摘要
DNA的凝聚是分子生物学的核心之一，而单分子操纵技术在分子生物学的发展中提供重要的手段，本文主要是采用单分子磁镊技术（MT）与原子力显微镜技术(AFM)，对DNA的凝聚过程的溶剂效应进行研究。主要研究内容包括：
1.利用原子力显微镜技术（AFM），系统地研究了由乙醇与多价离子（hexammine cobalt(III) [(Co(NH_3)_6~(3+)]）协同作用导致的lambda-DNA凝聚现象。单独测得三价Co(NH_3)_6~(3+)的临界凝聚浓度大约是10μM，乙醇的临界凝聚浓度大约是15% (v/v)。若三价离子Co(NH_3)_6~(3+)的浓度大于400μM时,可以观察到DNA的解凝聚现象。在DNA溶液中同时加入乙醇（12%）与( )3Co(NH_3)_6~(3+)（8μM），当其浓度各低于临界值时，也可观察到凝聚现象，说明乙醇与( )3Co(NH_3)_6~(3+)对DNA的凝聚有协同作用。而且在协同作用下，可以观察到典型的圆环结构（toroids）。其中解凝聚现象可能运用电荷逆转与离子释放机制来解释。
2.通过AFM与MT的技术，研究酒精导致的DNA凝聚。酒精一般被用作提纯DNA的沉淀剂，我们通过MT与AFM技术研究酒精导致的单分子DNA凝聚。首次证明酒精引起的DNA塌缩的中间亚稳球拍态的存在。对于凝聚力的测量，甚至在50%酒精浓度都不到0.2pN，这个值远远小于多价离子与表面活性剂。还证明了酒精导致的DNA形态的B-A转变，发现DNA的A形态的弹性模量比B形态的要大。与多价离子相比，酒精导致DNA凝聚的拉伸实验表现了不同的特性，其拉伸曲线的步长范围比较大，从几十纳米到几微米的范围都有，与多价离子相对统一的200nm的步矩形成对比。同时我们发现，随着酒精浓度的增加，DNA的持久长度成单调减小的趋势。在弱溶剂里，由于DNA片段之间的弱相互作用引起的DNA的凝聚形态，多是一些不规则球拍组成的松散花状的结构。通过AFM成像进一步证实这些现象与分析结果。得出结论，在酒精导致的DNA凝聚中溶剂排斥效应比电荷中和效应更占据主导地位。
3.多个识别位点的内切酶与DNA相互作用的方式有很多，其中通过结合成环状的方式在许多基础生物化学的过程中起着很重要的作用。限制性内切酶BspMI必须绑定DNA上面两个有效的识别位点才具有有效的活性,这是研究这种成环相互作用的有用模型。在实验中Ca~(2+)代替正常的内切酶辅助因子Mg~(2+),限制了内切酶的切割作用,导致内切酶与DNA的结合,而且这种内切酶一般是通过四聚体的形式与DNA的一个位点结合或者通过一个四聚体结合两个位点形成环状结构。我们通过AFM研究不同浓度内切酶作用下的DNA-内切酶成像。从云母片上面的成像可以清楚看见特异性结合的内切酶在DNA上面的位置,并且通过实验观察得出非特异性结合的内切酶数量占整个BspMI-DNA复合物的比例不到8%。当酶的浓度增加,在云母表面的内切酶与DNA的结合率与成环率就会增加,但当高到一定程度时,结合位点会达到饱和。在实验过程中我们还统计了BspMI-DNA复合物的平均成环大小。
DNA condensation is the core of molecular biology.Single molecule manipulation is the main method of the molecule biology. In this paper, we study DNA condensation by sinle molecule magnetic tweezer(sMT) and atomic force microscopy(AFM). The main contents are as fellows:
1. We performed systematic studies of lambda-DNA condensation on mica surfaces induced by alcohol and hexammine cobalt (III) [Co(NH_3)_6~(3+)] using AFM. The critical condensation concentration for Co(NH_3)_6~(3+) was found to be about 10μM; the DNA molecules extended freely on mica when the concentration was below the critical value. The morphology of condensed DNA became more compact with increasing concentration. At about 500μM Co(NH_3)_6~(3+) concentration, no condensation patterns could be observed due to charge inversion of the compact structures resulting in failure of adhesion to the positively charged surfaces. The critical concentration for alcohol was about 15% (v/v). At this concentration, a few intramolecular loops could be observed in the AFM images. With increasing ethanol concentration the condensation pattern became more complicated ranging from flower-like to pancake-like. When the solution contained both alcohol and hexammine cobalt (III), DNA condensation patterns could be observed even when the concentrations of the two condensation agents were lower than their critical values. We observed this phenomenon by adding mixtures of 10% alcohol and 8μM hexammine cobalt (III) to DNA solutions. The condensation patterns were more compact than those of the condensation agents separately. Typical toroids were found at an appropriate alcohol and hexammine cobalt (III) concentration. The collaborative condensation phenomenon was analyzed by electrostatic interaction and charge neutralization.
