Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA?

Journal of Chemical Physics

Volumn 133, Issue 3, 2010, Pages

  Woiczikowski, P Benjamin ^a   Kuba, Tomáš ^a   Gutírrez, Rafael ^b   Cuniberti, Gianaurelio ^b   Elstner, Marcus ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SYSTEM; CHARGE TRANSFER EFFICIENCY; CHARGE TRANSPORT; CONDUCTION PROPERTIES; CONFORMATIONAL SPACE; DOUBLE STRANDED DNA; DOUBLE-STRANDED DNA (DS-DNA); ELECTRICAL CONDUCTION; ELECTRICAL TRANSPORT PROPERTIES; ELECTRONIC STRUCTURE CALCULATIONS; HIGHER-DEGREE; HYBRID APPROACH; MATRIX ELEMENTS; MOLECULAR DYNAMICS SIMULATIONS; STRUCTURAL DISTORTIONS; STRUCTURAL STABILITIES; TIGHT BINDING MODEL; TRANSMISSION FUNCTION;

CHARGE TRANSFER; COMPUTER SIMULATION; CONFORMATIONS; DNA; ELECTRONIC STRUCTURE; GENES; ION EXCHANGE; MOLECULAR DYNAMICS; STABILITY; TRANSPORT PROPERTIES;

ELECTRIC PROPERTIES;

DNA; GUANINE QUADRUPLEX;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; ELECTRODE; ELECTRON; ELECTRON TRANSPORT; GENETICS; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; SOLUTION AND SOLUBILITY; THERMODYNAMICS;

BASE SEQUENCE; DNA; ELECTRODES; ELECTRON TRANSPORT; ELECTRONS; G-QUADRUPLEXES; MOLECULAR DYNAMICS SIMULATION; SOLUTIONS; THERMODYNAMICS;

EID: 77956255091     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3460132     Document Type: Article

References (78)

