DNA binding and bending protein-based DNA actuator and its practical realization

Nanobiotechnology

Volumn 4, Issue 1-4, 2008, Pages 43-49

  Endo, Tatsuro ^a   Yoda, Hiroki ^a   Yanagida, Yasuko ^a   Hatsuzawa, Takeshi ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Atomic force microscopy; DNA actuator; DNA binding and bending proteins; Single polypeptide chain integrated host factor 2 (scIHF2)

Indexed keywords

DEOXYRIBONUCLEOPROTEIN; DNA ACTUATOR; DNA BINDING PROTEIN; NANOPARTICLE; POLYPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; NANOBIOTECHNOLOGY; NANODEVICE; NANOFABRICATION; NANOTECHNOLOGY; PRIORITY JOURNAL; PROTEIN DOMAIN;

EID: 68949219599     PISSN: 15511286     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12030-009-9025-5     Document Type: Article

References (30)

1. WR Browne BL Feringa 2006 Making molecular machines work Nat Nanotechnol 1 25 35 10.1038/nnano.2006.45
2. M Sarikaya C Tamerler AK-Y Jen K Schulten F Baneyx 2003 Molecular biomimetics: nanotechnology through biology Nat Mater 2 577 585 10.1038/nmat964
3. E Winfree F Liu LA Wenzler NC Seeman 1998 Design and self-assembly of two-dimensional DNA crystals Nature 394 539 544 10.1038/28998
4. C Sönnichsen BM Reinhard J Liphardt AP Alivisatos 2005 A molecular ruler based on plasmon coupling of single gold and silver nanoparticles Nat Biotechnol 23 741 745 10.1038/nbt1100
5. DS Hopkins D Pekker PM Goldbart A Bezryadin 2005 Quantum interference device made by DNA templating of superconducting nanowires Science 308 1762 1765 10.1126/science.1111307
6. Y Chen C Mao 2004 Putting a brake on an autonomous DNA nanomotor J Am Chem Soc 126 8626 8627 10.1021/ja047991r
7. PWK Rothemund 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297 302 10.1038/nature04586
8. H Yan TH LaBean L Feng JH Reif 2003 Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices Proc Natl Acad Sci U S A 100 8103 8108 10.1073/pnas.1032954100
9. T Hatsuzawa H Osanai Y Yanagida 2006 Nano-particle positioning on DNA strand J Jpn Soc Precis Eng 72 1407 1410
10. S Khrapunov M Brenowitz PA Rice CE Catalano 2006 Binding then bending: a mechanism for wrapping DNA Proc Natl Acad Sci U S A 103 19217 19218 10.1073/pnas.0609223103
11. K Luger AW Mäder RK Richmond DF Sargent TJ Richmond 1997 Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature 389 251 260 10.1038/38444
12. RE Harrington 1992 DNA curving and bending in protein-DNA recognition Mol Microbiol 6 2549 2555 10.1111/j.1365-2958.1992.tb01431.x
13. PC van der Vliet CP Verrijzer 1993 Bending of DNA by transcription factors Bioessays 15 25 32 10.1002/bies.950150105
14. PA Rice SW Yang K Mizuuchi HA Nash 1996 Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn Cell 87 1295 1306 10.1016/S0092-8674(00) 81824-3
15. N Goosen P van de Putte 1995 The regulation of transcription initiation by integration host factor Mol Microbiol 16 1 7 10.1111/j.1365-2958.1995. tb02386.x
16. KK Swinger PA Rice 2007 Structure-based analysis of HU-DNA binding J Mol Biol 365 1005 1016 10.1016/j.jmb.2006.10.024
17. I Tanaka K Appelt J Dijk SW White KS Wilson 1984 3-Å resolution structure of a protein with histone-like properties in prokaryotes Nature 310 376 381 10.1038/310376a0
18. CC Yang HA Nash 1989 The interaction of E. coli IHF protein with its specific binding sites Cell 57 869 880 10.1016/0092-8674(89) 90801-5
19. KK Swinger PA Rice 2004 IHF and HU: flexible architects of bent DNA Curr Opin Struct Biol 14 28 35 10.1016/j.sbi.2003.12.003
20. S Sugimura DM Crothers 2006 Stepwise binding and bending of DNA by Escherichia coli integration host factor Proc Natl Acad Sci U S A 103 18510 18514 10.1073/pnas.0608337103
21. T Corona, et al. 2003 Activation of site-specific DNA integration in human cells by a single chain integration host factor Nucleic Acids Res 31 5140 5148 10.1093/nar/gkg711
22. Q Bao N Christ P Dröge 2004 Single-chain integration host factors as probes for high-precision nucleoprotein complex formation Gene 343 99 106 10.1016/j.gene.2004.08.030
23. J Widom 1992 A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells Proc Natl Acad Sci U S A 89 1095 1099 10.1073/pnas.89.3.1095
24. RT Dame, et al. 2005 Analysis of scanning force microscopy images of protein-induced DNA bending using simulations Nucleic Acids Res 33 e68 10.1093/nar/gni073
25. J van Noort S Verbrugge N Goosen C Dekker RT Dame 2004 Dual architectural roles of HU: formation of flexible hinges and rigid filaments Proc Natl Acad Sci U S A 101 6969 6974 10.1073/pnas.0308230101
26. JD Badjic V Balzani A Credi S Silvi JF Stoddart 2004 A molecular elevator Science 303 1845 1849 10.1126/science.1094791
27. BH Robinson NC Seeman 1987 The design of a biochip: a self-assembling molecular-scale memory device Protein Eng 1 295 300 10.1093/protein/1.4.295
28. V Balzani A Credi M Venturi 2007 Molecular devices and machines Nano Today 2 18 25 10.1016/S1748-0132(07) 70055-5
29. T Liedl TL Sobey FC Simmel 2007 DNA-based nanodevices Nano Today 2 36 41 10.1016/S1748-0132(07) 70057-9
30. JT Finer RM Simmons JA Spudich 1994 Single myosin molecule mechanics: piconewton forces and nanometer steps Nature 368 113 119 10.1038/368113a0