2. As a widely used precipitation agent for DNA extraction, ethanol is used to induce single molecule DNA condensation. This process is studied with force-measuring MT and AFM. Our experiments provide direct evidence of the metastable intermediate racquet states in DNA collapse induced by ethanol. The measured condensing force is less than 0.2pN even at 50% ethanol concentration, which is much less than those induced by multivalent cations and cationic surfactants. We confirmed the A-B transition of DNA in ethanol and found that the tensile modulus of A-form DNA is larger than that of B-form. Single molecule pulling experiment shows very different features of neutral ethanol from those of multivalent cations. The pulling curve contains a wide range of step sizes, ranging from tens of nanometers to a few micrometers, contrasting with the relatively uniform interval (about 200 nm) in multivalent cations. Meanwhile, the persistence length of DNA decreases monotonically with the increasing ethanol concentration. The condensing morphologies by the weak attraction of DNA segments in the less polar solvent are loose and flowerlike structures composed of many annealed irregular racquets. The analysis of pulling experiments is supported by AFM direct imaging. We concluded that the dominant factor in DNA condensation induced by ethanol is solvent exclusion rather than charge neutralization correlation effect.
3. Proteins interacting at multiple sites on DNA via looping play an important role on many fundamental biochemical processes. Restriction endonuclease BspMI that must bind at two recognition sites for efficient activity is a useful model system for studying such interactions. In our experiments, Ca~(2+) was substituted for the normal enzyme cofactor Mg~(2+). Under these conditions it was found that specific binding occurs but cleavage does not. Enzyme in tetramer way interact DNA in the manner of binding one site or forming loops on two sites. AFM images of DNA molecules adsorbed on mica in our experiments for different BspMI concentrations. The present of the enzyme at the specific position can be easily observed. It is worth noting that nonspecific binding to DNA represent less than 8% of the total BspMI-DNA complexes. When the enzyme concentration is increased, the high binding rate and the rate of forming loops were occurred on mica surface. The statistics on loop sizes about BspMI-DNA complexes were reported in this study.
引文
1. Strick, T.; Dessinges, M.; Charvin, G.; Dekker, N.; Allemand, J.; Bensimon, D.; Croquette, V., Stretching of macromolecules and proteins[J]. Reports on Progress in Physics 2003, 66, 1-45.
2. Florin, E.; Moy, V.; Gaub, H., Adhesion forces between individual ligand-receptor pairs[J]. Science 1994, 264 (5157), 415.
3. Simmons, R.; Finer, J.; Chu, S.; Spudich, J., Quantitative measurements of force and displacement using an optical trap[J]. Biophysical journal 1996, 70 (4), 1813-1822.
4. Amblard, F.; Yurke, B.; Pargellis, A.; Leibler, S., A magnetic manipulator for studying local rheology and micromechanical properties of biological systems[J]. Review of Scientific Instruments 1996, 67, 818.
5. Orte, A.; Birkett, N.; Clarke, R.; Devlin, G.; Dobson, C.; Klenerman, D., Direct characterization of amyloidogenic oligomers by single-molecule fluorescence[J]. Proceedings of the National Academy of Sciences 2008, 105 (38), 14424.
