Single DNA Molecules: Compaction and Decompaction

DNA Interactions with Polymers and Surfactants

Volumn , Issue , 2007, Pages 59-88

  Zinchenko, Anatoly A ^a   Pyshkina, Olga A ^b   Lezov, Andrey V ^c   Sergeyev, Vladimir G ^b   Yoshikawa, Kenichi ^d,e  

^a NAGOYA UNIVERSITY   (Japan)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

^c ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^d KYOTO UNIVERSITY   (Japan)

^e JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Cationic liposome DNA condensation; DNA compaction, decompaction and multivalent cations; Single DNA molecules compaction and decompaction

Indexed keywords

EID: 84875011618     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470286364.ch3     Document Type: Chapter

References (95)

1. V. P. Osica, T. L. Pyatigorskaya, O. F. Polyvtsev, A. T. Dembo, M. O. Klija, V. N. Vasilchenko, B. I. Venkin, B. Ya. Sukharevsky. Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt. Nucl. Acids Res. 4 (1977): 1083-1096.
2. K. Hayakawa, J. P. Santerre, J. C. T. Kwak. The binding of cationic surfactants by DNA. Biophys. Chem. 17 (1983): 175-181.
3. M. Morimoto, P. A. Ferchmin, E. L. Bennett. Spectrophotometric analysis of RNA and DNA using cetyltrimethylammonium bromide. Anal. Biochem. 62 (1978): 436-448.
4. R. Ghirlando, E. J. Wachtel, T. Arad, A. Minsky. DNA packaging induced by micellar aggregates: A novel in vitro DNA condensation system. Biochemistry 31 (1992): 7110-7119.
5. S. M. Mel'nikov, V. G. Sergeyev, K. Yoshikawa. Discrete coil-globule transition of large DNA induced by cationic surfactant. J. Am. Chem. Soc. 117 (1995): 2401-2408.
6. S. M. Mel'nikov V. G. Sergeyev, K. Yoshikawa. Transition of double-stranded DNA chains between random coil and compact globule states induced by cooperative binding of cationic surfactant. J. Am. Chem. Soc. 117 (1995): 9951-9957.
7. V. Sergeyev, S. Mikhailenko, O. Pyshkina, I. Yaminsky, K. Yoshikawa. How does alcohol dissolve the complex of DNAwith a cationic surfactant. J. Am. Chem. Soc. 121 (1999): 1780-1785.
8. V. G. Sergeyev, O. A. Pyshkina, A.V. Lezov, A.B. Mel'nikov, E. I. Ryumtsev, A. B. Zezin, V. A. Kabanov.DNA complexed with oppositely charged amphiphile in low-polar organic solvents. Langmuir 15 (1999): 4434-4440.
9. A. S. Komolov, A. B. Mel'nikov, K. Schaumburg, E. I. Ryumtsev, A. V. Lezov. Sizes and conformation of the molecules of DNA-surfactant complexes in dilute solutions and on the atomic smooth substrates. Coll. J. 64 (2002): 155-159.
10. V. A. Bloomfield. DNA condensation by multivalent cations. Biopolymers 44 (1997): 269-282.
11. T. Blessing, J. S. Remy, J. P. Behr. Monomolecular collapse of plasmid DNA into stable virus-like particles. Proc. Natl. Acad. Sci. USA 95 (1998): 1427-1431.
12. M. Ouyang, J. S. Remy, F. C. Szoka. Controlled template-assisted assembly of plasmid DNA into nanometric particles with high DNA concentration. Bioconj. Chem. 11 (2000): 104-112.
13. E. Dauty, J. S. Remy, T. Blessing, J. P. Behr. Template oligomerization of DNA-bound cations produces calibrated nanometric particles. J. Am. Chem. Soc. 123 (2001): 9227-9234.
