Organizing protein-DNA hybrids as nanostructures with programmed functionalities

Trends in Biotechnology

Volumn 28, Issue 12, 2010, Pages 619-628

  Teller, Carsten ^a,b   Willner, Itamar ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b FRAUNHOFER INSTITUTE FOR BIOMEDICAL ENGINEERING   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BASE SEQUENCES; BIOSENSING; DNA NANOSTRUCTURES; FUNCTIONAL INFORMATION; FUNCTIONAL PROTEINS; FUTURE PROSPECTS; METALLIC NANOSTRUCTURE; PROTEIN HYBRIDS; REDOX ENZYME;

CATALYSTS; ENZYMES; IONIC LIQUIDS; NANOSTRUCTURES; NUCLEIC ACIDS;

DNA;

CHOLINE OXIDASE; DNA; DNA HYBRID; DNA NANOWIRE; ENZYME; GLUCOSE OXIDASE; GOLD SALT; HORSERADISH PEROXIDASE; HYDROGEN PEROXIDE; LUMINOL; METAL NANOPARTICLE; NANOMATERIAL; NANOWIRE; NITRIC OXIDE; NITRITE; NUCLEIC ACID; OXIDOREDUCTASE; PROTEIN; UNCLASSIFIED DRUG;

ACTION POTENTIAL; BIOCATALYSIS; BIOTRANSFORMATION; CHEMOLUMINESCENCE; COMPLEX FORMATION; DNA HYBRIDIZATION; DNA PROTEIN COMPLEX; ENZYME ACTIVATION; ENZYME CONFORMATION; ENZYMIC BIOSENSOR; OPTICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; REVIEW; SUPRAMOLECULAR CHEMISTRY;

BIOSENSING TECHNIQUES; BIOTECHNOLOGY; DNA; ENZYMES; METALS; NANOSTRUCTURES; PROTEINS;

EID: 78149468482     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2010.09.005     Document Type: Review

References (57)