1. E. Boon, A. Livingston, N. Chmiel, S. David, and J. Barton, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 100, 12543 (2003). 10.1073/pnas.2035257100
2. K. Keren, R. S. Berman, E. Buchstab, U. Sivan, and E. Braun, Science SCIEAS 0036-8075 302, 1380 (2003). 10.1126/science.1091022
3. E. Braun, Y. Eichen, U. Sivan, and G. Ben-Yoseph, Nature (London) NATUAS 0028-0836 391, 775 (1998). 10.1038/35826
4. M. Mertig, R. Kirsch, W. Pompe, and H. Engelhardt, Eur. Phys. J. D EPJDF6 1434-6060 9, 45 (1999). 10.1007/s100530050397
5. P. Rothemund, Nature (London) NATUAS 0028-0836 440, 297 (2006). 10.1038/nature04586
6. W. Shih, J. Quispe, and G. Joyce, Nature (London) NATUAS 0028-0836 427, 618 (2004). 10.1038/nature02307
7. S. M. Douglas, H. Dietz, T. Liedl, B. Hoegberg, F. Graf, and W. M. Shih, Nature (London) NATUAS 0028-0836 459, 414 (2009). 10.1038/nature08016
8. A. J. Storm, J. V. Noort, S. D. Vries, and C. Dekker, Appl. Phys. Lett. APPLAB 0003-6951 79, 3881 (2001). 10.1063/1.1421086
9. D. Porath, A. Bezryadin, S. D. Vries, and C. Dekker, Nature (London) NATUAS 0028-0836 403, 635 (2000). 10.1038/35001029
10. K. -H. Yoo, D. H. Ha, J. -O. Lee, J. W. Park, J. Kim, J. J. Kim, H. -Y. Lee, T. Kawai, and H. Y. Choi, Phys. Rev. Lett. PRLTAO 0031-9007 87, 198102 (2001). 10.1103/PhysRevLett.87.198102
11. B. Xu, P. Zhang, X. Li, and N. Tao, Nano Lett. NALEFD 1530-6984 4, 1105 (2004). 10.1021/nl0494295
12. H. Cohen, C. Nogues, R. Naaman, and D. Porath, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 102, 11589 (2005). 10.1073/pnas.0505272102
13. N. Kang, A. Erbe, and E. Scheer, Appl. Phys. Lett. APPLAB 0003-6951 96, 023701 (2010). 10.1063/1.3291113
14. X. Xiao, B. Q. Xu, and N. J. Tao, Nano Lett. NALEFD 1530-6984 4, 267 (2004). 10.1021/nl035000m
15. Y. A. Berlin, I. V. Kurnikov, D. Beratan, M. A. Ratner, and A. L. Burin, Top. Curr. Chem. FCFOA2 0071-7894 237, 1 (2004).
16. F. C. Grozema, L. D. A. Siebbeles, Y. A. Berlin, and M. A. Ratner, ChemPhysChem CPCHFT 1439-4235 3, 536 (2002). 10.1002/1439-7641(20020617)3: 6<536::AID-CPHC536>3.0.CO;2-6
17. K. Senthilkumar, F. C. Grozema, C. F. Guerra, F. M. Bickelhaupt, F. D. Lewis, Y. A. Berlin, M. A. Ratner, and L. D. A. Siebbeles, J. Am. Chem. Soc. JACSAT 0002-7863 127, 14894 (2005). 10.1021/ja054257e
18. T. Cramer, S. Krapf, and T. Koslowski, J. Phys. Chem. C JPCCCK 1932-7447 111, 8105 (2007). 10.1021/jp071618z
19. R. Gutírrez, R. A. Caetano, B. P. Woiczikowski, T. Kuba, M. Elstner, and G. Cuniberti, Phys. Rev. Lett. PRLTAO 0031-9007 102, 208102 (2009). 10.1103/PhysRevLett.102.208102
20. P. B. Woiczikowski, T. Kuba, R. Gutírrez, R. A. Caetano, G. Cuniberti, and M. Elstner, J. Chem. Phys. JCPSA6 0021-9606 130, 215104 (2009). 10.1063/1.3146905
21. E. Hatcher, A. Balaeff, S. Keinan, R. Venkatramani, and D. N. Beratan, J. Am. Chem. Soc. JACSAT 0002-7863 130, 11752 (2008). 10.1021/ja802541e
22. D. N. Beratan, S. S. Skourtis, I. A. Balabin, A. Balaeff, S. Keinan, R. Venkatramani, and D. Xiao, Acc. Chem. Res. ACHRE4 0001-4842 42, 1669 (2009). 10.1021/ar900123t
23. A. Paul, S. Bezer, R. Venkatramani, L. Kocsis, E. Wierzbinski, A. Balaeff, S. Keinan, D. N. Beratan, C. Achim, and D. H. Waldeck, J. Am. Chem. Soc. JACSAT 0002-7863 131, 6498 (2009). 10.1021/ja9000163
24. A. Phan and J. Mergny, Nucleic Acids Res. NARHAD 0305-1048 30, 4618 (2002). 10.1093/nar/gkf597