14. G. J. Benham. Elastic model of supercoiling. Proc. Natl. Acad. Sci. USA 74 (1977): 2397-2401.
15. Y. Shi, J. Hearst. The Kirchhoff elastic rod, the nonlinear Schrödinger equation, and DNA supercoiling. J. Chem. Phys. 101 (1994): 5186-5200.
16. S. M. Mel'nikov, K. Yoshikawa. First-order phase transition in large single duplex DNA induced by a non-ionic surfactant. Biochem. Biophys. Res. Comm. 230 (1997): 514-517.
17. Y. S. Mel'nikova, B. Lindman. pH-controlled DNA condensation in the presence of dodecyldimethylamine oxide. Langmuir 16 (2000): 5871-5878.
18. S. M. Mel'nikov, V. G. Sergeyev, K. Yoshikawa, H. Takahashi, I. Hatta. Cooperativity or phase transition? Unfolding transition of DNA cationic surfactant complex. J. Chem. Phys. 107 (1997): 6917-6924.
19. S. M. Mel'nikov, V. G. Sergeyev, K. Yoshikawa. Cooperation between salt induced globule-coil transition in single duplex DNA complexed with cationic surfactant and sphere-rod transition of surfactant micelles. Prog. Coll. Polym. Sci. 106 (1997): 209-214.
20. S. M. Mel'nikov, V. G. Sergeyev, Yu. S. Mel'nikova, K. Yoshikawa. Folding of long DNA chains in the presence of distearyldimethylammonium bromide and unfolding induced by neutral liposomes. J. Chem. Soc. Faraday Trans. 93 (1997): 283-288.
21. P. L. Felgner, T. R. Gadek, M. Holm, R. Roman, H. W. Chan, M. Wenz, J. P. Northrop, G. M. Ringold, M. Danielsen. Lipofection: A highly efficient, lipid-mediated DNAtransfection procedure. Proc. Natl. Acad. Sci. USA 84 (1987): 7413-7417.
22. N. Ballas, N. Zakai, I. Sela, A. Loyter. Liposomes bearing a quaternary ammonium detergent as an efficient vehicle for functional transfer of TMV-RNA into plant protoplasts. Biochim. Biophys. Acta 939 (1988): 8-18.
23. P. L. Felgner, M. Holm. Cationic liposome-mediated transfection. Focus 11 (1989): 21-25.
24. R.W. Malone, P. L. Felgner, I. L. Verma. Cationic liposome-mediated RNA transfection. Proc. Natl. Acad. Sci. USA 86 (1989): 6077-6081.
25. J. P. Behr. DNA strongly binds to micelles and vesicles containing lipopolyamines or lipointercalants. Tetrahedron Lett. 27 (1986): 5861-5864.
26. P. L. Felgner, G. M. Ringold. Cationic liposome-mediated transfection. Nature 337 (1989): 387-388.
27. W. M. Bertling, M. Gareis, A. Zimmer, J. Kreuter, E. Nurenberg, P. Harre. Use of liposomes, viral capsids, and nanoparticles as DNA carriers. Biotechnol. Appl. Biochem. 13 (1991): 390-405.
28. M. Maccarone, L. Dini, L. Marzio, A. Giulio, A. Rossi, G. Mossa, A. F. Agro. Interaction of DNA with cationic liposomes: Ability of transfecting lentil protoplasts. Biochem. Biophys. Res. Commun. 186 (1992): 1417-1422.
29. H. Gershon, R. Ghirlando, S. Guttman, A. Minsky. Mode of formation and structural features of DNA-cationic liposome complexes used for transfection. Biochemistry 32 (1993): 7143-7151.
30. B. Sternberg, F. L. Sorgi, L. Huang. New structures in complex formation between DNA and cationic liposomes visualized by freeze-fracture electron microscopy. FEBS Lett. 356 (1994): 361-366.
31. J. Gustafsson, A. Almgrem, G. Arvidson, M. Almgren. Complexes between cationic liposomes and DNA visualized by cryo-TEM. Biochim. Biophys. Acta 1235 (1995): 305-312.
