Nanoscale programmable sequence-specific patterning of DNA scaffolds using RecA protein

Nanotechnology

Volumn 23, Issue 36, 2012, Pages

  Sharma, R ^a   Davies, A G ^a   Walti C ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MOLECULE; DNA MOLECULES; DNA STRANDS; HOST DEVICES; MOLECULAR SCAFFOLDS; MOLECULAR SELF ASSEMBLY; NANO SCALE; NANO-SCALE OBJECTS; NANOSCALE ASSEMBLIES; NANOSCALE COMPLEXES; NUCLEOPROTEIN FILAMENTS; PATTERNING TECHNIQUES; RECA PROTEINS; SINGLE-STRANDED (SS) DNA; SPECIFIC LOCATION;

DNA; MOLECULES; NANOTECHNOLOGY; PROTEINS;

SCAFFOLDS (BIOLOGY);

DNA; RECA PROTEIN; RESTRICTION ENDONUCLEASE;

ARTICLE; CHEMISTRY; CONFORMATION; ESCHERICHIA COLI; GENETICS; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS;

BASE SEQUENCE; DNA; DNA RESTRICTION ENZYMES; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ESCHERICHIA COLI; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; REC A RECOMBINASES;

EID: 84865421507     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/23/36/365301     Document Type: Article

References (33)

