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Journal of Biological Physics logoLink to Journal of Biological Physics
. 2005 Dec;31(3-4):243–248. doi: 10.1007/s10867-005-7285-4

Single Macromolecules: Hierarchic Thermodynamics, Irreversibility and Biological Function

Kenichi Yoshikawa 1,
PMCID: PMC3456320  PMID: 23345896

Abstract

Single homo-polymers show two different paths in the folding transition; a liquid-like spherical globule is generated for flexible polymers, whereas a rich variety of ordered structures are formed for semi-flexible polymers. This unique characteristic is discussed in relation to its biological significance.

Key words: giant DNA, coil-globule transition, DNA condensation, genetic switching, genetic regulation

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References

  1. Jacob F., Monod J. Genetic Regulatory Mechanisms in the Synthesis of Proteins. J. Mol. Biol. 1961;3:318–356. doi: 10.1016/S0022-2836(61)80072-7. [DOI] [PubMed] [Google Scholar]
  2. Grosberg, A. Yu. and Khokhlov, A.R.: Statistical Physics Of Macromolecules, AIP Press, NY (1994).
  3. de Gennes, P.-G.: Scaling Concepts In Polymer Physics, Cornell University Press, NY (1979).
  4. Yoshikawa K., Takahashi M., Vasilevskaya V.V., Khokhlov A.R.Large Discrete Transition in a Single DNA Molecule Appears Continuous in the Ensemble Phys. Rev. Lett. 1996763029–3031. 10.1103/PhysRevLett.76.30291996PhRvL..76.3029Y [DOI] [PubMed] [Google Scholar]
  5. Yoshikawa, K. and Yoshikawa, Y.: Compaction and condensation of DNA, in Mahato, R.I. et al. (eds.), Pharmaceutical Perspectives of Nucleic Acid-Based Therapeutics, 137–163; Taylor & Francis (2002) and references therein.
  6. Yoshikawa K. Field Hypothesis on the Self-Regulation of Gene Expression. J. Biol. Phys. 2002;28:701–712. doi: 10.1023/A:1021251125101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Noguchi H., Yoshikawa K.First-Order Phase Transition in a Stiff Polymer Chain Chem. Phys. Lett. 1997278184–188. 10.1016/S0009-2614(97)00974-31997CPL...278..184N [DOI] [Google Scholar]
  8. Noguchi H., Yoshikawa K.Morphological Variation in a Collapsed Single Homopolymer Chain J. Chem. Phys. 19981095070–5077. 10.1063/1.4771211998JChPh.109.5070N [DOI] [Google Scholar]
  9. Bloomfield V.A. DNA Condensation. Curr. Opin. Struct. Biol. 1996;6:334–341. doi: 10.1016/S0959-440X(96)80052-2. [DOI] [PubMed] [Google Scholar]
  10. Yamazaki Y., Teramoto Y., Yoshikawa K. Disappearance of the Negative Charge in Giant DNA with a Folding Transition. Biophys. J. 2001;80:2823–2832. doi: 10.1016/S0006-3495(01)76249-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Essafi W., Lafuma F., Williams C.E.Effect of Solvent Quality on the Behaviour of Highly Charged Polyelectrolytes J. de Phys. II 199551269–1275.1995JPhy2...5.1269E [Google Scholar]
  12. Dobrynin A., Rubinstein M., Obukhov S.P.Cascade Transition of Polyelectrolytes in Poor Solvents Macromolecules 1996292974–2979. 10.1021/ma95079581996Mamol..29.2974D [DOI] [Google Scholar]
  13. Lyulin A.V., Duenweg B., Borisov O., Darinskii A.A.Computer Simulation Studies of a Single Polyelectrolyte Chain in Poor Solvent Macromolecules 1999323264–3278. 10.1021/ma981818w1999Mamol..32.3264L [DOI] [Google Scholar]
  14. Micka U., Kremer K.Strongly Charged Flexible Polyelectrolytes in Poor Solvents – From stable Spheres to Necklace Chains Europhys. Lett. 200049189–195. 10.1209/epl/i2000-00133-62000EL.....49..189M [DOI] [Google Scholar]
  15. Kiriy A., Gorodyska G., Minko S., Jaeger W., Stepanek P., Stamm M. Cascade of Coil-Globule Conformational Transitions of Single Flexible Polyelectrolyte Molecules in Poor Solvent. J. Am. Chem. Soc. 2002;124:13454–13462. doi: 10.1021/ja0261168. [DOI] [PubMed] [Google Scholar]
  16. Baigl D., Sferrazza M., Williams C.E.On the Pearl Size of Hydrophobic Polyelectrolytes Europhys. Lett. 200362110–116.2003EL.....62..110B [Google Scholar]
  17. Yoshikawa K., Yoshikawa Y., Kanbe T. Highly Effective Compaction of Long Duplex DNA Induced by Polyethylene Glycol with Pendant Amino Group. J. Am. Chem. Soc. 1997;119:6473–6477. [Google Scholar]
  18. Takagi S., Tsumoto K., Yoshikawa K.Intra-Molecular Phase Segregation in a Single Polyelectrolyte Chain J. Chem. Phys. 20011146942–6849.2001JChPh.114.6942T [Google Scholar]
  19. Iwaki T., Yoshikawa K.Competition Between Interchain and Intrachain Phase Segregation Phys. Rev. E. 200368031902. 10.1103/PhysRevE.68.0319022003PhRvE..68c1902I [DOI] [PubMed] [Google Scholar]
  20. Zinchenko A.A., Sergeyev V.G., Murata S., Yoshikawa K. Controlling the Intrachain Segregation on a Single DNA Molecule. J. Am. Chem. Soc. 2003;125:4414–4415. doi: 10.1021/ja028804x. [DOI] [PubMed] [Google Scholar]
  21. Takagi S.T., Yoshikawa K. Stepwise Collapse of Polyelectrolyte Chains Entrapped in a Finite Space as Predicted by Theoretical Considerations. Langmuir. 1999;15:4143–4146. doi: 10.1021/la981158o. [DOI] [Google Scholar]
  22. Yoshikawa, K. and Noguchi, H.: A Working Hypothesis on the Mechanism of Molecular Machinery, Chem. Phys. Lett. 303 (1999), 10–14.
  23. Akitaya T., Tsumoto K., Yamada A., Makita N., Kubo K., Yoshikawa K. NTP Concentration Switches Transcriptional Activity by Changing the Large-Scale Structure of DNA. Biomacromolecules. 2003;4:1121–1125. doi: 10.1021/bm034017w. [DOI] [PubMed] [Google Scholar]
  24. Tsumoto K., Francois L., Yoshikawa K. Giant DNA Molecules Exhibit on/off Switching of Transcriptional Activity Through Conformational Transition. Biophys. Chem. 2003;106:23–29. doi: 10.1016/S0301-4622(03)00138-8. [DOI] [PubMed] [Google Scholar]
  25. Yamada, A., Kubo, K., Nakai, T., Tsumoto, K. and Yoshikawa, K.: All-or-none Switching of Transcriptional Activity on Single DNA Molecules Caused by a Discrete Conformational Transition. arXiv:q-bio.BM/0408015.

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