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
Full Text
The Full Text of this article is available as a PDF (154.2 KB).
References
- 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]
- Grosberg, A. Yu. and Khokhlov, A.R.: Statistical Physics Of Macromolecules, AIP Press, NY (1994).
- de Gennes, P.-G.: Scaling Concepts In Polymer Physics, Cornell University Press, NY (1979).
- 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]
- 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.
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- Baigl D., Sferrazza M., Williams C.E.On the Pearl Size of Hydrophobic Polyelectrolytes Europhys. Lett. 200362110–116.2003EL.....62..110B [Google Scholar]
- 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]
- 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]
- 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]
- 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]
- 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]
- Yoshikawa, K. and Noguchi, H.: A Working Hypothesis on the Mechanism of Molecular Machinery, Chem. Phys. Lett. 303 (1999), 10–14.
- 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]
- 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]
- 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.