25. J. Williamson, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 23, 703 (1994). 10.1146/annurev.bb.23.060194.003415
26. H. Arthanari and P. Bolton, Chem. Biol. CBOLE2 1074-5521 8, 221 (2001). 10.1016/S1074-5521(01)00007-2
27. J. Mergny, P. Mailliet, F. Lavelle, J. Riou, A. Laoui, and C. Helene, Anti-Cancer Drug Des. ACDDEA 0266-9536 14, 327 (1999).
28. N. Maizels, Nat. Struct. Mol. Biol. NSMBCU 1545-9993 13, 1055 (2006). 10.1038/nsmb1171
29. D. Sen and W. Gilbert, Nature (London) NATUAS 0028-0836 334, 364 (1988). 10.1038/334364a0
30. D. Sen and W. Gilbert, Nature (London) NATUAS 0028-0836 344, 410 (1990). 10.1038/344410a0
31. D. Sen and W. Gilbert, Methods Enzymol. MENZAU 0076-6879 211, 191 (1992). 10.1016/0076-6879(92)11012-8
32. K. Hoogsteen, Acta Crystallogr. ACSEBH 1600-5368 16, 907 (1963). 10.1107/S0365110X63002437
33. J. Davis, Angew. Chem., Int. Ed. ACIEF5 1433-7851 43, 668 (2004). 10.1002/anie.200300589
34. T. Simonsson, Biol. Chem. BICHF3 1431-6730 382, 621 (2001). 10.1515/BC.2001.073
35. H. Cohen, T. Sapir, N. Borovok, T. Molotsky, R. Di Felice, A. B. Kotlyar, and D. Porath, Nano Lett. NALEFD 1530-6984 7, 981 (2007). 10.1021/nl070013b
36. A. B. Kotlyar, N. Borovok, T. Molotsky, H. Cohen, E. Shapir, and D. Porath, Adv. Mater. ADVMEW 0935-9648 17, 1901 (2005). 10.1002/adma.200401997
37. N. Borovok, T. Molotsky, J. Ghabboun, D. Porath, and A. Kotlyar, Anal. Biochem. ANBCA2 0003-2697 374, 71 (2008). 10.1016/j.ab.2007.10.017
38. N. Špačková, I. Berger, and J. Šponer, J. Am. Chem. Soc. JACSAT 0002-7863 121, 5519 (1999). 10.1021/ja984449s
39. N. Špačková, I. Berger, and J. Šponer, J. Am. Chem. Soc. JACSAT 0002-7863 123, 3295 (2001). 10.1021/ja002656y
40. M. Cavallari, A. Calzolari, A. Garbesi, and R. Di Felice, J. Phys. Chem. B JPCBFK 1089-5647 110, 26337 (2006). 10.1021/jp064522y
41. R. D. Felice and A. Calzolari, Modern Methods for Theoretical Physical Chemistry of Biopolymers (Elsevier, New York, 2006), Chap., pp. 485-508.
42. A. Calzolari, R. Di Felice, E. Molinari, and A. Garbesi, J. Phys. Chem. B JPCBFK 1089-5647 108, 2509 (2004). 10.1021/jp036689m
43. A. Calzolari, R. Di Felice, E. Molinari, and A. Garbesi, Appl. Phys. Lett. APPLAB 0003-6951 80, 3331 (2002). 10.1063/1.1476700
44. A. Calzolari, R. Di Felice, and E. Molinari, Solid State Commun. SSCOA4 0038-1098 131, 557 (2004). 10.1016/j.ssc.2004.05.032
45. R. Di Felice, A. Calzolari, and H. Zhang, Nanotechnology NNOTER 0957-4484 15, 1256 (2004). 10.1088/0957-4484/15/9/025
46. R. Di Felice, A. Calzolari, A. Garbesi, S. Alexandre, and J. M. Soler, J. Phys. Chem. B JPCBFK 1089-5647 109, 22301 (2005). 10.1021/jp054274q
47. A. -M. Guo and S. -J. Xiong, Phys. Rev. B PLRBAQ 0556-2805 80, 035115 (2009). 10.1103/PhysRevB.80.035115
48. A. -M. Guo, Z. Yang, H. -J. Zhu, and S. -J. Xiong, J. Phys.: Condens. Matter JCOMEL 0953-8984 22, 065102 (2010). 10.1088/0953-8984/22/6/065102
49. I. A. Balabin, D. N. Beratan, and S. S. Skourtis, Phys. Rev. Lett. PRLTAO 0031-9007 101, 158102 (2008). 10.1103/PhysRevLett.101.158102
50. A. A. Voityuk, K. Siriwong, and N. Rösch, Angew. Chem., Int. Ed. ACIEF5 1433-7851 43, 624 (2004). 10.1002/anie.200352824
51. Y. A. Berlin, F. C. Grozema, L. D. A. Siebbeles, and M. A. Ratner, J. Phys. Chem. C JPCCCK 1932-7447 112, 10988 (2008). 10.1021/jp801646g
52. A. Sadowska-Aleksiejew, J. Rak, and A. A. Voityuk, Chem. Phys. Lett. CHPLBC 0009-2614 429, 546 (2006). 10.1016/j.cplett.2006.08.050
