Reversible bond formation enables the replication and amplification of a crosslinking salen complex as an orthogonal base pair

Nature Chemistry

Volumn 3, Issue 10, 2011, Pages 794-800

  Kaul, Corinna ^a   Müller, Markus ^a   Wagner, Mirko ^b   Schneider, Sabine ^a   Carell, Thomas ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION COMPOUND; COPPER SULFATE; DNA; DNA DIRECTED DNA POLYMERASE BETA; ETHYLENEDIAMINE; ETHYLENEDIAMINE DERIVATIVE; N,N' DISALICYLIDENEETHYLENEDIAMINE;

ARTICLE; BASE PAIRING; CHEMISTRY; METABOLISM; POLYMERASE CHAIN REACTION; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; COORDINATION COMPLEXES; COPPER SULFATE; CRYSTALLOGRAPHY, X-RAY; DNA; DNA POLYMERASE I; ETHYLENEDIAMINES; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, TERTIARY;

EID: 80053292275     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.1117     Document Type: Article

References (50)

1. Giuseppone, N., Schmitt, J.-L. & Lehn, J.-M. Generation of dynamic constitutional diversity and driven evolution in helical molecular strands under Lewis acid catalyzed component exchange. Angew. Chem. Int. Ed. 43, 4902-4906 (2004). (Pubitemid 39312140)
2. Lehn, J.-M. From supramolecular chemistry towards constitutional dynamic chemistry and adaptive chemistry. Chem. Soc. Rev. 36, 151-160 (2007).
3. Lu, Y. & Liu, J. Functional DNA nanotechnology: Emerging applications of DNAzymes and aptamers. Curr. Opin. Biotechnol. 17, 580-588 (2006). (Pubitemid 44791909)
4. Niemeyer, C. M. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew. Chem. Int. Ed. 49, 1200-1216 (2010).
5. Seeman, N. C. DNA in a material world. Nature 421, 427-431 (2003). (Pubitemid 36157949)
6. Switzer, C., Moroney, S. E. & Benner, S. A. Enzymatic incorporation of a new base pair into DNA and RNA. J. Am. Chem. Soc. 111, 8322-8323 (1989). (Pubitemid 19255518)
7. Crick, F. H. C., Barnett, L., Brenner, S. &Watts-Tobin, R. J. General nature of the genetic code for proteins. Nature 192, 1227-1232 (1961).
8. Kool, E. T. Synthetically modified DNAs as substrates for polymerases. Curr. Opin. Chem. Biol. 4, 602-608 (2000).
9. Henry, A. A. & Romesberg, F. E. Beyond A, C, G and T: Augmenting Nature's alphabet. Curr. Opin. Chem. Biol. 7, 727-733 (2003).
10. Hirao, I. Unnatural base pair systems for DNA/RNA-based biotechnology. Curr. Opin. Chem. Biol. 10, 622-627 (2006). (Pubitemid 44822665)
11. Kool, E. T. Replacing the nucleobases in DNA with designer molecules. Acc. Chem. Res. 35, 936-943 (2002).
12. Kool, E. T., Morales, J. C. & Guckian, K. M. Mimicking the structure and function of DNA: Insights into DNA stability and replication. Angew. Chem. Int. Ed. 39, 990-1009 (2000). (Pubitemid 30217233)
13. Krueger, A. T. & Kool, E. T. Redesigning the architecture of the base pair: Toward biochemical and biological function of new genetic sets. Chem. Biol. 16, 242-248 (2009).
14. Switzer, C. Y., Moroney, S. E. & Benner, S. A. Enzymic recognition of the base pair between isocytidine and isoguanosine. Biochemistry 32, 10489-10496 (1993). (Pubitemid 23320175)
15. Killelea, T. et al. Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues. Biochemistry 49, 5772-5781 (2010).
16. Kimoto, M., Mitsui, T., Yokoyama, S. & Hirao, I. A unique fluorescent base analogue for the expansion of the genetic alphabet. J. Am. Chem. Soc. 132, 4988-4989 (2010).
17. Leconte, A. M. et al. Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet. J. Am. Chem. Soc. 130, 2336-2343 (2008). (Pubitemid 351288011)
18. Lu, H., Krueger, A. T., Gao, J., Liu, H. & Kool, E. T. Toward a designed genetic system with biochemical function: Polymerase synthesis of single and multiple size-expanded DNA base pairs. Org. Biomol. Chem. 8, 2704-2710 (2010).
19. Matsuda, S. et al. Efforts toward expansion of the genetic alphabet: Structure and replication of unnatural base pairs. J. Am. Chem. Soc. 129, 10466-10473 (2007). (Pubitemid 47330265)
20. Moran, S., Ren, R. X. F. & Kool, E. T. A thymidine triphosphate shape analog lackingWatson-Crick pairing ability is replicated with high sequence selectivity. Proc. Natl Acad. Sci. USA 94, 10506-10511 (1997). (Pubitemid 27430764)
21. Moran, S., Ren, R. X. F., Rumney, S. I. V. & Kool, E. T. Difluorotoluene, a nonpolar isostere for thymine, codes specifically and efficiently for adenine in DNA replication. J. Am. Chem. Soc. 119, 2056-2057 (1997). (Pubitemid 27148124)
22. Hirao, I. et al. An unnatural hydrophobic base pair system: Site-specific incorporation of nucleotide analogs into DNA and RNA. Nature Methods 3, 729-735 (2006). (Pubitemid 44275742)
