View Item 

Show simple item record

Unnatural Nucleosides with Unusual Base Pairing Properties
dc.contributor.authorBergstrom, Donald E.
dc.date.accessioned2020-01-13T15:11:41Z
dc.date.available2020-01-13T15:11:41Z
dc.date.issued2001-07
dc.identifier.citationBergstrom, Donald E. (2001). "Unnatural Nucleosides with Unusual Base Pairing Properties." Current Protocols in Nucleic Acid Chemistry 5(1): 1.4.1-1.4.13.
dc.identifier.issn1934-9270
dc.identifier.issn1934-9289
dc.identifier.urihttps://hdl.handle.net/2027.42/152854
dc.description.abstractSynthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in nucleic acid biochemistry. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered including base pairs with alternative H‐bonding schemes, hydrophobic base pairs, degenerate bases, universal nucleosides, and triplex constituents.
dc.publisherJohn Wiley & Sons
dc.titleUnnatural Nucleosides with Unusual Base Pairing Properties
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelBiological Chemistry
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelEngineering
dc.subject.hlbtoplevelHealth Sciences
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/152854/1/cpnc0104.pdf
dc.identifier.doi10.1002/0471142700.nc0104s05
dc.identifier.sourceCurrent Protocols in Nucleic Acid Chemistry
dc.identifier.citedreferenceOda, Y., Uesugi, S., Ikehara, M., Kawase, Y., and Ohtsuka, E. 1991. NMR studies for identification of dI:dG mismatch base‐pairing structure in DNA. Nucl. Acids Res. 19: 5263 ‐ 5267.
dc.identifier.citedreferenceNguyen, N.K., Bonfils, E., Auffray, P., Costaglioli, P., Schmitt, P., Asseline, U., Durand, M., Maurizot, J.C., Dupret, D., and Thuong, N.T. 1998. The stability of duplexes involving AT and/or G(4Et)C base pairs is not dependent on their AT/G(4Et)C ratio content. Implication for DNA sequencing by hybridization. Nucl. Acids Res. 26: 4249 ‐ 4258.
dc.identifier.citedreferenceOgawa, A.K., Wu, Y., McMinn, D.L., Liu, J., Schultz, P.G., and Romesberg, F.E. 2000. Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs. J. Am. Chem. Soc. 122: 3274 ‐ 3287.
dc.identifier.citedreferenceOhtsuka, E., Matsuki, S., Ikehara, M., Takahashi, Y., and Matsubara, K. 1985. An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions. J. Biol. Chem. 260: 2605 ‐ 2608.
dc.identifier.citedreferencePiccirilli, J.A., Krauch, T., Moroney, S.E., and Benner, S.A. 1990. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343: 33 ‐ 37.
dc.identifier.citedreferencePochet, S. and Marliére, P. 1996. Construction of a self‐complementary nucleoside from deoxyguanosine. C. R. Acad. Sci. (Paris) 319: 1 ‐ 7.
dc.identifier.citedreferencePrévot‐Halter, I. and Leumann, C.J. 1999. Selective recognition of a C‐G base pair in the parallel DNA triple‐helical binding motif. Bioorg. Med. Chem. Lett. 9: 2657 ‐ 2660.
dc.identifier.citedreferenceRothman, J.H. and Richards, W.G. 1996. Novel Hoogsteen‐like bases for configurational recognition of the T‐A base pair by DNA triplex formation. Biopolymers 39: 795 ‐ 812.
dc.identifier.citedreferenceSaenger, W. 1984. Principles of Nucleic Acid Structure. Springer‐Verlag, New York.
dc.identifier.citedreferenceSchweitzer, B.A. and Kool, E. 1995. Hydrophobic, non‐hydrogen‐bonding bases and base pairs DNA. J. Am. Chem. Soc. 117: 1864 ‐ 1872.
dc.identifier.citedreferenceSeela, F. and Debelak, H. 2000. The N 8 ‐(2′‐deoxyribofuranoside) of 8‐aza‐7‐deazaadenine: A universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents. Nucl. Acids Res. 28: 3224 ‐ 3232.
