Azobenzene photoisomerization-induced destabilization of B-DNA

Biophysical Journal

Volumn 107, Issue 4, 2014, Pages 932-940

  Biswas, Mithun ^a   Burghardt, Irene ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINOALCOHOL; AZO COMPOUND; AZOBENZENE; BUTANEDIOL; DNA B; THREONINOL;

CHEMISTRY; ISOMERISM; MOLECULAR DYNAMICS; PHOTOCHEMISTRY; TEMPERATURE;

AMINO ALCOHOLS; AZO COMPOUNDS; BUTYLENE GLYCOLS; DNA, B-FORM; ISOMERISM; MOLECULAR DYNAMICS SIMULATION; PHOTOCHEMICAL PROCESSES; TEMPERATURE;

EID: 84904974211     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.06.044     Document Type: Article

References (43)

1. D. Liu, and S.H. Park T.H. LaBean DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires Proc. Natl. Acad. Sci. USA 101 2004 717 722 (Pubitemid 38121023)
2. J.S. Shin, and N.A. Pierce A synthetic DNA walker for molecular transport J. Am. Chem. Soc. 126 2004 10834 10835 (Pubitemid 39180556)
3. B. Yurke, and A.J. Turberfield J.L. Neumann A DNA-fueled molecular machine made of DNA Nature 406 2000 605 608 (Pubitemid 30641042)
4. J. Bath, and A.J. Turberfield DNA nanomachines Nat. Nanotechnol. 2 2007 275 284 (Pubitemid 46882966)
5. H. Asanuma, and T. Ito M. Komiyama Photoregulation of the formation and dissociation of a DNA duplex by using the cis-trans isomerization of azobenzene Angew. Chem. Int. Ed. Engl. 38 1999 2393 2395 (Pubitemid 29399571)
6. H. Asanuma, and T. Takarada M. Komiyama Enantioselective incorporation of azobenzenes into oligodeoxyribonucleotide for effective photoregulation of duplex formation Angew. Chem. Int. Ed. Engl. 40 2001 2671 2673 (Pubitemid 32691711)
7. J. Andersson, and S. Li J. Andréasson Photoswitched DNA-binding of a photochromic spiropyran J. Am. Chem. Soc. 130 2008 11836 11837
8. H.M.D. Bandara, and S.C. Burdette Photoisomerization in different classes of azobenzene Chem. Soc. Rev. 41 2012 1809 1825
9. G.S. Hartley Cis-form of azobenzene Nature 140 1937 281
10. H. Asanuma, and X. Liang M. Komiyama Photocontrol of DNA duplex formation by using azobenzene-bearing oligonucleotides ChemBioChem 2 2001 39 44 (Pubitemid 33722526)
11. X. Liang, and H. Asanuma M. Komiyama NMR study on the photoresponsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form J. Am. Chem. Soc. 125 2003 16408 16415 (Pubitemid 38020665)
12. X. Liang, and N. Takenaka H. Asanuma Molecular design for reversing the photoswitching mode of turning ON and OFF DNA hybridization Chem. Asian J. 3 2008 553 560
13. X. Liang, T. Mochizuki, and H. Asanuma A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices Small 5 2009 1761 1768
14. M. Liu, H. Asanuma, and M. Komiyama Azobenzene-tethered T7 promoter for efficient photoregulation of transcription J. Am. Chem. Soc. 128 2006 1009 1015 (Pubitemid 43153050)
15. A. Yamazawa, and X. Liang M. Komiyama Photoregulation of the DNA polymerase reaction by oligonucleotides bearing an azobenzene Angew. Chem. Int. Ed. Engl. 39 2000 2356 2357 (Pubitemid 30482258)
16. X. Liang, and H. Nishioka H. Asanuma Construction of photon-fueled DNA nanomachines by tethering azobenzenes as engines A. Goel, F. Simmel, P. Sosík, DNA Computing, Vol. 5347, Lecture Notes in Computer Science 2009 Springer Berlin 21 32
17. P.H. Nguyen, R.D. Gorbunov, and G. Stock Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study Biophys. J. 91 2006 1224 1234 (Pubitemid 44174243)
18. P.H. Nguyen, and H. Staudt G. Stock Real time observation of ultrafast peptide conformational dynamics: molecular dynamics simulation vs infrared experiment J. Phys. Chem. B 115 2011 13084 13092