23. Hirao, I., Mitsui, T., Kimoto, M. & Yokoyama, S. Development of an unnatural base pair for efficient PCR amplification. Nucleic Acids Symp. Ser. 51, 9-10 (2007).
24. Johnson, S. C., Sherrill, C. B., Marshall, D. J., Moser, M. J. & Prudent, J. R. A third base pair for the polymerase chain reaction: Inserting isoC and isoG. Nucleic Acids Res. 32, 1937-1941 (2004). (Pubitemid 38849351)
25. Yang, Z., Chen, F., Chamberlin, S. G. & Benner, S. A. Expanded genetic alphabets in the polymerase chain reaction. Angew. Chem. Int. Ed. 49, 177-180 (2010).
26. Piccirilli, J. A., Krauch, T., Moroney, S. E. & Benner, S. A. Enzymic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343, 33-37 (1990).
27. Lutz, M. J., Horlacher, J. & Benner, S. A. Recognition of a non-standard base pair by thermostable DNA polymerases. Bioorg. Med. Chem. Lett. 8, 1149-1152 (1998). (Pubitemid 28231388)
28. Urata, H., Yamaguchi, E., Funai, T., Matsumura, Y. & Wada, S.-i. Incorporation of thymine nucleotides by DNA polymerases through T-HgII-T base pairing. Angew. Chem. Int. Ed. 49, 6516-6519 (2010).
29. Katz, S. The reversible reaction of sodium thymonucleate and mercuric chloride. J. Am. Chem. Soc. 74, 2238-2245 (1952).
30. Kuklenyik, Z. & Marzilli, L. G. Mercury(II) site-selective binding to a DNA hairpin. Relationship of sequence-dependent intra- and interstrand crosslinking to the hairpin-duplex conformational transition. Inorg. Chem. 35, 5654-5662 (1996). (Pubitemid 126453014)
31. Miyake, Y. et al. MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. J. Am. Chem. Soc. 128, 2172-2173 (2006).
32. Park, K. S., Jung, C. & Park, H. G. 'Illusionary' polymerase activity triggered by metal ions: Use for molecular logic-gate operations. Angew. Chem. Int. Ed. 49, 9757-9760 (2010).
33. Ono, A. et al. Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes. Chem. Commun. 39, 4825-4827 (2008).
34. Urata, H., Yamaguchi, E., Nakamura, Y. & Wada, S-i. Pyrimidine-pyrimidine base pairs stabilized by silver(I) ions. Chem. Commun. 47, 941-943 (2011).
35. Carell, T. Molecular computing: DNA as a logic operator. Nature 469, 45-46 (2011).
36. Czlapinski, J. L. & Sheppard, T. L. Nucleic acid template-directed assembly of metallosalen-DNA conjugates. J. Am. Chem. Soc. 123, 8618-8619 (2001). (Pubitemid 32808092)
37. Czlapinski, J. L. & Sheppard, T. L. Template-directed assembly of metallosalen- DNA hairpin conjugates. ChemBioChem 5, 127-129 (2004). (Pubitemid 38095030)
38. Gothelf, K. V., Thomsen, A., Nielsen, M., Cló, E. & Brown, R. S. Modular DNA-programmed assembly of linear and branched conjugated nanostructures. J. Am. Chem. Soc. 126, 1044-1046 (2004). (Pubitemid 38140733)
39. Nielsen, M., Thomsen, A. H., Cló, E., Kirpekar, F. & Gothelf, K. V. Synthesis of linear and tripoidal oligo(phenylene ethynylene)-based building blocks for application in modular DNA-programmed assembly. J. Org. Chem. 69, 2240-2250 (2004). (Pubitemid 38419031)
40. Clever, G. H., Polborn, K. & Carell, T. A highly DNA-duplex- stabilizing metal-salen base pair. Angew. Chem. Int. Ed. 44, 7204-7208 (2005). (Pubitemid 41641731)
41. Clever, G. H. & Carell, T. Controlled stacking of 10 transition-metal ions inside a DNA duplex. Angew. Chem. Int. Ed. 46, 250-253 (2007). (Pubitemid 46071711)
42. Clever, G. H., Reitmeier, S. J., Carell, T. & Schiemann, O. Antiferromagnetic coupling of stacked cuII-salen complexes in DNA. Angew. Chem. Int. Ed. 49, 4927-4929 (2010).
43. Clever, G. H., Soeltl, Y., Burks, H., Spahl, W. & Carell, T. Metal-salen-base-pair complexes inside DNA: Complexation overrides sequence information. Chem. Eur. J. 12, 8708-8718 (2006). (Pubitemid 44852456)
44. Clever, G. H., Kaul, C. & Carell, T. DNA-metal base pairs. Angew. Chem. Int. Ed. 46, 6226-6236 (2007). (Pubitemid 47329411)
45. Müller, J. Metal-ion-mediated base pairs in nucleic acids. Eur. J. Inorg. Chem. 3749-3763 (2008).
46. Clever, G. H. & Shionoya, M. Metal-base pairing in DNA. Coord. Chem. Rev. 254, 2391-2402 (2010).
47. Yoon, T. P. & Jacobsen, E. N. Privileged chiral catalysts. Science 299, 1691-1693 (2003). (Pubitemid 36337187)
48. Atwell, S., Meggers, E., Spraggon, G. & Schultz, P. G. Structure of a copper-mediated base pair in DNA. J. Am. Chem. Soc. 123, 12364-12367 (2001). (Pubitemid 33136073)
49. Johannsen, S., Megger, N., Boehme, D., Sigel, R. K. O. & Mueller, J. Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nature Chem. 2, 229-234 (2010).
50. Johannsen, S., Paulus, S., Düpre, N., Müller, J. & Sigel, R. K. O. Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions. J. Inorg. Biochem. 102, 1141-1151 (2008).