6. Smith, S.; Finzi, L.; Bustamante, C., Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads[J]. Science 1992, 258 (5085), 1122.
7. Masuda, H.; Fukuda, K., Ordered metal nanohole arrays made by a two-step replication of honeycomb structures of anodic alumina[J]. Science 1995, 268 (5216), 1466.
8.孟宪敏;赵荣瑞, DNA解链分析法的原理及应用[J].山西医科大学学报1998, 29 (003), 199-200.
9. Guo, P.; Peterson, C.; Anderson, D., Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29[J]. Journal of molecular biology 1987, 197 (2), 229.
10. Morita, M.; Tasaka, M.; Fujisawa, H., DNA packaging ATPase of bacteriophage T3[J]. Virology 1993, 193 (2), 748-752.
11. Gosule, L. C.; Schellman, J. A., Compact form of DNA induced by spermidine[J]. Nature 1976,259,333.
12. Baumann, C.; Smith, S.; Bloomfield, V.; Bustamante, C., Ionic effects on the elasticity of single DNA molecules[J]. Proceedings of the National Academy of Sciences 1997, 94 (12), 6185.
13. Bloomfield, V., DNA condensation[J]. Current Opinion in Structural Biology 1996, 6 (3), 334-341.
14. Ou, Z.; Muthukumar, M., Langevin dynamics of semiflexible polyelectrolytes: Rod-toroid–globule-coil structures and counterion distribution[J]. The Journal of chemical physics 2005, 123, 074905.
15. Schnurr, B.; MacKintosh, F.; Williams, D., Dynamical intermediates in the collapse of semiflexible polymers in poor solvents[J]. EPL (Europhysics Letters) 2000, 51, 279-285.
16. Vilfan, N. V. H. a. I. D., TOROIDAL DNA CONDENSATES: Unraveling the Fine Structure and the Role of Nucleation in Determining Size[J]. Annual Review of Biophysics and Biomolecular Structure 2005, 34, 295-318.
17. Arscott, P.; Ma, C.; Wenner, J.; Bloomfield, V., DNA condensation by cobalt hexaammine (III) in alcohol-water mixtures: dielectric constant and other solvent effects[J]. Peptide Science 1995,36 (3), 345-364.
18. Kundu, T.; Rao, M., DNA condensation by the rat spermatidal protein TP2 shows GC-rich sequence preference and is zinc dependent[J]. Biochemistry 1995, 34 (15), 5143-5150.
19. Lerman, L., A transition to a compact form of DNA in polymer solutions[J]. Proceedings of the National Academy of Sciences of the United States of America 1971, 68 (8), 1886-1890.
20. Louie, D.; Serwer, P., Quantification of the effect of excluded volume on double-stranded DNA[J]. Journal of molecular biology 1994, 242 (4), 547.
21. Murphy, L.; Zimmerman, S., Macromolecular crowding effects on the interaction of DNA with Escherichia coli DNA-binding proteins: a model for bacterial nucleoid stabilization[J]. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression 1994, 1219 (2), 277-284.
22. Murphy, L.; Zimmerman, S., Condensation and cohesion ofλDNA in cell extracts and other media: Implications for the structure and function of DNA in prokaryotes[J]. Biophysical chemistry 1995, 57 (1), 71-92.
23. Vasilevskaya, V.; Khokhlov, A.; Matsuzawa, Y.; Yoshikawa, K., Collapse of single DNA molecule in poly (ethylene glycol) solutions[J]. The Journal of chemical physics 1995, 102, 6595.
24. Zimmerman, S.; Minton, A., Macromolecular crowding: biochemical, biophysical, and physiological consequences[J]. Annual Review of Biophysics and Biomolecular Structure 1993,22 (1), 27-65.
25. Farhood, H.; Gao, X.; Son, K.; Yang, Y.; Lazo, J.; Huang, L.; Barsoum, J.; Bottega, R.; Epand, R., Cationic liposomes for direct gene transfer in therapy of cancer and other diseases[J]. Annals of the New York Academy of Sciences 1994, 716, 23.
