, vol. 38, no. 3, pp. 952–963, 1999.
[131]
D. C. Ward, E. Reich, and L. Stryer, “Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives,” The Journal of Biological Chemistry, vol. 244, no. 5, pp. 1228–1237, 1969.
[132]
R. A. Hochstrasser, T. E. Carver, L. C. Sowers, and D. P. Millar, “Melting of a DNA helix terminus within the active site of a DNA polymerase,” Biochemistry, vol. 33, pp. 11971–11979, 1994.
[133]
C. M. Joyce, O. Potapova, A. M. DeLucia, X. Huang, V. P. Basu, and N. D. Grindley, “Fingers-closing and other rapid conformational changes in DNA polymerase I (Klenow fragment) and their role in nucleotide selectivity,” Biochemistry, vol. 47, no. 23, pp. 6103–6116, 2008.
[134]
H. R. Lee, M. Wang, and W. Konigsberg, “The reopening rate of the fingers domain is a determinant of base selectivity for RB69 DNA polymerase,” Biochemistry, vol. 48, no. 10, pp. 2087–2098, 2009.
[135]
A. M. DeLucia, N. D. Grindley, and C. M. Joyce, “Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence,” Biochemistry, vol. 46, no. 38, pp. 10790–10803, 2007.
[136]
U. Subuddhi, M. Hogg, and L. J. Reha-Krantz, “Use of 2-aminopurine fluorescence to study the role of the beta hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases,” Biochemistry, vol. 47, no. 23, pp. 6130–6137, 2008.
[137]
A. A. Marti, S. Jockusch, Z. Li, J. Ju, and N. J. Turro, “Molecular beacons with intrinsically fluorescent nucleotides,” Nucleic Acids Research, vol. 34, no. 6, article e50, 2006.
[138]
C. Dash, J. W. Rausch, and S. F. J. Le Grice, “Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 polypurine tract,” Nucleic Acids Research, vol. 32, no. 4, pp. 1539–1547, 2004.
[139]
X. Zhang and R. M. Wadkins, “DNA hairpins containing the cytidine analog pyrrolo-dC: structural, thermodynamic, and spectroscopic studies,” Biophysical Journal, vol. 96, no. 5, pp. 1884–1891, 2009.
[140]
K. Yang and R. J. Stanley, “The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study,” Photochemistry and Photobiology, vol. 84, no. 3, pp. 741–749, 2008.
[141]
J. Petruska and M. F. Goodman, “Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity,” The Journal of Biological Chemistry, vol. 260, no. 12, pp. 7533–7539, 1985.
[142]
K. Y. Lin, R. J. Jones, and M. Matteucci, “Tricyclic -deoxycytidine analogs: syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA,” Journal of the American Chemical Society, vol. 117, no. 13, pp. 3873–3874, 1995.
[143]
L. M. Wilhelmsson, A. Holmen, P. Lincoln, P. E. Nielsen, and B. Norden, “A highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine,” Journal of the American Chemical Society, vol. 123, pp. 2434–2435, 2001.
[144]
G. Stengel, J. P. Gill, P. Sandin et al., “Conformational dynamics of DNA polymerase probed with a novel fluorescent DNA base analogue,” Biochemistry, vol. 46, no. 43, pp. 12289–12297, 2007.
[145]
P. Sandin, P. Lincoln, T. Brown, and L. M. Wilhelmsson, “Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe,” Nature Protocols, vol. 2, no. 3, pp. 615–623, 2007.
[146]
P. Sandin, G. Stengel, T. Ljungdahl, K. Borjesson, B. Macao, and L. M. Wilhelmsson, “Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCo by Klenow fragment,” Nucleic Acids Research, vol. 37, no. 12, pp. 3924–3933, 2009.
[147]
J. M. Walsh, I. Bouamaied, T. Brown, L. M. Wilhelmsson, and P. J. Beuning, “Discrimination against the cytosine analog tC by Escherichia coli DNA polymerase IV DinB,” Journal of Molecular Biology, vol. 409, no. 2, pp. 89–100, 2011.
[148]
T. J. Lund, N. A. Cavanaugh, N. Joubert et al., “B family DNA polymerases asymmetrically recognize pyrimidines and purines,” Biochemistry, vol. 50, pp. 7243–7250, 2011.
[149]
P. Sandin, K. Borjesson, H. Li et al., “Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue,” Nucleic Acids Research, vol. 36, pp. 157–167, 2008.
[150]
G. Stengel, B. W. Purse, L. M. Wilhelmsson, M. Urban, and R. D. Kuchta, “Ambivalent incorporation of the fluorescent cytosine analogues tC and tCo by human DNA polymerase alpha and Klenow fragment,” Biochemistry, vol. 48, no. 31, pp. 7547–7555, 2009.
[151]
G. Stengel, M. Urban, B. W. Purse, and R. D. Kuchta, “High density labeling of polymerase chain reaction products with the fluorescent base analogue tCo,” Analytical Chemistry, vol. 81, no. 21, pp. 9079–9085, 2009.
[152]
E. T. Kool, J. C. Morales, and K. M. Guckian, “Mimicking the structure and function of DNA: insights into DNA stability and replication,” Angewandte Chemie, vol. 39, pp. 990–1009, 2000.
[153]
A. A. Henry and F. E. Romesberg, “Beyond A, C, G and T: augmenting nature's alphabet,” Current Opinion in Chemical Biology, vol. 7, no. 6, pp. 727–733, 2003.
[154]
K. Seo, J. Yin, P. Donthamsetti, S. Chandani, C. Lee, and E. Loechler, “Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli,” Journal of Molecular Biology, vol. 392, no. 2, pp. 270–282, 2009.
[155]
D. Loakes and P. Holliger, “Polymerase engineering: towards the encoded synthesis of unnatural biopolymers,” Chemical Communications, no. 31, pp. 4619–4631, 2009.
[156]
C. Bailly and M. J. Waring, “Use of DNA molecules substituted with unnatural nucleotides to probe specific drug-DNA interactions,” Methods in Enzymology, vol. 340, pp. 485–502, 2001.