32. Y. Yoshikawa, N. Emi, T. Kanbe, K. Yoshikawa, H. Saito. Folding and aggregation of DNA chains induced by complexation with lipospermine: Formation of a nucleosomelike structure and network assembly. FEBS Lett. 396 (1996): 71-76.
33. N. S. Templeton, D. D. Lasic, P. M. Frederik, H. H. Strey, D. D. Roberts, G. N. Pavlakis. Improved DNA:liposome complexes for increased systemic delivery and gene expression. Nature Biotechnology 15 (1997): 647-652.
34. J. O. Radler, I. Koltover, T. Salditt, C. R. Safinya. An inverted hexagonal phase of DNA-cationic liposome complexes related to DNA release. Science 275 (1997): 810-814.
35. D. D. Lasic, H. Strey, M. C. A. Stuart, R. Podgornik, P. M. Frederik. DNA - cationic liposome complexes: Structure and structure-activity relationships. J. Am. Chem. Soc. 119 (1997): 832-833.
36. B. Pitard, O. Aguerre, M. Airiau, A. M. Lachages, T. Boukhnikachvili, G. Byk, C. Dubertret, C. Herviou, D. Scherman, J.-F. Mayaux, J. Crouzet. Virus-sized selfassembling lamellar complexes between plasmid DNA and cationic micelles promote gene transfer. Proc. Natl. Acad. Sci. USA 94 (1997): 14412-14417.
37. J. O. Radler, I. Koltover, A. Jamieson, T. Salditt, C. Safinya. Structure and interfacial aspects of self-assembled cationic lipid-DNA gene carrier complexes. Langmuir 14 (1998): 4272-4283.
38. Y. S. Mel'nikova, S. M. Mel'nikov, J. E. Lofroth. Single-molecule visualization of interaction between DNA and oppositely charged mixed liposomes. J. Phys. Chem. B. 102 (1998): 9367-9369.
39. Y. S. Mel'nikova, S. M. Mel'nikov, J. E. Lofroth. Physico-chemical aspects of the interaction between DNA and oppositely charged mixed liposomes. Biophys. Chem. 81 (1999): 125-141.
40. S. Huebner, B. J. Battersby, R. Grimm, G. Cevc. Lipid-DNA complex formation: Reorganization and rupture of lipid vesicles in the presence of DNA as observed by cryoelectron microscopy. Biophys. J., 76 (1999): 3158-3166.
41. M. Schmutz, D. Durand, A. Debin, Y. Palvadeau, A. Etienne, A. R. Thierry. DNA packing in stable lipid complexes designed for gene transfer imitates DNA compaction in bacteriophage. Proc. Natl. Acad. Sci. USA 96 (1999): 12293-12298.
42. J. Smisterova, A. Wagenaar, M. C. A. Stuart, E. Polushkin, G. ten Brinke, R. Hulst, J. Engberts, D. Hoekstraa. Molecular shape of the cationic lipid controls the structure of cationic lipid/dioleylphosphatidylethanolamine-DNA complexes and the efficiency of gene delivery. J. Biol. Chem. 276 (2001): 47615-47622.
43. M. Takahashi, K. Yoshikawa, V. V. Vasilevskaya, A. R. Khokhlov. Discrete coil-globule transition of single duplex DNA induced by polyamines. J. Phys. Chem. B. 101 (1997): 9396-9401.
44. K. Khokhlov, M. Takahashi, V. V. Vasilevskaya, A. R. Khokhlov. Large discrete transition in a single DNA molecule appears continuous in the ensemble. Phys. Rev. Lett. 76 (1996): 3029-3031.
45. T. Akitaya, A. Seno, T. Nakai, N. Hazemoto, S. Murata, K. Yoshikawa.Weak interaction induces an ON/OFF Switch, whereas strong interaction causes gradual change: Folding transition of a long duplex DNA chain by poly-l-lysine. Biomacromolecules 8 (2007): 273-278.