1. Phan A.T., Mergny J. Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix. Nucleic Acids Res. 2002, 30:4618-4625.
2. Mayer G. The chemical biology of aptamers. Angew. Chem. Int. Ed. 2009, 48:2672-2689.
3. Liu J., et al. Functional nucleic acid sensors. Chem. Rev. 2009, 109:1948-1998.
4. Seeman N.C. From genes to machines: DNA nanomechanical devices. Trends Biochem. Sci. 2005, 30:119-125.
5. Ezziane Z. DNA computing: applications and challenges. Nanotechnology 2006, 17:R27-R39.
6. Aldaye F.A., et al. Assembling materials with DNA as the guide. Science 2008, 321:1795-1799.
7. Cissell K.A., et al. Reassembly of a bioluminescent protein Renilla luciferase directed through DNA hybridization. Bioconjug. Chem. 2009, 20:15-19.
8. Niemeyer C.M., et al. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H:FMN oxidoreductase and luciferase. ChemBioChem 2002, 3:242-245.
9. Müller J., Niemeyer C.M. DNA-directed assembly of artificial multienzyme complexes. Biochem. Biophys. Res. Commun. 2008, 377:62-67.
10. Piperberg G., et al. Control of bioelectrocatalytic transformations on DNA scaffolds. J. Am. Chem. Soc. 2009, 131:8724-8725.
11. Tepper A.W.J.W. Electrical contacting of an assembly of pseudoazurin and nitrite reductase using DNA-directed immobilization. J. Am. Chem. Soc. 2010, 132:6550-6557.
12. 2+ Ions. J. Am. Chem. Soc. 2010, 132:6878-6879.
13. Katz S. The reversible reaction of Hg (II) and double-stranded polynucleotides. A step-function theory and its significance. BBA-Spec. Sect. Nucleic Acids and Rel. Subj. 1963, 68:240-253.
14. II-thymine base pairs in DNA duplexes. J. Am. Chem. Soc. 2006, 128:2172-2173.
15. Yan H., et al. A robust DNA mechanical device controlled by hybridization topology. Nature 2002, 415:62-65.
16. Ding B., Seeman N.C. Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate. Science 2006, 314:1583-1585.
17. Weizmann Y., et al. A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:5289-5294.
18. Centi S., et al. Different approaches for the detection of thrombin by an electrochemical aptamer-based assay coupled to magnetic beads. Biosens. Bioelectron. 2008, 23:1602-1609.
19. Golub E., et al. Electrochemical, photoelectrochemical, and surface plasmon resonance detection of cocaine using supramolecular aptamer complexes and metallic or semiconductor nanoparticles. Anal. Chem. 2009, 81:9291-9298.
20. Tombelli S., Mascini M. Aptamers as molecular tools for bioanalytical methods. Curr. Opin. Mol. Ther. 2009, 11:179-188.
21. Willner I., Zayats M. Electronic aptamer-based sensors. Angew. Chem. Int. Ed. Engl. 2007, 46:6408-6418.
22. Stojanovic M.N., et al. Fluorescent sensors based on aptamer self-assembly. J. Am. Chem. Soc. 2000, 122:11547-11548.
23. Jose A.M., et al. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res. 2001, 29:1631-1637.
24. Noeske J., et al. Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain. Nucleic Acids Res. 2007, 35:5262-5273.
25. Freeman R., et al. Supramolecular cocaine-aptamer complexes activate biocatalytic cascades. J. Am. Chem. Soc. 2009, 131:5028-5029.
26. Freeman R., et al. Control of biocatalytic transformations by programmed DNA assemblies. Chem. Eur. J. 2010, 16:3690-3698.
27. Pavlov V., et al. Fluorescence detection of DNA by the catalytic activation of an aptamer/thrombin complex. J. Am. Chem. Soc. 2005, 127:6522-6523.
28. Willner I., et al. DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem. Soc. Rev. 2008, 37:1153-1165.
29. Liu J., Lu Y. A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc. 2003, 125:6642-6643.
30. Elbaz J., et al. DNA computing circuits using libraries of DNAzyme subunits. Nat. Nano. 2010, 5:417-422.
31. Travascio P., et al. DNA-enhanced peroxidase activity of a DNA aptamer-hemin complex. Chem. Biol. 1998, 5:505-517.
32. Rojas A., et al. Specificity of a DNA-based (DNAzyme) peroxidative biocatalyst. Biotechnol. Lett. 2007, 29:227-232.
33. Xiao Y., et al. Lighting up biochemiluminescence by the surface self-assembly of DNA-hemin complexes. ChemBioChem 2004, 5:374-379.
34. Shlyahovsky B., et al. Proteins modified with DNAzymes or aptamers act as biosensors or biosensor labels. Biosens. Bioelectron. 2007, 22:2570-2576.
35. Modi S., et al. Structural DNA nanotechnology: from bases to bricks, from structure to function. J. Phys. Chem. Lett. 2010, 1:1994-2005.
36. LaBean T.H., et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 2000, 122:1848-1860.
37. Liu D., et al. DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:717-722.
38. Rothemund P.W.K. Folding DNA to create nanoscale shapes and patterns. Nature 2006, 440:297-302.
39. Dietz H., et al. Folding DNA into twisted and curved nanoscale shapes. Science 2009, 325:725-730.
40. Douglas S.M., et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 2009, 459:414-418.
41. Andersen E.S., et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 2009, 459:73-76.
42. Wilner O.I., et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nano. 2009, 4:249-254.
43. Cheglakov Z., et al. Increasing the complexity of periodic protein nanostructures by the rolling-circle-amplified synthesis of aptamers. Angew. Chem. Int. Ed. 2008, 47:126-130.
44. Rinker S., et al. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nat. Nano. 2008, 3:418-422.
45. Liu Y., et al. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew. Chem. Int. Ed. 2005, 44:4333-4338.
46. Chhabra R., et al. Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures. J. Am. Chem. Soc. 2007, 129:10304-10305.
47. Numajiri K., et al. Stepwise and reversible nanopatterning of proteins on a DNA origami scaffold. Chem. Commun. 2010, 46:5127-5129.
48. Wilner O.I., et al. Self-assembly of enzymes on DNA scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires. Nano. Lett. 2009, 9:2040-2043.
49. Willner I., et al. Growing metal nanoparticles by enzymes. Adv. Mat. 2006, 18:1109-1120.
50. Zayats M., et al. Biocatalytic growth of Au nanoparticles: from mechanistic aspects to biosensors design. Nano Lett. 2005, 5:21-25.
51. Basnar B., et al. Synthesis of nanowires using dip-pen nanolithography and biocatalytic inks. Adv. Mat. 2006, 18:713-718.
52. Fruk L., et al. Apoenzyme reconstitution as a chemical tool for structural enzymology and biotechnology. Angew. Chem. Int. Ed. 2009, 48:1550-1574.
53. Niemeyer C.M. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew. Chem. Int. Ed. 2010, 49:1200-1216.
54. Riklin A., et al. Improving enzyme-electrode contacts by redox modification of cofactors. Nature 1995, 376:672-675.
55. Hu Y., et al. Construction of artificial photosynthetic reaction centers on a protein surface: vectorial, multistep, and proton-coupled electron transfer for long-lived charge separation. J. Am. Chem. Soc. 2000, 122:241-253.
56. Fruk L., et al. Kinetic analysis of semisynthetic peroxidase enzymes containing a covalent DNA-heme adduct as the cofactor. Chem. Eur. J. 2006, 12:7448-7457.
57. Kostiainen M.A., et al. Optically degradable dendrons for temporary adhesion of proteins to DNA. Chem. Eur. J. 2010, 16:6912-6918.