dc.identifier.citedreferenceSeela, F. and Kaiser, K. 1986. Phosphoramidites of base‐modified 2′‐deoxyinosine isosteres and solid‐phase synthesis of d(GCI*CGC) oligomers containing an ambiguous base. Nucl. Acids Res. 14: 1825 ‐ 1844.
dc.identifier.citedreferenceSwitzer, C.Y., Moroney, S.E., and Benner, S.A. 1993. Enzymatic recognition of the base pair between isocytidine and isoguanosine. Biochemistry 32: 10489 ‐ 10496.
dc.identifier.citedreferenceTanaka, K. and Shionoya, M. 1999. Synthesis of a novel nucleoside for alternative DNA base pairing through metal complexation. J. Org. Chem. 64: 5002 ‐ 5003.
dc.identifier.citedreferenceUeno, Y., Mikawa, M., and Matsuda, A. 1998. Synthesis and properties of oligodeoxynucleotides containing 5‐[N‐[2[N,N‐bis(2‐aminoethyl)‐amino]ethyl]carbamoyl]‐2′‐deoxyuridine and 5‐[N‐[3‐[N,N‐Bis(3‐aminopropyl)amino]propyl] carbamoyl]‐2′‐deoxyuridine. Bioconjugate Chem. 9: 33 ‐ 39.
dc.identifier.citedreferenceUesugi, S., Oda, Y., Ikehara, M., Kawase, Y., and Ohtsuka, E. 1987. Identification of I‐A mismatch base‐pairing structure in DNA. J. Biol. Chem. 262: 6965 ‐ 6968.
dc.identifier.citedreferenceVoegel, J.J. and Benner, S.A. 1994. Nonstandard hydrogen bonding in duplex oligonucleotides. The base pair between an acceptor‐donor‐donor pyrimidine analog and donor‐acceptor‐acceptor analog. J. Am. Chem. Soc. 116: 6929 ‐ 6930.
dc.identifier.citedreferenceWagner, R.W., Matteucci, M.D., Lewis, J.G., Gutierrez, A.J., Moulds, C., and Froehler, B.C. 1993. Antisense gene inhibition by oligonucleotides containing C‐5 propyne pyrimidines. Science 260: 1510 ‐ 1513.
dc.identifier.citedreferenceWu, Y., Ogawa, A.K., Berger, M., McMinn, D.L., Schultz, P.G., and Romesberg, F.E. 2000. Efforts toward expansion of the genetic alphabet: Optimization of interbase hydrophobic interactions. J. Am. Chem. Soc. 122: 7621 ‐ 7632.
dc.identifier.citedreferenceYu, H., Eritja, R., Bloom, L.B., and Goodman, M.F. 1993. Ionization of bromouracil and fluorouracil stimulates base mispairing frequencies with guanine. J. Biol. Chem. 268: 15935 ‐ 15943.
dc.identifier.citedreferenceZhang, P., Johnson, W.T., Klewer, D., Paul, N., Hoops, G., Davisson, V.J., and Bergstrom, D.E. 1998. Exploratory studies on azole carboxamides as nucleobase analogs: Thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole‐3‐carboxamide. Nucl. Acids Res. 26: 2208 ‐ 2215.
dc.identifier.citedreferenceBerger, M., Ogawa, A.K., McMinn, D.L., Wu, Y., Schultz, P.G., and Romesberg, F.E. 2000a. Stable and selective hybridization of oligonucleotides with unnatural hydrophobic bases. Angew. Chem. Int. Ed. Engl. 39: 2940 ‐ 2942.
dc.identifier.citedreferenceBerger, M., Wu, Y., Ogawa, A.K., McMinn, D.L., Schultz, P.G., and Romesberg, F.E. 2000b. Universal bases for hybridization, replication and chain termination. Nucl. Acids Res. 28: 2911 ‐ 2914.
dc.identifier.citedreferenceBergstrom, D.E., Zhang, P., Toma, P.H., Andrews, C.A., and Nichols, R. 1995. Synthesis, structure, and deoxyribonucleic acid sequencing with a universal nucleoside: 1‐(2′‐Deoxy‐β‐ D ‐ribofuranosyl)‐3‐nitropyrrole. J. Am. Chem. Soc. 117: 1201 ‐ 1209.
dc.identifier.citedreferenceBergstrom, D.E., Zhang, P., and Johnson, W.T. 1996. Design and synthesis of heterocyclic carboxamides as natural nucleic acid mimics. Nucleosides Nucleotides 15: 59 ‐ 68.
dc.identifier.citedreferenceBergstrom, D.E., Zhang, P., and Johnson, W.T. 1997. Comparison of the base pairing properties of a series of nitroazole nucleobase analogs in the oligodeoxyribonucleotide sequence 5′‐d(CGCXAATTYGCG)‐3′. Nucl. Acids Res. 25: 1935 ‐ 1942.