46. Y. Yoshikawa, K. Yoshikawa. Diaminoalkanes with an odd number of carbon atoms induce compaction of a single double-stranded DNA chain. FEBS Lett. 361 (1995): 277-281.
47. A. A. Zinchenko, V. G. Sergeyev, K. Yamabe, S. Murata, K. Yoshikawa. DNA compaction by divalent cations: Structural specificity revealed by the potentiality of designed quaternary diammonium salts. ChemBioChem 5 (2004): 360-368.
48. A. A. Zinchenko, V. G. Sergeyev, V. A. Kabanov, S. Murata, K. Yoshikawa. Stereoisomeric discrimination in DNA compaction. Angew. Chem. Int. Ed. 43 (2004): 2378-2381.
49. K. Yoshikawa, Y. Matsuzawa. Nucleation and growth in single DNA molecules. J. Am. Chem. Soc. 118 (1996): 929-930.
50. H. Noguchi, S. Saito, S. Kidoaki, K.Yoshikawa. Self-organized nanostructure constructed with a single polymer chain. Chem. Phys. Lett. 261 (1996): 527-533.
51. M. Suwalsky, W. Traub, U. Shmueli, J. Subirana. An X-ray study of the interaction of DNA with spermine. J. Mol. Biol. 42 (1969): 363-373.
52. A. A. Zinchenko, N. Chen, S. Murata, K. Yoshikawa. How does DNA compaction favor chiral selectivity with cationic species? Higher selectivity with lower cationic charge. ChemBioChem 6 (2005): 1419-1422.
53. A. A. Zinchenko, V. G. Sergeyev, S. Murata, K. Yoshikawa. Controlling the intrachain segregation on a single DNA molecule. J. Am. Chem. Soc. 125 (2003): 4414-4415.
54. N. Chen, A. A. Zinchenko, S. Murata, K. Yoshikawa. Specific formation of beads-on-achain structures on giant DNA using a designed polyamine derivative. J. Am. Chem. Soc. 127 (2005): 10910-10916.
55. T. Saito, T. Iwaki, K. Yoshikawa. Why is the compact state of DNA preferred at higher temperature? Folding transition of a single DNA chain in the presence of a multivalent cation. Europhys. Lett. 71 (2005): 304-310.
56. N. Makita, K. Yoshikawa. Proton concentration (pH) switches the higher-order structure of DNA in the presence of spermine. Biophys. Chem. 99 (2002): 43-53.
57. T. Akitaya, K. Tsumoto, A. Yamada, N. Makita, K. Kubo, K. Yoshikawa. NTP concentration switches transcriptional activity by changing the large-scale structure of DNA. Biomacromolecules 4 (2003): 1121-1125.
58. Y. Murayama, Y. Sakamaki. M. Sano. Elastic response of singleDNAmolecules exhibits a reentrant collapsing transition. Phys. Rev. Lett. 90 (2003): 018102.
59. H.Wada, Y. Murayama, M. Sano. Model of elastic response of single DNA molecules in collapsing transition. Phys. Rev. E. 66 (2002): 061912.
60. +. Chem. Phys. Lett. 426 (2006): 405-409.
61. H. Mayama, S. M. Nomura, H. Oana, K. Yoshikawa. Self-oscillating polymer chain. Chem. Phys. Lett. 330 (2000): 361.
62. F. Luckel, K. Kubo, K. Tsumoto, K. Yoshikawa. Enhancement and inhibition of DNA transcriptional activity by spermine: A marked difference between linear and circular templates. FEBS Lett. 579 (2005): 5119-5122.
63. A.V. Kabanov, V.A. Kabanov. DNA complexes with polycations for the delivery of genetic material into cells. Bioconj. Chem. 6 (1995): 7-20, (and references quoted therein).
64. A. V. Kabanov, V. A. Kabanov. Interpolyelectrolyte complexes of nucleic acids as means for targeted delivery of genetic material to the cell. Vysokomolek. Soed., A, B 36 (1994): 198-211.
