Construction of semisynthetic DNA-protein conjugates with phi X174 gene-A* protein

Bioconjugate Chemistry

Volumn 23, Issue 6, 2012, Pages 1349-1355

  Mashimo, Yasumasa ^a   Maeda, Hitomi ^a   Mie, Masayasu ^a   Kobatake, Eiry ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOSYNTHESIS; CHEMICAL MODIFICATION; DNA; GENES; OLIGONUCLEOTIDES;

DNA FUNCTION; DNA-PROTEINS; ECONOMICAL METHODS; ENHANCED GREEN FLUORESCENT PROTEIN; FIREFLY LUCIFERASE; MOLECULAR TOOLS; PROTEIN CONJUGATES; PROTEIN FUNCTIONS; SITE-SPECIFIC; SYNERGISTIC EFFECT;

RECOMBINANT PROTEINS;

APTAMER; ENHANCED GREEN FLUORESCENT PROTEIN; FIREFLY LUCIFERASE; GENE A PROTEIN; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHOTYROSINE; RECOMBINANT PROTEIN; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIOPHAGE PHI X 174; CATALYSIS; CONJUGATE; DNA SYNTHESIS; DOT HYBRIDIZATION; GENE FUSION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CLEAVAGE; PROTEIN DNA INTERACTION; PROTEIN SYNTHESIS; SEMISYNTHETIC DNA PROTEIN CONJUGATE; STEADY STATE;

ANIMALS; APTAMERS, NUCLEOTIDE; BACTERIOPHAGE PHI X 174; BASE SEQUENCE; DNA, SINGLE-STRANDED; GREEN FLUORESCENT PROTEINS; HUMANS; LUCIFERASES, FIREFLY; OLIGODEOXYRIBONUCLEOTIDES; RECOMBINANT FUSION PROTEINS; THROMBIN; VIRAL PROTEINS;

EID: 84862686067     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc300118m     Document Type: Article

References (34)