dc.identifier.citedreferenceBijapur, J., Keppler, M.D., Bergqvist, S., Brown, T., and Fox, K.R. 1999. 5‐(1‐Propargylamino)‐2′‐deoxyuridine (Up): A novel thymidine analogue for generating DNA triplexes with increased stability. Nucl. Acids Res. 27: 1802 ‐ 1809.
dc.identifier.citedreferenceBrown, D.M. and Lin, P.K.T. 1991a. The structure and application of oligodeoxyribonucleotides containing modified, degenerate bases. Nucl. Acids Symp. Ser. 24: 209 ‐ 212.
dc.identifier.citedreferenceBrown, D.M. and Lin, P.K.T. 1991b. Synthesis and duplex stability of oligonucleotides containing adenine‐guanine analogues. Carbohydr. Res. 216: 129 ‐ 139.
dc.identifier.citedreferenceCarbonnaux, C., Fazakerley, G.V., and Sowers, L.C. 1990. An NMR structural study of deaminated base pairs in DNA. Nucl. Acids Res. 18: 4075 ‐ 4081.
dc.identifier.citedreferenceCassidy, S.A., Slickers, P., Trent, J.O., Capaldi, D.C., Roselt, P.D., Reese, C.B., Neidle, S., and Fox, K.R. 1997. Recognition of GC base pairs by triplex‐forming oligonucleotides containing nucleosides derived from 2‐aminopyridine. Nucl. Acids Res. 25: 4891 ‐ 4898.
dc.identifier.citedreferenceCorfield, P.W.R., Hunter, W.N., Brown, T., Robinson, P., and Kennard, O. 1987. Inosine‐adenine base pairs in a B‐DNA duplex. Nucl. Acids. Res. 15: 7935 ‐ 7949.
dc.identifier.citedreferenceCruse, W.B.T., Aymani, J., Kennard, O., Brown, T., Jack, A.G.C., and Leonard, G.A. 1989. Refined crystal structures of an octanucleotide duplex with I.T. mismatch base pairs. Nucl. Acids Res. 17: 55 ‐ 72.
dc.identifier.citedreferenceDay, J.P., Bergstrom, D., Hammer, R.P., and Barany, F. 1999a. Nucleotide analogs facilitate base conversion with 3′‐mismatch primers. Nucl. Acids Res. 27: 1810 ‐ 1818.
dc.identifier.citedreferenceDay, J.P., Hammer, R.P., Bergstrom, D., and Barany, F. 1999b. Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations. Nucl. Acids Res. 27: 1819 ‐ 1827.
dc.identifier.citedreferenceDervan, P.B. and Burli, R.W. 1999. Sequence‐specific DNA recognition by polyamides. Curr. Opin. Chem. Biol. 3: 688 ‐ 693.
dc.identifier.citedreferenceDoronina, S.O. and Behr, J.‐P. 1997. Towards a general triple helix mediated DNA recognition scheme. Chem. Soc. Rev. 26: 63 ‐ 71.
dc.identifier.citedreferenceEritja, R., Horowitz, D.M., Walker, P.A., Ziehler‐Martin, J.P., Boosalis, M.S., Goodman, M.F., Itakura, M., and Kaplan, B.E. 1986. Synthesis and properties of oligonucleotides containing 2′‐deoxynebularine and 2′‐deoxyxanthosine. Nucl. Acids Res. 14: 8135 ‐ 8153.
dc.identifier.citedreferenceGanesh, K.N., Kumar, V.A., and Barawkar, D.A. 1996. Synthetic control of DNA triplex structure through chemical modifications. In Supramolecular Control of Structure and Bonding ( A.D. Hamilton, ed.) pp. 263 ‐ 327. John Wiley & Sons, New York.
dc.identifier.citedreferenceGottesfeld, J.M., Turner, J.M., and Dervan, P.B. 2000. Chemical approaches to control of gene expression. Gene Expr. 9: 77 ‐ 91.
dc.identifier.citedreferenceGowers, D.M. and Fox, K.R. 1999. Towards mixed sequence recognition by triple helix formation. Nucl. Acids Res. 27: 1569 ‐ 1577.
dc.identifier.citedreferenceGuckian, K.M. and Kool, E.T. 1997. Highly precise shape mimicry by a difluorotoluene deoxynucleoside, a replication‐competent substitute for thymidine. Angew. Chem. Int. Ed. Engl. 36: 2825 ‐ 2828.
dc.identifier.citedreferenceGuckian, K.M., Morales, J.C., and Kool, E.T. 1998. Structure and base pairing properties of a replicable nonpolar isostere for deoxyadenosine. J. Org. Chem. 63: 9652 ‐ 9656.
dc.identifier.citedreferenceGuo, Z., Liu, Q., and Smith, L.M. 1997. Enhanced discrimination of single nucleotide polymorphisms by artificial mismatch hybridization. Nat. Biotechnol. 15: 331 ‐ 335.