1. Lu W and Lieber C M 2007 Nanoelectronics from the bottom up Nature Mater. 6 841-50 (Pubitemid 350050579)
2. Aldaye F A, Palmer A L and Sleiman H F 2008 Assembling materials with DNA as the guide Science 321 1795-9
3. Mirkin C A, Letsinger R L, Mucic R C and Storhoff J J 1996 A DNA-based method for rationally assembling nanoparticles into macroscopic materials Nature 382 607-9 (Pubitemid 26268949)
4. Cha J N, Noh H, Choi C, Hung A M and Jin S H 2010 Site-specific patterning of highly ordered nanocrystal super lattices through biomolecular surface confinement ACS Nano 4 5076-80
5. Sarikaya M, Tamerler C, Jen A K, Schulten K and Baneyx F 2003 Molecular biomimetics: nanotechnology through biology Nature Mater. 2 577-85
6. Brown S 2001 Protein-mediated particle assembly Nano Lett. 1 391-4 (Pubitemid 33673011)
7. Niemeyer C M, Burger W and Peplies J 1998 Covalent DNA-streptavidin conjugates as building blocks for novel biometallic nanostructures Angew. Chem. Int. Edn 37 2265-8 (Pubitemid 28450892)
8. Johnson S, Evans D, Laurenson S, Paul D, Davies A G, Ko Ferrigno P and Wälti C 2008 Surface-immobilized peptide aptamers as probe molecules for protein detection Anal. Chem. 80 978-83 (Pubitemid 351272327)
9. Seeman N C 2010 Nanomaterials based on DNA Annu. Rev. Biochem. 79 65-87
10. Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297-302
11. Seeman N C and Lukeman P S 2005 Nucleic acid nanostructures: bottom-up control of geometry on the nanoscale Rep. Prog. Phys. 68 237-70
12. Liu Y, Lin C, Li H and Yan H 2005 Aptamer-directed self-assembly of protein arrays on a DNA nanostructure Angew. Chem. Int. Edn Engl. 44 4333-8 (Pubitemid 41026362)
13. Yan H, Chhabra R, Sharma J, Ke Y G, Liu Y, Rinker S and Lindsay S 2007 Spatially addressable multiprotein nanoarrays templated by aptamer-tagged DNA nanoarchitectures J. Am. Chem. Soc. 129 10304-5 (Pubitemid 47330226)
14. Folta-Stogniew E, OMalley S, Gupta R, Anderson K S and Radding C M 2004 Exchange of DNA base pairs that coincides with recognition of homology promoted by E-coli RecA protein Mol. Cell 15 965-75 (Pubitemid 39277992)
15. Lusetti S L, Shaw J J and Cox M M 2003 Magnesium ion-dependent activation of the RecA protein involves the C terminus J. Biol. Chem. 278 16381-8 (Pubitemid 36799765)
16. Hegner M, Smith S B and Bustamante C 1999 Polymerization and mechanical properties of single RecA-DNA filaments Proc. Natl Acad. Sci. USA 96 10109-14 (Pubitemid 29422520)
17. Kowalczykowski S C and Krupp R A 1995 DNA-strand exchange promoted by RecA protein in the absence of ATP: implications for the mechanism of energy transduction in protein-promoted nucleic acid transactions Proc. Natl Acad. Sci. USA 92 3478-82
18. Joo C, McKinney S A, Nakamura M, Rasnik I, Myong S and Ha T 2006 Real-time observation of RecA filament dynamics with single monomer resolution Cell 126 515-27 (Pubitemid 44163610)
19. van Loenhout M T, van der Heijden T, Kanaar R, Wyman C and Dekker C 2009 Dynamics of RecA filaments on single-stranded DNA Nucl. Acids Res. 37 4089-99
20. Story R M, Weber I T and Steitz T A 1992 The structure of the E. coli RecA protein monomer and polymer Nature 355 318-25
21. Chen Z, Yang H and Pavletich N P 2008 Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Nature 453 489-4 (Pubitemid 351733325)
22. VanLoock M S, Yu X, Yang S, Lai A L, Low C, Campbell M J and Egelman E H 2003 ATP-mediated conformational changes in the RecA filament Structure 11 187-96 (Pubitemid 36183643)
23. Cox M M 2007 Motoring along with the bacterial RecA protein Nature Rev. Mol. Cell Biol. 8 127-38 (Pubitemid 46432527)
24. Lindsley J E and Cox M M 1990 Assembly and disassembly of RecA protein filaments occur at opposite filament ends. Relationship to DNA strand exchange J. Biol. Chem. 265 9043-54
25. Tracy R B and Kowalczykowski S C 1996 In vitro selection of preferred DNA pairing sequences by the Escherichia coli RecA protein Genes Dev. 10 1890-903 (Pubitemid 26281684)
26. Bar-Ziv R and Libchaber A 2001 Effects of DNA sequence and structure on binding of RecA to single-stranded DNA Proc. Natl Acad. Sci. USA 98 9068-73 (Pubitemid 32743870)
27. Shigemori Y and Oishi M 2005 Stable triple-stranded DNA formation and its application to the SNP detection DNA Res. 12 441-9 (Pubitemid 43843813)
28. Keren K, Krueger M, Gilad R, Ben-Yoseph G, Sivan U and Braun E 2002 Sequence-specific molecular lithography on single DNA molecules Science 297 72-5 (Pubitemid 34743092)
29. Nishinaka T, Takano A, Doi Y, Hashimoto M, Nakamura A, Matsushita Y, Kumaki J and Yashima E 2005 Conductive metal nanowires templated by the nucleoprotein filaments, complex of DNA and RecA protein J. Am. Chem. Soc. 127 8120-5 (Pubitemid 40799669)
30. Ferrin L J and Camerini-Otero R D 1991 Selective cleavage of human DNA: RecA-assisted restriction endonuclease (RARE) cleavage Science 254 1494-7 (Pubitemid 21917486)
31. Tosch P, Wälti C, Middelberg A P and Davies A G 2006 Generic technique to generate large branched DNA complexes Biomacromolecules 7 677-81
32. Koob M, Burkiewicz A, Kur J and Szybalski W 1992 RecA-Ac - single-site cleavage of plasmids and chromosomes at any predetermined restriction site Nucl. Acids Res. 20 5831-6
33. Honigberg S M, Rao B J and Radding C M 1986 Ability of RecA protein to promote a search for rare sequences in duplex DNA Proc. Natl Acad. Sci. USA 83 9586-90 (Pubitemid 17223403)