53. A. A. Voityuk, Chem. Phys. Lett. CHPLBC 0009-2614 439, 162 (2007). 10.1016/j.cplett.2007.03.066
54. F. C. Grozema, S. Tonzani, Y. A. Berlin, G. C. Schatz, L. D. A. Siebbeles, and M. A. Ratner, J. Am. Chem. Soc. JACSAT 0002-7863 130, 5157 (2008). 10.1021/ja078162j
55. R. Gutírrez, R. Caetano, P. B. Woiczikowski, T. Kuba, M. Elstner, and G. Cuniberti, New J. Phys. NJOPFM 1367-2630 12, 023022 (2010). 10.1088/1367-2630/12/2/023022
56. G. Laughlan, A. Murchie, D. Norman, M. Moore, P. Moody, D. Lilley, and B. Luisi, Science SCIEAS 0036-8075 265, 520 (1994). 10.1126/science.8036494
57. See http://structure.usc.edu/make-na/server.html for website for building nucleic acid structures.
58. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. JCPSA6 0021-9606 79, 926 (1983). 10.1063/1.445869
59. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. JCCHDD 0192-8651 26, 1701 (2005). 10.1002/jcc.20291
60. J. Wang, P. Cieplak, and P. A. Kollman, J. Comput. Chem. JCCHDD 0192-8651 21, 1049 (2000). 10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F
61. A. Ṕrez, I. Marchán, D. Svozil, J. Šponer, T. E. Cheatham III, C. A. Laughton, and M. Orozco, Biophys. J. BIOJAU 0006-3495 92, 3817 (2007). 10.1529/biophysj.106.097782
62. T. Kuba and M. Elstner, J. Phys. Chem. B JPCBFK 1089-5647 112, 8788 (2008). 10.1021/jp803661f
63. T. Kuba, P. B. Woiczikowski, G. Cuniberti, and M. Elstner, J. Phys. Chem. B JPCBFK 1089-5647 112, 7937 (2008). 10.1021/jp801486d
64. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B PLRBAQ 0556-2805 58, 7260 (1998). 10.1103/PhysRevB.58.7260
65. P. O. Löwdin, J. Chem. Phys. JCPSA6 0021-9606 18, 365 (1950). 10.1063/1.1747632
66. V. Mujica, M. Kemp, and M. A. Ratner, J. Chem. Phys. JCPSA6 0021-9606 101, 6849 (1994). 10.1063/1.468314
67. V. Mujica, M. Kemp, and M. A. Ratner, J. Chem. Phys. JCPSA6 0021-9606 101, 6856 (1994). 10.1063/1.468315
68. E. Fadrná, N. Špačková, R. Štefl, J. Koča, T. Cheatham III, and J. Šponer, Biophys. J. BIOJAU 0006-3495 87, 227 (2004). 10.1529/biophysj.103.034751
69. T. Ndlebe and G. Schuster, Org. Biomol. Chem. OBCRAK 1477-0520 4, 4015 (2006). 10.1039/b610159c
70. T. Steinbrecher, T. Koslowski, and D. A. Case, J. Phys. Chem. B JPCBFK 1089-5647 112, 16935 (2008). 10.1021/jp8076134
71. D. eha, W. Barford, and S. Harris, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10, 5436 (2008). 10.1039/b719619a
72. T. Kuba, U. Kleinekathöfer, and M. Elstner, J. Phys. Chem. B JPCBFK 1089-5647 113, 13107 (2009). 10.1021/jp9073587
73. S. P. Liu, S. H. Weisbrod, Z. Tang, A. Marx, E. Scheer, and A. Erbe, Angew. Chem., Int. Ed. ACIEF5 1433-7851 49, 3313 (2010).
74. 5-thiol-dG-GGC GGC GAC CTT CCC GCA GCT GGT ACG GAC.
75. Note, generally, the two last tetrads (base pairs) at the 5′ and 3′ end are not considered for CT calculations to avoid end effects, although the simulations were done with 12 tetrads and base pairs for G4 and dsDNA, respectively.
76. Only T2 interstrand couplings between adjacent strands are considered. See also the scheme in Fig..
77. Note, that this only applies when the whole structure is homogeneous. If other bases such as A or T enter the sequence, the behavior may be the opposite.
78. See supplementary material at http://dx.doi.org/10.1063/1.3460132 E-JCPSA6-133-023026 for further data analysis.