Theoretical Chemistry Accounts

, Volume 125, Issue 3–6, pp 185–191 | Cite as

Charge transfer between DNA and proteins in the nucleosomes

Regular Article


Recently X-ray diffraction provided the structure of nucleosomes. External disturbances can unwrap DNA from the histone–protein and their genetic information becomes readable. This is strongly connected with cancer initiation. Therefore, first we performed charge transfer (CT) calculations between polythymidine and a periodic model-protein chain with a lysine or arginine and three glycines. The CT calculations were repeated between the infinite chains using combined solid state physical and quantum chemical methods. We found that the CT between the unit cells of an infinite polythymidine and poly(lysine-triglycine) is 0.04 e and 0.03 e for poly(arginine-triglycine). We investigated the influence of the basis set quality on the calculated CT values using a molecular model built of a thymidine and lysine or arginine. We have calculated also the bands of polythymidine and the two protein model chains. We have found that the differences between the highest level of the valence band of single polythymidine chain and the lowest level of the conduction bands of the model protein chains (6-11 eV depending on the basis set) are too large to assume a direct CT between these two bands.


Nucleosome structure Charge transfer between PO4¯–Lys+ Charge transfer between PO4¯–Arg+ Band structure of poly[Lys–triglycine] Band structure of poly[Arg–triglycine] 



We should like to express our gratitude to Professor F. Beleznay for the very fruitful discussions.