65. K. Minagawa. Y. Matsuzawa, K. Yoshikawa, M. Matsumoto, M. Doi. Direct observation of the biophasic conformational change ofDNA induced by cationic polymers. FEBS Lett. 295 (1991): 67-69.
66. W. Zauner, M. Ogris, E. Wagner. Polylysine-based transfection systems utilizing receptormediated delivery. Adv. Drug Deliv. Rev. 30 (1998): 97-113.
67. W. T. Godbey, K. K. Wu, A. G. Mikos. Tracking the intracellular path of poly. (ethylnimine)/DNA complexes for gene delivery. Proc. Natl. Acad. Sci. USA 96 (1999): 5177-5181.
68. M. X. Tang, C. T. Redemann, F. C. J. Szoka. In vitro gene delivery by degraded polyamidoamine dendrimers. Bioconj. Chem. 7 (1996): 703-714, (and references therein).
69. Y. B. Li, S. M. Kim, Y. Lee, W. K. Lee, T. G. Yang, M. J. Lee, H. Suh, J. S. Park. Cationic hyperbranched poly(amino ester): A novel class of DNA condensing molecule with cationic surface, biodegradable three-dimensional structure, and teriary amine groups in the interior. J. Am. Chem. Soc. 123 (2001): 2460-2461.
70. A. J. Rackstraw, A. L. Martin, S. Stolnik, C. J. Roberts, M. C. Garnett, M. C. Davies, S. J. B. Tendler. Microscopic investigations into PEG-cationic polymer-induced DNA condensation. Langmuir 17 (2001): 3185-3193.
71. H. Petersen, P. M. Fechner, A. L. Martin, K. Kunath, S. Stolnik, C. J. Roberts, D. Fischer, M. C. Davies, T. Kissel. Polyethylenimine-graft-poly(ethylene glycol) copolymers: Influence of copolymer block structure on DNA complexation and biological activities as gene delivery system. Bioconj. Chem. 13 (2002): 845-854.
72. V. G. Sergeyev, O. A. Novoskoltseva, O. A. Pyshkina, A. A. Zinchenko, V. B. Rogacheva, A. B. Zezin, K. Yoshikawa, V. A. Kabanov. Secondary structure of DNA is recognized by slightly cross-linked cationic hydrogel. J. Am. Chem. Soc. 124 (2002): 11324-11333.
73. O. Philippova, T. Akitaya, I. Mullagaliev, A. Khokhlov, K. Yoshikawa. Salt-controlled intrachain/interchain segregation in DNA complexed with polycation of natural origin. Macromolecules 38 (2005): 9359-9365.
74. H. G. Hansma, R. Golan, W. Hsieh, C. P. Lollo, P. Mullen-Ley, D. Kwoh. DNA condensation for gene therapy as monitored by atomic force microscopy. Nucl. Acids Res. 26 (1998): 2481-2487.
75. J. C. Perales, T. Ferkol, H. Beegen, O. D. Ratnoff, R. W. Hanson. Gene transfer in vivo: Sustained expression and regulation of genes introduced into the liver by receptor-targeted uptake. Proc. Natl. Acad. Sci. USA 91 (1994): 4086-4090.
76. M. Wittmar, J. S. Ellis, F. Morell, F. Unger, J. C. Schumacher, C. J. Roberts, S. J. B. Tendler, M. C. Davies, T. Kissel. Biophysical and transfection studies of an aminemodified poly(vinyl alcohol) for gene delivery. Bioconj. Chem. 16 (2005): 1390-1398.
77. S. Kidoaki, K. Yoshikawa. Controlling the folding transition of giant DNA: Cooperative effect between neutral polymer and basic polypeptide, Nucl. Acids Res. Symp. Ser. 35 (1996): 115-116.
78. Y.Yamasaki, S. Katayose, K. Kataoka, K.Yoshikawa. PEG-PLL block copolymers induce reversible large discrete coil-globule transition in a single DNA molecule through cooperative complex formation. Macromolecules 36 (2003): 6276-6279.