dc.identifier.citedreferenceHabener, J.F., Vo, C.D., Le, D.B., Gryan, G.P., Ercolani, L., and Wang, A.H.J. 1988. 5‐Fluorodeoxyuridine as an alternative to the synthesis of mixed hybridization probes for the detection of specific gene sequences. Proc. Natl. Acad. Sci. U.S.A. 85: 1735 ‐ 1739.
dc.identifier.citedreferenceHill, F., Loakes, D., and Brown, D.M. 1998. Polymerase recognition of synthetic oligodeoxyribonucleotides incorporating degenerate pyrimidine and purine bases. Proc. Natl. Acad. Sci. U.S.A. 95: 4258 ‐ 4263.
dc.identifier.citedreferenceHoops, G.C., Zhang, P., Johnson, W.T., Paul, N., Bergstrom, D.E., and Davisson, V.J. 1997. Template directed incorporation of nucleotide mixtures using azole‐nucleobase analogs. Nucl. Acids Res. 25: 4866 ‐ 4871.
dc.identifier.citedreferenceHorlacher, J., Hottiger, M., Podust, V.N., Hubscher, U., and Benner, S.A. 1995. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc. Natl. Acad. Sci. U.S.A. 92: 6329 ‐ 6333.
dc.identifier.citedreferenceHuang, C.‐Y., Bi, G., and Miller, P.S. 1996. Triplex formation by oligonucleotides containing novel deoxycytidine derivatives. Nucl. Acids. Res. 24: 2606 ‐ 2613.
dc.identifier.citedreferenceInoue, H., Imura, A., and Ohtsuka, E. 1985. Synthesis and hybridization of dodecadeoxyribonucleotides containing a fluorescent pyridopyrimidine deoxynucleoside. Nucl. Acids Res. 13: 7119 ‐ 7128.
dc.identifier.citedreferenceJohnson, W.T., Zhang, P., and Bergstrom, D.E. 1997. The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1‐(2′‐deoxy‐β‐ D ‐ribofuranosyl)imidazole‐4‐carboxamide. Nucl. Acids Res. 25: 559 ‐ 567.
dc.identifier.citedreferenceKawase, Y., Iwai, S., and Ohtsuka, E. 1989. Synthesis and thermal stability of dodecadeoxyribonucleotides containing deoxyinosine pairing with four major bases. Chem. Phamacol. Bull. 37: 599 ‐ 601.
dc.identifier.citedreferenceKlewer, D., Zhang, P., Bergstrom, D.E., Davisson, V.J., and Liwang, A.C. 2001. Conformations of nucleoside analog 1‐(2′‐deoxy‐β‐ D ‐ribofuranosyl)‐1,2,4‐triazole‐3‐carboxamide in DNA duplexes with different sequence contexts. Biochemistry 40: 1518 ‐ 1527.
dc.identifier.citedreferenceKoh, J.S. and Dervan, P.B. 1992. Design of a nonnatural deoxyribonucleoside for recognition of GC base pairs by oligonucleotide‐directed triple‐helix formation. J. Am. Chem. Soc. 114: 1470 ‐ 1478.
dc.identifier.citedreferenceKool, E.T. 1998. Replication of non‐hydrogen bonded bases by DNA polymerases: A mechanism for steric matching. Biopolymers 48: 3 ‐ 17.
dc.identifier.citedreferenceKrawczyk, S.H., Milligan, J.F., Wadwani, S., Moulds, C., Froehler, B.C., and Matteucci, M.D. 1992. Oligonucleotide‐mediated triple helix formation using an N3‐protonated deoxycytidine analog exhibiting pH‐independent binding within the physiological range. Proc. Natl. Acad. Sci. U.S.A. 89: 3761 ‐ 3764.
dc.identifier.citedreferenceKutyavin, I.V., Lukhtanov, E.A., Gorn, V.V., Meyers, R.B. Jr., and Gamper, H.B. Jr. 1996. Oligonucleotides containing 2‐aminoadenine and 2‐thiothymine act as selectively binding complementary agents. Biochemistry 35: 11170 ‐ 11176.
dc.identifier.citedreferenceLin, T.K.T. and Brown, D.M. 1989. Synthesis and duplex stability of oligonucleotides containing cytosine‐thymine analogues. Nucl. Acids Res. 17: 10373 ‐ 10383.
dc.identifier.citedreferenceLoakes, D. and Brown, D.M. 1994. 5‐Nitroindole as an universal base analogue. Nucl. Acids Res. 22: 4039 ‐ 4043.
dc.identifier.citedreferenceLoakes, D., Brown, D.M., Linde, S., and Hill, F. 1995. 3‐Nitropyrrole and 5‐nitroindole as universal bases in primers for DNA sequencing and PCR. Nucl. Acids Res. 23: 2361 ‐ 2366.