  1. 1.
    Luger K, Mäder W, Richmond RK et al (1997) Nature 389:251. doi:10.1038/38444 CrossRefGoogle Scholar
  2. 2.
    Richmond TJ, Davey CA (2003) Nature 423:145. doi:10.1038/nature01595 CrossRefGoogle Scholar
  3. 3.
    Elgin CR, Workman JL (2000) Chromatin structure and gene expression. Oxford University Press, OxfordGoogle Scholar
  4. 4.
    Muthurajan UM, Bao Y, Forsberg LJ et al (2004) EMBO J 23:260. doi:10.1038/sj.emboj.7600046 CrossRefGoogle Scholar
  5. 5.
    Schalch T, Duda S, Sargent DF et al (2005) Nature 436:138. doi:10.1038/nature03686 CrossRefGoogle Scholar
  6. 6.
    Dorigo B, Schalch T, Kulangara A et al (2004) Science 306:1571. doi:10.1126/science.1103124 CrossRefGoogle Scholar
  7. 7.
    Weinstein B personal communicationGoogle Scholar
  8. 8.
  9. 9.
    Ladik J, Förner W (1994) The beginnings of cancer in the cell. Springer, HeidelbergGoogle Scholar
  10. 10.
    Ladik J, Bende A, Bogár F (2007) J Chem Phys 127:055102. doi:10.1063/1.2752806 CrossRefGoogle Scholar
  11. 11.
    Ladik J, Bende A, Bogár F (2008) J Chem Phys 128:105101. doi:10.1063/1.2832860 CrossRefGoogle Scholar
  12. 12.
    Blumen A, Merkel C (1977) Phys Status Solid 383:425. doi:10.1002/pssb.2220830208 CrossRefGoogle Scholar
  13. 13.
    Porath D, Berzyadin A, de Vriesand S, Dekker C (2000) Nature 403:635. doi:10.1038/35001029 CrossRefGoogle Scholar
  14. 14.
    Porath D, Cuniberti G, Di Felice R (2004) Top Curr Chem 237:183–227. doi:10.1007/b94477 Google Scholar
  15. 15.
    Guo X, Gorodetsky AA, Hone J, Barton JK, Nuckolls C (2008) Nat Nanotechnol 3:163. doi:10.1038/nnano.2008.4 CrossRefGoogle Scholar
  16. 16.
    Bende A, Bogár F, Ladik J (2007) Chem Phys Lett 437:117. doi:10.1016/j.cplett.2007.01.089 CrossRefGoogle Scholar
  17. 17.
    Bende A, Bogár F, Ladik J (2008) Chem Phys Lett 463:211. doi:10.1016/j.cplett.2008.08.036 CrossRefGoogle Scholar
  18. 18.
    Maseras F, Morokuma K (1995) J Comput Chem 16:1170. doi:10.1002/jcc.540160911 CrossRefGoogle Scholar
  19. 19.
    Svensson M, Humbel S, Froese RDJ et al (1996) J Phys Chem 100:19357. doi:10.1021/jp962071j CrossRefGoogle Scholar
  20. 20.
    Dapprich S, Komáromi I, Byun KS et al (1999) J Mol Struct Theochem 462:1. doi:10.1016/S0166-1280(98)00475-8 CrossRefGoogle Scholar
  21. 21.
    Schaefer A, Huber C, Ahlrichs R (1994) J Chem Phys 100:5829. doi:10.1063/1.467146 CrossRefGoogle Scholar
  22. 22.
    Mulliken RS (1955) J Chem Phys 23:1833. doi:10.1063/1.1740588 CrossRefGoogle Scholar
  23. 23.
    Foster JP, Weinhold F (1980) J Am Chem Soc 102:7211. doi:10.1021/ja00544a007 CrossRefGoogle Scholar
  24. 24.
    Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys 83:735. doi:10.1063/1.449486 CrossRefGoogle Scholar
  25. 25.
    Gianolo L, Clementi E (1980) Gazz Chim Ital 110:179Google Scholar
  26. 26.
    Olson WK, Bansal M, Burley MK et al (2001) J Mol Biol 313:229. doi:10.1006/jmbi.2001.4987 CrossRefGoogle Scholar
  27. 27.
    Jérome D, Shultz H (1982) Adv Phys 31:299. doi:10.1080/00018738200101398 CrossRefGoogle Scholar
  28. 28.
    Sing M, Schwingenschlögl U, Claessen R et al (2003) Phys Rev B 68:125111. doi:10.1103/PhysRevB.68.125111 CrossRefGoogle Scholar
  29. 29.
    Mintmire JW (1991) In: Labanowski J, Anzelm J (eds) Density functional methods in chemistry. Springer, New York, pp 125–138Google Scholar
  30. 30.
    Del Re G, Ladik J, Biczo G (1967) Phys Rev 155:997. doi:10.1103/PhysRev.155.997 CrossRefGoogle Scholar
  31. 31.
    Gaussian 03, Revision C.02, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels A. D, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian, Inc., Wallingford CTGoogle Scholar
  32. 32.
    Hehre WJ, Ditchfield R, Pople JA (1972) J Chem Phys 56:2257. doi:10.1063/1.1677527 CrossRefGoogle Scholar
  33. 33.
    Dill JD, Pople JA (1975) J Chem Phys 62:2921. doi:10.1063/1.430801 CrossRefGoogle Scholar
  34. 34.
    Francl MM, Petro WJ, Hehre WJ, Binkley JS, Gordon MS, DeFrees DJ, Pople JA (1982) J Chem Phys 77:3654. doi:10.1063/1.444267 CrossRefGoogle Scholar
  35. 35.
    Bogár F, Ladik J (2000) J Mol Struct Theochem 501–502:445. doi:10.1016/S0166-1280(99)00458-3 CrossRefGoogle Scholar
  36. 36.
    Shockley W (1950) Electron and holes in semiconductors. Van Nostrand, New YorkGoogle Scholar
  37. 37.
    Beleznay F, Bogár F, Ladik J (2003) J Chem Phys 119:5690. doi:10.1063/1.1595634 CrossRefGoogle Scholar
  38. 38.
    Bende A, Bogár F, Beleznay F, Ladik J (2008) Phys Rev E Stat Nonlinear Soft Matter Phys 78:061923. doi:10.1103/PhysRevE.78.061923 Google Scholar
  39. 39.
    Ladik J (1988) Chapter 4 in: quantum theory of polymers as solids. Plenum, New YorkGoogle Scholar
  40. 40.
    Sarmento RG, Albuquerque EL, Sesion PD Jr, Fulcob UL, de Oliveira BPW (2009) Phys Lett A 373:1486. doi:10.1016/j.physleta.2009.02.043 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Laboratory of the National Foundation for Cancer ResearchFriedrich-Alexander-University-Erlangen-NürnbergErlangenGermany
  2. 2.Department of Molecular and Biomolecular PhysicsNational Institute for Research and Development of Isotopic and Molecular TechnologiesCluj NapocaRomania
  3. 3.Supramolecular and Nanostructured Materials Research Group of the Hungarian Academy of SciencesUniversity of SzegedSzegedHungary

Personalised recommendations