1. Saccà, B., and Niemeyer, C. M. (2011) Functionalization of DNA nanostructures with proteins. Chem. Soc. Rev. 40, 5910-5921.
2. Röglin, L., and Seitz, O. (2008) Controlling the activity of peptides and proteins with smart nucleic acid-protein hybrids. Org. Biomol. Chem. 6, 3881-3887.
3. Burbulis, I., Yamaguchi, K., Gordon, A., Carlson, R., and Brent, R. (2005) Using protein-DNA chimeras to detect and count small numbers of molecules. Nat. Methods 2, 31-37.
4. Morin, I., Dixon, N. E., and Schaeffer, P. M. (2010) Ultrasensitive detection of antibodies using a new Tus-Ter-lock immunoPCR system. Mol. Biosyst. 6, 1173-1175.
5. Tang, Y. C., Wan, G., Ng, J. K., Ajikumar, P. K., and Too, H. P. (2008) DNA-directed assembly of protein microarrays. Front. Biosci. 13, 5755-5771.
6. Demidov, V. V., Dokholyan, N. V., Witte-Hoffmann, C., Chalasani, P., Yiu, H. W., Ding, F., Yu, Y., Cantor, C. R., and Broude, N. E. (2006) Fast complementation of split fluorescent protein triggered by DNA hybridization. Proc. Natl. Acad. Sci. U.S.A. 103, 2052-2056.
7. Takeda, S., Tsukiji, S., Ueda, H., and Nagamune, T. (2008) Covalent split protein fragment-DNA hybrids generated through N-terminus-specific modification of proteins by oligonucleotides. Org. Biomol. Chem. 6, 2187-2194.
8. Chen, C. H., Dellamaggiore, K. R., Ouellette, C. P., Sedano, C. D., Lizadjohry, M., Chernis, G. A., Gonzales, M., Baltasar, F. E., Fan, A. L., Myerowitz, R., and Neufeld, E. F. (2008) Aptamer-based endocytosis of a lysosomal enzyme. Proc. Natl. Acad. Sci. U.S.A. 105, 15908-15913.
9. Tong, G. J., Hsiao, S. C., Carrico, Z. M., and Francis, M. B. (2009) Viral capsid DNA aptamer conjugates as multivalent cell-targeting vehicles. J. Am. Chem. Soc. 131, 11174-11178.
10. Aldaye, F. A., Senapedis, W. T., Silver, P. A., and Way, J. C. (2010) A structurally tunable DNA-based extracellular matrix. J. Am. Chem. Soc. 132, 14727-14729.
11. Niemeyer, C. M., Sano, T., Smith, C. L., and Cantor, C. R. (1994) Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA-streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates. Nucleic Acids Res. 22, 5530-5539.
12. Kukolka, F., and Niemeyer, C. M. (2004) Synthesis of fluorescent oligonucleotide-EYFP conjugate: towards supramolecular construction of semisynthetic biomolecular antennae. Org. Biomol. Chem. 2, 2203-2206.
13. Lapiene, V., Kukolka, F., Kiko, K., Arndt, A., and Niemeyer, C. M. (2010) Conjugation of fluorescent proteins with DNA oligonucleotides. Bioconjugate Chem. 21, 921-927.
14. Niemeyer, C. M. (2010) Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew. Chem., Int. Ed. Engl. 49, 1200-1216.
15. Lovrinovic, M., Seidel, R., Wacker, R., Schroeder, H., Seitz, O., Engelhard, M., Goody, R. S., and Niemeyer, C. M. (2003) Synthesis of protein-nucleic acid conjugates by expressed protein ligation. Chem. Commun., 822-823.
16. Pritz, S., Wolf, Y., Kraetke, O., Klose, J., Bienert, M., and Beyermann, M. (2007) Synthesis of biologically active peptide nucleic acid-peptide conjugates by sortase-mediated ligation. J. Org. Chem. 72, 3909-3912.
17. Tominaga, J., Kemori, Y., Tanaka, Y., Maruyama, T., Kamiya, N., and Goto, M. (2007) An enzymatic method for site-specific labeling of recombinant proteins with oligonucleotides. Chem. Commun., 401-403.
18. Kitaoka, M., Tsuruda, Y., Tanaka, Y., Goto, M., Mitsumori, M., Hayashi, K., Hiraishi, Y., Miyawaki, K., Noji, S., and Kamiya, N. (2011) Transglutaminase-mediated synthesis of a DNA-(enzyme)n probe for highly sensitive DNA detection. Chemistry 17, 5387-5392.
19. Smith, S. S., Niu, L., Baker, D. J., Wendel, J. A., Kane, S. E., and Joy, D. S. (1997) Nucleoprotein-based nanoscale assembly. Proc. Natl. Acad. Sci. U.S.A. 94, 2162-2167.
20. Jongsma, M. A., and Litjens, R. H. (2006) Self-assembling protein arrays on DNA chips by auto-labeling fusion proteins with a single DNA address. Proteomics 6, 2650-2655.
21. Linney, E., and Hayashi, M. (1973) Two proteins of Gene A of φX174. Nat. New Biol. 245, 6-8.
22. Langeveld, S. A., van Mansfeld, A. D., Baas, P. D., Jansz, H. S., van Arkel, G. A., and Weisbeek, P. J. (1978) Nucleotide sequence of the origin of replication in bacteriophage φX174 RF DNA. Nature 271, 417-420.
23. Sanhueza, S., and Eisenberg, S. (1984) Cleavage of single-stranded DNA by the φX174 A* protein: The A*-single-stranded DNA covalent linkage. Proc. Natl. Acad. Sci. U.S.A. 81, 4285-4289.
24. Hanai, R., and Wang, J. C. (1993) The mechanism of sequence-specific DNA cleavage and strand transfer by phi X174 gene A*protein. J. Biol. Chem. 268, 23830-23836.
25. Heidekamp, F., Baas, P. D., and Jansz, H. S. (1982) Nucleotide sequences at the φX gene A protein cleavage site in replicative form I DNAs of bacteriophages U3, G14, and α3. J. Virol. 42, 91-99.
26. Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., and Toole, J. J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355, 564-566.
27. van Mansfeld, A. D., van Teeffelen, H. A., Baas, P. D., and Jansz, H. S. (1986) Two juxtaposed tyrosyl-OH groups participate in phi X174 gene A protein catalysed cleavage and ligation of DNA. Nucleic Acids Res. 14, 4229-4238.
28. Venkatesh, B., Arifuzzaman, M., Mori, H., Suzuki, S., Taguchi, T., and Ohmiya, Y. (2005) Use of GFP tags to monitor localization of different luciferases in E. coli. Photochem. Photobiol. Sci. 4, 740-743.
29. Baldrich, E., Restrepo, A., and O'Sullivan, C. K. (2004) Aptasensor development: elucidation of critical parameters for optimal aptamer performance. Anal. Chem. 76, 7053-7063.
30. Sekiguchi, J., and Shuman, S. (1994) Requirements for noncovalent binding of vaccinia topoisomerase I to duplex DNA. Nucleic Acids Res. 22, 5360-5365.
31. Nangreave, J., Han, D., Liu, Y., and Yan, H. (2010) DNA origami: a history and current perspective. Curr. Opin. Chem. Biol. 14, 608-615.
32. Rajendran, A., Endo, M., and Sugiyama, H. (2012) Single-molecule analysis using DNA origami. Angew. Chem., Int. Ed. Engl. 51, 874-890.
33. Lin, C., Liu, Y., and Yan, H. (2009) Designer DNA nanoarchitectures. Biochemistry 48, 1663-1674.
34. Zhang, D. Y., and Seelig, G. (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103-113.