26. Felgner, P.; Gadek, T.; Holm, M.; Roman, R.; Chan, H.; Wenz, M.; Northrop, J.; Ringold, G.; Danielsen, M., Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure[J]. Proceedings of the National Academy of Sciences 1987, 84 (21), 7413.
27. Hou, X.; Zhang, X.; Wei, K.; Ji, C.; Dou, S.; Wang, W.; Li, M.; Wang, P., Cisplatin induces loop structures and condensation of single DNA molecules[J]. Nucleic Acids Research 2009, 37 (5), 1400.
28. Widom, J.; Baldwin, R. L., Monomolecular condensation ofλ‐DNA induced by cobalt hexammine[J]. Biopolymers 1983, 22 (6), 1595-1620.
29. Gosule, L. C.; Schellman, J. A., DNA condensation with polyamines. Spectroscopic studies[J]. Journal of molecular biology 1978, 121 (3), 311-326.
30. Laemmli, U., Characterization of DNA condensates induced by poly (ethylene oxide) and polylysine[J]. Proceedings of the National Academy of Sciences of the United States of America 1975, 72 (11), 4288.
31. Hsiang, M. W.; Cole, R. D., Structure of histone H1-DNA complex: Effect of histone H1 on DNA condensation[J]. Proceedings of the National Academy of Sciences of the United States of America 1977, 74 (11), 4852.
32. Garcia‐Ramírez, M.; Subirana, J. A., Condensation of DNA by basic protiens does not depend on protien composition[J]. Biopolymers 1994, 34 (2), 285-292.
33. Ma, C.; Bloomfield, V. A., Condensation of supercoiled DNA induced by MnCl2[J]. Biophysical journal 1994, 67 (4), 1678-1681.
34. Arscott, P. G.; Ma, C.; Wenner, J. R.; Bloomfield, V. A., DNA condensation by cobalt hexaammine (III) in alcohol–water mixtures: dielectric constant and other solvent effects[J]. Biopolymers 1995, 36 (3), 345-364.
35. Eickbush, T. H.; Moudrianakis, E. N., The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids[J]. Cell 1978, 13 (2), 295-306.
36. Bloomfield, V. A., DNA condensation[J]. Current Opinion in Structural Biology 1996, 6 (3),334-341.
37. Lang, D.; Taylor, T.; Dobyan, D.; Gray, D., Dehydrated circular DNA: electron microscopy of ethanol-condensed molecules[J]. Journal of molecular biology 1976, 106 (1), 97-107.
38. Arscott, P. G.; Li, A. Z.; Bloomfield, V. A., Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles[J]. Biopolymers 1990, 30 (5‐6), 619-630.
39. Fu, W.; Wang, X.; Zhang, X.; Ran, S.; Yan, J.; Li, M., Compaction dynamics of single DNA molecules under tension[J]. J. Am. Chem. Soc 2006, 128, 15040-15041.
40. Besteman, K.; Hage, S.; Dekker, N.; Lemay, S., Role of tension and twist in single-molecule DNA condensation[J]. Physical review letters 2007, 98 (5), 58103.
41. Ali, B.; Amit, R.; Braslavsky, I.; Oppenheim, A.; Gileadi, O.; Stavans, J., Compaction of single DNA molecules induced by binding of integration host factor (IHF)[J]. Proceedings of the National Academy of Sciences of the United States of America 2001, 98 (19), 10658.
42. Amit, R.; Oppenheim, A.; Stavans, J., Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor[J]. Biophysical journal 2003, 84 (4), 2467-2473.
43. van Noort, J.; Verbrugge, S.; Goosen, N.; Dekker, C.; Dame, R., Dual architectural roles of HU: formation of flexible hinges and rigid filaments[J]. Proceedings of the National Academy of Sciences of the United States of America 2004, 101 (18), 6969.
44. Fang, Y.; Spisz, T.; Hoh, J., Ethanol-induced structural transitions of DNA on mica[J]. Nucleic Acids Research 1999, 27 (8), 1943.
45. Zhang, C.; van der Maarel, J., Surface-Directed and Ethanol-Induced DNA Condensation on Mica[J]. Journal of Physical Chemistry B-Condensed Phase 2008, 112 (11), 3552-3557.
