Unnatural base pair systems for DNA/RNA-based biotechnology

Current Opinion in Chemical Biology

Volumn 10, Issue 6, 2006, Pages 622-627

  Hirao, Ichiro ^a  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; DNA POLYMERASE; RNA;

AMINO TERMINAL SEQUENCE; BASE PAIRING; BIOTECHNOLOGY; DNA TEMPLATE; GENE REPLICATION; GENE STRUCTURE; GENETIC TRANSCRIPTION; HYDROGEN BOND; HYDROPHOBICITY; NONHUMAN; REVIEW; RNA TRANSLATION;

BASE PAIRING; BIOTECHNOLOGY; DNA; HYDROGEN BONDING; RNA;

EID: 33846393737     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.09.021     Document Type: Review

References (32)

1. Henry A.A., and Romesberg F.E. Beyond A, C, G and T: augmenting nature's alphabet. Curr Opin Chem Biol 7 (2003) 727-733
2. Kool E.T. Synthetically modified DNAs as substrates for polymerases. Curr Opin Chem Biol 4 (2000) 602-608
3. Benner S.A., Burgstaller P., Battersby T.R., and Jurczyk S. Did the RNA world exploit an expanded genetic alphabet?. In: Gesteland R.F., Cech T.R., and Atkins J.F. (Eds). The RNA World (1999), Cold Spring Harbor Laboratory Press 163-181
4. Switzer C., Moroney S.E., and Benner S.A. Enzymatic incorporation of a new base pair into DNA and RNA. J Am Chem Soc 111 (1989) 8322-8323
5. Piccirilli J.A., Krauch T., Moroney S.E., and Benner S.A. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343 (1990) 33-37
6. Morales J.C., and Kool E.T. Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat Struct Biol 5 (1998) 950-954
7. McMinn D.L., Ogawa A.K., Wu Y., Liu J., Schultz P.G., and Romesberg F.E. Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base. J Am Chem Soc 121 (1999) 11585-11586
8. Ogawa A.K., Wu Y., McMinn D.L., Liu J., Schultz P.G., and Romesberg F.E. Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs. J Am Chem Soc 122 (2000) 3274-3287
9. Wu Y., Ogawa A.K., Berger M., McMinn D.L., Schultz P.G., and Romesberg F.E. Efforts toward expansion of the genetic alphabet: Optimization of interbase hydrophobic interactions. J Am Chem Soc 122 (2000) 7621-7632
10. Ohtsuki T., Kimoto M., Ishikawa M., Mitsui T., Hirao I., and Yokoyama S. Unnatural base pairs for specific transcription. Proc Natl Acad Sci USA 98 (2001) 4922-4925
11. Hirao I., Ohtsuki T., Fujiwara T., Mitsui T., Yokogawa T., Okuni T., Nakayama H., Takio K., Yabuki T., Kigawa T., et al. An unnatural base pair for incorporating amino acid analogs into proteins. Nat Biotechnol 20 (2002) 177-182
12. Mitsui T., Kimoto M., Harada Y., Yokoyama S., and Hirao I. An efficient unnatural base pair for a base-pair-expanded transcription system. J Am Chem Soc 127 (2005) 8652-8658
13. Hirao I. Placing extra components into RNA by specific transcription using unnatural base pair systems. BioTechniques 40 (2006) 711-717
14. Sismour A.M., Lutz S., Park J.H., Lutz M.J., Boyer P.L., Hughes S.H., and Benner S.A. PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1. Nucleic Acids Res 32 (2004) 728-735
15. Johnson S.C., Sherrill C.B., Marshall D.J., Moser M.J., and Prudent J.R. A third base pair for the polymerase chain reaction: inserting isoC and isoG. Nucleic Acids Res 32 (2004) 1937-1941
16. s and G-C pairs by KF-Taq.
17. Kimoto M., Endo M., Mitsui T., Okuni T., Hirao I., and Yokoyama S. Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. Chem Biol 11 (2004) 47-55
18. Moriyama K., Kimoto M., Mitsui T., Yokoyama S., and Hirao I. Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs. Nucleic Acids Res 33 (2005) e129
19. Kawai R., Kimoto M., Ikeda S., Mitsui T., Endo M., Yokoyama S., and Hirao I. Site-specific fluorescent labeling of RNA molecules by specific transcription using unnatural base pairs. J Am Chem Soc 127 (2005) 17286-17295
20. Fujiwara T., Kimoto M., Sugiyama H., Hirao I., and Yokoyama S. Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides. Bioorg Med Chem Lett 11 (2001) 2221-2223
21. Leconte A.M., Chen L., and Romesberg F.E. Polymerase evolution: efforts toward expansion of the genetic code. J Am Chem Soc 127 (2005) 12470-12471. Evolution of Sf-Taq for the improvement of the PICS-PICS extension.
22. Hirao I., Kimoto M., Mitsui T., Fujiwara T., Kawai R., Sato A., Harada Y., and Yokoyama S. An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. Nat Methods 3 (2006) 729-735. PCR amplification experiments using a Ds-Pa pair system in combination with γ-amidotriphosphates by Vent DNA polymerase and the transcription.
23. Mitsui T., Kitamura A., Kimoto M., To T., Sato A., Hirao I., and Yokoyama S. An unnatural hydrophobic base pair with shape complementarity between pyrrole-2-carbaldehyde and 9-methylimidazo[(4,5)-b]pyridine. J Am Chem Soc 125 (2003) 5298-5307
24. Morales J.C., and Kool E.T. Minor groove interactions between polymerase and DNA: more essential to replication than Watson-Crick hydrogen bonds?. J Am Chem Soc 121 (1999) 2323-2324
25. Leconte A.M., Matsuda S., Hwang G.T., and Romesberg F.E. Efforts towards expansion of the genetic alphabet: pyridone and methyl pyridone nucleobases. Angew Chem Int Ed Engl 45 (2006) 4326-4329
26. Matsuda S., Henry A.A., and Romesberg F.E. Optimization of unnatural base pair packing for polymerase recognition. J Am Chem Soc 128 (2005) 6369-6375
27. Collins M.L., Irvine B., Tyner D., Fine E., Zayati C., Chang C., Horn T., Ahle D., Detmer J., Shen L.P., et al. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res 25 (1997) 2979-2984
28. Sherrill C.B., Marshall D.J., Moser M.J., Larsen C.A., Daudé-Snow L., Jurczyk S., Shapiro G., and Prudent J.R. Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence. J Am Chem Soc 126 (2004) 4550-4556
29. Moser M.J., Marshall D.J., Grenier J.K., Kieffer C.D., Killeen A.A., Ptacin J.L., Richmond C.S., Roesch E.B., Scherrer C.W., Sherrill C.B., et al. Exploiting the enzymatic recognition of an unnatural base pair to develop a universal genetic analysis system. Clin Chem 49 (2003) 407-414
30. Liu H., Gao J., Lynch S.R., Saito Y.D., Maynard L., and Kool E.T. A four-base paired genetic helix with expanded size. Science 302 (2003) 868-871. High thermal stability of DNA duplexes composed of the xA-T and A-xT pairs.
31. Lu H., He K., and Kool E.T. yDNA: a new geometry for size-expanded base pairs. Angew Chem Int Ed Engl 43 (2004) 5834-5836
32. Lee A.H., and Kool E.T. A new four-base genetic helix, yDNA, composed of widened benzopyrimidine-purine pairs. J Am Chem Soc 127 (2005) 3332-3338