79. K. Yoshikawa, Y. Yoshikawa, T. Kanbe. Highly effective compaction of long duplexDNA induced by polyethylene glycol with pendant amino groups. J. Am. Chem. Soc. 119 (1997): 6473-6477.
80. V. A. Kabanov, V. G. Sergeyev, O. A. Pyshkina, A. A. Zinchenko, A. B. Zezin, J. G. H. Joosten, J. Brackman, K.Yoshikawa. Interpolyelectrolyte complexes formed by DNA and astramol TM poly(propyleneimine) dendrimers. Macromolecules 33 (2000): 9587-9593.
81. A. U. Bielinska, J. F. Kukowska-Latallo, J. R. Baker. Interpolyelectrolyte complexes formed by DNA and stramol™ poly(propyleneimine) dendrimers, Biochim. Biophys. Acta 1353 (1997). 180-190.
82. M. F. Ottaviani, F. Furini, A. Casini, N. J. Turro, S. Jockusch, D. A. Tomalia, L. Messori. Formation of supramolecular structures between DNA and starburst dendrimers studied by EPR, CD, UV, and melting profiles. Macromolecules 33 (2000): 7842-7851.
83. Yu. S. Mel'nikova, N. Kumazawa, K. Yoshikawa. Positively charged surface induces discontinuous transition for the high order structure in duplex DNA. Biochem. Biophys. Res. Commun. 214 (1995): 1040-1044.
84. M. J. Allen, E. M. Bradburyl, R. Balhorn. AFM analysis of DNA-protamine complexes bound to mica. Nucl. Acids Res. 25 (1997): 2221-2226.
85. Y. Fang, J. H. Hoh. Surface-directed DNA condensation in the absence of soluble multivalent cations. Nucl. Acids Res. 26 (1998): 588-593.
86. Y. Fang, J. H. Hoh. Early intermediates in spermidine induced DNA condensation. J. Am. Chem. Soc. 120 (1998): 8903-8909.
87. A. A. Zinchenko, K. Yoshikawa, D. Baigl. Compaction of Single-chain DNA by histoneinspired nanoparticles. Phys. Rev. Lett. 95 (2005): 228101, 1-4.
88. C. B. Post, B. H. Zimm. Internal condensation of a single DNA molecule. Biopolymers 18 (1979): 1487-1501.
89. V. V. Vasilevskaya, A. R. Khokhlov, Y. Matsuzawa, K. Yoshikawa. Collapse of single DNA molecule in poly(ethylene glycol) solutions. J. Chem. Phys. 102 (1995): 6595-6602.
90. A.Y. Grosberg, I.Y. Erukhimovitch, E. I. Shakhnovitch. On the theory of ψ-condensation. Biopolymers 21 (1982): 2413-2432.
91. Y. M. Evdokimov, T. L. Pyatigorskaya, O. F. Polyvtsev, N. M. Akimenko, V. A. Kadykov, D. Y. Tsvanki, Y. M. Marshavsky.A comparative X-ray diffraction and circular dichroism study of DNA compact particles formed in water-salt solutions, containing poly(ethylene glycol). Nucl. Acids Res. 3 (1976): 2353-2366.
92. H. Mayama, T. Iwataki, K.Yoshikawa. Thermodynamics in the folding phase-transition of single T4DNAmolecules in poly(ethylene glycol) solution. Chem. Phys. Lett. 318 (2000): 113-117.
93. + in DNA compaction in a crowded environment. Biophys. J. 88 (2005): 4118-4123.
94. S. G. Starodoubtsev, K.Yoshikawa. Intrachain segregation in single giantDNAmolecules induced by poly(2-vinylpyrrolidone). J. Phys. Chem. 100 (1996): 19702-19705.
95. S. G. Starodoubtsev, K. Yoshikawa. Conformational transition of large duplex T4 DNA embedded in poly(acrilamide) gel. Langmuir 14 (1998): 214-217.