46. Lyo, I. W.; Avouris, P., Field-induced nanometer-to atomic-scale manipulation of silicon surfaces with the STM[J]. Science 1991, 253 (5016), 173.
47. Binnig, G.; Quate, C. F.; Gerber, C., Atomic force microscope. APS: 1986,56, 930-933.
48. Hansma, H.; Laney, D., DNA binding to mica correlates with cationic radius: assay by atomic force microscopy[J]. Biophysical Journal 1996, 70 (4), 1933-1939.
49. Vesenka, J.; Guthold, M.; Tang, C.; Keller, D.; Delaine, E.; Bustamante, C., Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope[J]. Ultramicroscopy 1992, 42, 1243-1249.
50. Lyubchenko, Y.; Oden, P.; Lampner, D.; Lindsay, S.; Dunker, K., Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces[J]. Nucleic Acids Research 1993, 21 (5), 1117.
51. Binnig, G.; Quate, C.; Gerber, C., Atomic force microscope[J]. physical review letters 1986, 56 (9), 930-933.
52. Hansma, H.; Vesenka, J.; Siegerist, C.; Kelderman, G.; Morrett, H.; Sinsheimer, R.; Elings, V.; Bustamante, C.; Hansma, P., Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope[J]. Science 1992, 256, 1180-1184.
53. Zheng, J.; Li, Z.; Wu, A.; Zhou, H., AFM studies of DNA structures on mica in the presence of alkaline earth metal ions[J]. Biophysical chemistry 2003, 104 (1), 37-43.
54. Bustamante, C.; Erie, D.; Keller, D., Biochemical and structural applications of scanning force microscopy[J]. Current Opinion in Structural Biology 1994, 4 (5), 750-760.
55. Hansma, H.; Hoh, J., Biomolecular imaging with the atomic force microscope[J]. Annual Review of Biophysics and Biomolecular Structure 1994, 23 (1), 115-140.
56. Bustamante, C.; Rivetti, C., Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope[J]. Annual Review of Biophysics and Biomolecular Structure 1996, 25 (1), 395-429.
57. Tanigawa, M.; Okada, T., Atomic force microscopy of supercoiled DNA structure on mica[J]. Analytica Chimica Acta 1998, 365 (1-3), 19-25.
58. Besteman, K.; van Eijk, K.; Vilfan, I.; Ziese, U.; Lemay, S., Influence of charged surfaces on the morphology of DNA condensed with multivalent ions[J]. Biopolymers 2007, 87 (2), 141-148.
59. Zhang, X.; Hou, X.; Ji, C.; Li, M.; Dou, S.; Wang, P., Spermidine-induced two-dimensional DNA condensations on mica surfaces: A different pathway from condensations in solution[J]. Chinese Science Bulletin 2009, 54 (14), 2425-2433.
60. Lin, Z.; Wang, C.; Feng, X.; Liu, M.; Li, J.; Bai, C., The observation of the local ordering characteristics of spermidine-condensed DNA: atomic force microscopy and polarizing microscopy studies[J]. Nucleic Acids Research 1998, 26 (13), 3228.
61. Lyubchenko, Y.; Gall, A.; Shlyakhtenko, L.; Harrington, R.; Jacobs, B.; Oden, P.; Lindsay, S., Atomic force microscopy imaging of double stranded DNA and RNA[J]. Journal ofbiomolecular structure & dynamics 1992, 10 (3), 589.
62. Lyubchenko, Y.; Blankenship, R.; Gall, A.; Lindsay, S.; Thiemann, O.; Simpson, L.; Shlyakhtenko, L., Atomic force microscopy of DNA, nucleoproteins and cellular complexes: the use of functionalized substrates[J]. Scanning microscopy. Supplement 1996, 10, 97.
63. Lyubchenko, Y.; Jacobs, B.; Lindsay, S., Atomic force microscopy of reovirus dsRNA: a routine technique for length measurements[J]. Nucleic Acids Research 1992, 20 (15), 3983.
64. Lyubchenko, Y.; Shlyakhtenko, L., Visualization of supercoiled DNA with atomic force microscopy in situ[J]. Proceedings of the National Academy of Sciences 1997, 94 (2), 496.