dc.identifier.citedreferenceLuo, J., Bergstrom, D.E., and Barany, F. 1996. Improving the fidelity of Thermus thermophilus DNA ligase. Nucl. Acids Res. 24: 3071 ‐ 3078.
dc.identifier.citedreferenceLuyten, I. and Herdewijn, P. 1998. Hybridization properties of base‐modified oligonucleotides within the double and triple helix motif. Eur. J. Med. Chem. 33: 515 ‐ 576.
dc.identifier.citedreferenceMartin, F.H. and Castro, M.M. 1985. Base pairing involving deoxyinosine: Implications for probe design. Nucl. Acids Res. 13: 8927 ‐ 8938.
dc.identifier.citedreferenceMatray, T.J. and Kool, E.T. 1999. A specific partner for abasic damage in DNA. Nature 399: 704 ‐ 708.
dc.identifier.citedreferenceMatray, T., Gamsey, S., Pongracz, K., and Gryaznov, S. 2000. A remarkable stabilization of complexes formed by 2,6‐diaminopurine oligonucleotide N3′→︀P5′ phosphoramidates. Nucleosides Nucleotides Nucleic Acids 19: 1553 ‐ 1567.
dc.identifier.citedreferenceMcMinn, D.L., Ogawa, A.K., Wu, Y., Liu, J., Schultz, P.G., and Romesberg, F.E. 1999. Efforts towards expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self pairing hydrophobic base. J. Am. Chem. Soc. 121: 11585 ‐ 11586.
dc.identifier.citedreferenceMeggers, E., Holland, P.L., Tolman, W.B., Romesberg, F.E., and Schultz, P.G. 2000. A novel copper‐mediated DNA base pair. J. Am. Chem. Soc. 122: 10714 ‐ 10715.
dc.identifier.citedreferenceMillican, T.A., Mock, G.A., Chauncey, M.A., Patel, T.P., Eaton, M.A.W., Gunning, J., Cutbush, S.D., Neidle, S., and Mann, J. 1984. Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: A possible approach to the problem of mixed base oligodeoxynucleotide synthesis. Nucl. Acids Res. 12: 7435 ‐ 7453.
dc.identifier.citedreferenceMorales, J.C. and Kool, E.T. 1999. Minor groove interactions between polymerase and DNA: More essential to replication than Watson‐Crick hydrogen bonds? J. Am. Chem. Soc. 121: 2323 ‐ 2324.
dc.identifier.citedreferenceMoran, S., Ren, R.X.‐F., and Kool, E.T. 1997a. A thymidine triphosphate shape analog lacking Watson‐Crick pairing ability is replicated with high sequence selectivity. Proc. Natl. Acad. Sci. U.S.A. 94: 10506 ‐ 10511.
dc.identifier.citedreferenceMoran, S., Ren, R.X.‐F., Rumney, S.I., and Kool, E.T. 1997b. Difluorotoluene, a nonpolar isostere for thymine, codes specifically and efficiently for adenine in DNA replication. J. Am. Chem. Soc. 119: 2056 ‐ 2057.
dc.identifier.citedreferenceNakatani, K., Sando, S., and Saito, I. 2001. Scanning of guanine‐guanine mismatches in DNA by synthetic ligands using surface plasmon resonance. Nat. Biotechnol. 19: 51 ‐ 55.
dc.identifier.citedreferenceNegishi, K., Williams, D.M., Inoue, Y., Moriyama, K., Brown, D.M., and Hayatsu, H. 1997. The mechanism of mutation induction by a hydrogen bond ambivalent, bicyclic N‐4‐oxy‐2′‐deoxycytidine in Escherichia coli. Nucl. Acids Res. 25: 1548 ‐ 1552.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


Files in this item

Name:
cpnc0104.pdf
Size:
267.6KB
Format:
PDF
View/Open

Show simple item record

Remediation of Harmful Language

The University of Michigan Library aims to describe library materials in a way that respects the people and communities who create, use, and are represented in our collections. Report harmful or offensive language in catalog records, finding aids, or elsewhere in our collections anonymously through our metadata feedback form. More information at Remediation of Harmful Language.

Accessibility

If you are unable to use this file in its current format, please select the Contact Us link and we can modify it to make it more accessible to you.