19. M. Böckmann, and S. Braun D. Marx Mimicking photoisomerization of azo-materials by a force field switch derived from nonadiabatic ab initio simulations: application to photoswitchable helical foldamers in solution J. Chem. Phys. 139 2013 084108
20. D. Case, and T. Darden P. Kollman AMBER 12 2012 University of California San Francisco, CA
21. H. Asanuma, D. Matsunaga, and M. Komiyama Clear-cut photo-regulation of the formation and dissociation of the DNA duplex by modified oligonucleotide involving multiple azobenzenes Nucl. Acids Symp. Ser. (Oxf) 49 2005 35 36
22. P. Duchstein, and C. Neiss D. Zahn Molecular mechanics modeling of azobenzene-based photoswitches J. Mol. Model. 18 2012 2479 2482
23. T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an N log (N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089
24. T.E. Cheatham 3rd, P. Cieplak, and P.A. Kollman A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 16 1999 845 862 (Pubitemid 29157655)
25. D.A. Case, and T.E. Cheatham 3rd R.J. Woods The AMBER biomolecular simulation programs J. Comput. Chem. 26 2005 1668 1688 (Pubitemid 43076180)
26. A. Pérez, and I. Marchán M. Orozco Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 92 2007 3817 3829 (Pubitemid 46910569)
27. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802 (Pubitemid 43078511)
28. J.-P. Ryckaert, G. Ciccotti, and H.J. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
29. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant pressure molecular dynamics algorithms J. Chem. Phys. 101 1994 4177
30. S.E. Feller, and Y. Zhang B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613
31. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28 (Pubitemid 26152973)
32. S. Pronk, and S. Páll E. Lindahl GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 2013 845 854
33. R. Lavery, and M. Moakher K. Zakrzewska Conformational analysis of nucleic acids revisited: CURVES+ Nucleic Acids Res. 37 2009 5917 5929
34. H. Rau Further evidence for rotation in the π,π and inversion in the n,π photoisomerization of azobenzenes J. Photochem. 26 1984 221 225
35. P. Bortolus, and S. Monti Cis-trans photoisomerization of azobenzene. Solvent and triplet donors effects J. Phys. Chem. 83 1979 648 652
36. M. Böckmann, N.L. Doltsinis, and D. Marx Nonadiabatic hybrid quantum and molecular mechanic simulations of azobenzene photoswitching in bulk liquid environment J. Phys. Chem. A 114 2010 745 754
37. J.A. Gámez, and O. Weingart W. Thiel Cooperating dinitrogen and phenyl rotations in trans-azobenzene photoisomerization J. Chem. Theory Comput. 8 2012 2352 2358
38. S. Neidle Oxford Handbook of Nucleic Acid Structure Vol. 326 1999 Oxford University Press New York
39. D. Rastädter, M. Biswas, and I. Burghardt Molecular Dynamics Study of the Controlled Destabilization of an RNA Hairpin Structure by a Covalently Attached Azobenzene Switch J. Phys. Chem. B. 118 2014 8478 8488
40. M. Böckmann, and D. Marx N.L. Doltsinis Multiscale modeling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond Phys. Chem. Chem. Phys. 13 2011 7604 7621
41. X.-J. Lu, Z. Shakked, and W.K. Olson A-form conformational motifs in ligand-bound DNA structures J. Mol. Biol. 300 2000 819 840
42. M. McCullagh, and I. Franco G.C. Schatz Defects in DNA: lessons from molecular motor design J. Phys. Chem. Lett. 3 2012 689 693
43. H. Ma, and C. Wan A.H. Zewail DNA folding and melting observed in real time redefine the energy landscape Proc. Natl. Acad. Sci. USA 104 2007 712 716 (Pubitemid 46154675)