65. Shlyakhtenko, L.; Potaman, V.; Sinden, R.; Lyubchenko, Y., Structure and dynamics of supercoil-stabilized DNA cruciforms1[J]. journal of molecular biology 1998, 280 (1), 61-72.
66. Pelta, J.; Durand, D.; Doucet, J.; Livolant, F., DNA mesophases induced by spermidine: structural properties and biological implications[J]. Biophysical journal 1996, 71 (1), 48-63.
67. Raspaud, E.; Durand, D.; Livolant, F., Interhelical spacing in liquid crystalline spermine and spermidine-DNA precipitates[J]. Biophysical journal 2005, 88 (1), 392-403.
68. Hud, N.; Vilfan, I., Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size[J]. Annual Review of Biophysics and Biomolecular Structure.2005,23,2995.
69. Lasic, D., Liposomes in gene delivery[M]. CRC PRESS: 1997.295
70. Templeton, N.; Lasic, D., New directions in liposome gene delivery[J]. Molecular biotechnology 1999, 11 (2), 175-180.
71. Ewert, K.; Ahmad, A.; Bouxsein, N.; Evans, H.; Safinya, C., Non-viral gene delivery with cationic liposome-DNA complexes[J]. Methods Mol Biol 2008, 433, 159-175.
72. Gelbart, W.; Bruinsma, R.; Pincus, P.; Parsegian, V., DNA-inspired electrostatics[J]. Physics Today 2000, 53 (9), 38-44.
73. Strey, H.; Podgornik, R.; Rau, D.; Parsegian, V., Dna-dna interactions[J]. Current Opinion in Structural Biology 1998, 8 (3), 309-313.
74. Bloomfield, V., Condensation of DNA by multivalent cations: considerations on mechanism[J]. Biopolymers 1991, 31 (13), 1471-1481.
75. Wilson, R.; Bloomfield, V., Counterion-induced condensation of deoxyribonucleic acid. A light-scattering study[J]. Biochemistry 1979, 18 (11), 2192-2196.
76. Schellman, J.; Parthasarathy, N., X-ray diffraction studies on cation-collapsed DNA[J].
85Journal of molecular biology 1984, 175 (3), 313.
77. Widom, J.; Baldwin, R., Cation-induced toroidal condensation of DNA studies with Co3+ (NH3) 6[J]. Journal of molecular biology 1980, 144 (4), 431.
78. Gaillard, C.; Strauss, F., Ethanol precipitation of DNA with linear polyacrylamide as carrier[J]. Nucleic acids research 1990, 18 (2), 378.
79. Paithankar, K. R.; Prasad, K. S., Precipitation of DNA by polyethylene glycol and ethanol[J]. Nucleic acids research 1991, 19 (6), 1346.
80. Roy, K.; Antony, T.; Saxena, A.; Bohidar, H., Ethanol-induced condensation of calf thymus DNA studied by laser light scattering[J]. J. Phys. Chem. B 1999, 103 (24), 5117-5121.
81. Xiao, Z.; Xu, M.; Sagisaka, K.; Fujita, D., AFM observations of self-assembled lambda DNA network on silanized mica[J]. Thin Solid Films 2003, 438, 114-117.
82. Song, Y.; Li, Z.; Liu, Z.; Wei, G.; Wang, L.; Sun, L.; Guo, C.; Sun, Y.; Yang, T., A novel strategy to construct a flat-lying DNA monolayer on a mica surface[J]. J. Phys. Chem. B 2006, 110 (22), 10792-10798.
83. Noy, A.; Perez, A.; Laughton, C.; Orozco, M., Theoretical study of large conformational transitions in DNA: the B {leftrightarrow} A conformational change in water and ethanol/water[J]. Nucleic acids research 2007, 35 (10), 3330.
84. Schultz, J.; Rupprecht, A.; Song, Z.; Piskur, J.; Nordenski ld, L.; Lahajnar, G., A mechanochemical study of MgDNA fibers in ethanol-water solutions[J]. Biophysical journal 1994, 66 (3), 810-819.
85. Widom J, B. R., Cation-induced toroidal condensation of DNA studies with Co3+(NH3) 6[J]. J Mol Biol 1980, 144, 431-453.
86. He, S.; Arscott, P.; Bloomfield, V., Condensation of DNA by multivalent cations: experimental studies of condensation kinetics[J]. Biopolymers 2000, 53 (4), 329.
87. Balhorn, R.; Cosman, M.; Thornton, K.; Krishnan, V. V.; Corzett, M.; Bench, G.; Kramer, C.; Hud, N. V.; Allen, M.; Prieto, M., Protamine mediated condensation of DNA in mammalian sperm[M]. Cache River Press ,1999.10-20
88. Cerritelli, M. E.; Cheng, N.; Rosenberg, A. H.; McPherson, C. E.; Booy, F. P.; Steven, A. C., Encapsidated conformation of bacteriophage T7 DNA[J]. Cell 1997, 91 (2), 271-280.
89. Mahato, R. I.; Takakura, Y.; Hashida, M., Nonviral vectors for in vivo gene delivery:physicochemical and pharmacokinetic considerations[J]. Critical reviews in therapeutic drug carrier systems 1997, 14 (2), 133.
90. Shen, M.; Downing, K.; Balhorn, R.; Hud, N., Nucleation of DNA condensation by static loops: formation of DNA toroids with reduced dimensions[J]. J. Am. Chem. Soc 2000, 122 (19), 4833-4834.
91. Conwell, C.; Vilfan, I.; Hud, N., Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength[J]. Proceedings of the National Academy of Sciences 2003, 100 (16), 9296.
92. Zinchenko, A.; Sergeyev, V.; Murata, S.; Yoshikawas, K., Controlling the intrachain segregation on a single DNA molecule[J]. J. Am. Chem. Soc 2003, 125 (15), 4414-4415.
93. Chen, N.; Zinchenko, A.; Murata, S.; Yoshikawa, K., Specific formation of beads-on-a-chain structures on giant DNA using a designed polyamine derivative[J]. J. Am. Chem. Soc 2005, 127 (31), 10910-10916.
94. Baumann, C.; Bloomfield, V.; Smith, S.; Bustamante, C.; Wang, M.; Block, S., Stretching of single collapsed DNA molecules[J]. Biophysical journal 2000, 78 (4), 1965-1978.
95. Bloomfield, V. A., Condensation of DNA by multivalent cations[J]. Biopolymers/Nucleic Acid Sci. 1998, 44, 269-282.
96. Baumann, C. G.; Bloomfield, V. A.; Smith, S. B.; Bustamante, C.; Wang, M. D.; Block, S. M., Stretching of single collapsed DNA molecules[J]. Biophysical journal 2000, 78 (4), 1965-1978.
97. Murayama, Y.; Sakamaki, Y.; Sano, M., Elastic response of single DNA molecules exhibits a reentrant collapsing transition[J]. Physical review letters 2003, 90 (1), 18102.
98. Husale, S.; Grange, W.; Karle, M.; Burgi, S.; Hegner, M., Interaction of cationic surfactants with DNA: a single-molecule study[J]. Nucleic acids research 2008, 36 (5), 1443.
99. Strick, T.; Allemand, J.; Bensimon, D.; Croquette, V., Behavior of supercoiled DNA[J]. Biophysical journal 1998, 74 (4), 2016-2028.
100.Yan, J.; Skoko, D.; Marko, J., Near-field-magnetic-tweezer manipulation of single DNA molecules[J]. Physical Review E 2004, 70 (1), 11905.
101.Bouchiat, C.; Wang, M.; Allemand, J.; Strick, T.; Block, S.; Croquette, V., Estimating the persistence length of a worm-like chain molecule from force-extension measurements[J].Biophysical journal 1999, 76 (1), 409-413.
102.Baase, W. A.; Staskus, P. W.; Allison, S. A., Precollapse of T7 DNA by spermidine at low ionic strength: a linear dichroism and intrinsic viscosity study[J]. Biopolymers 1984, 23 (12), 2835-2851.
103.Marquet, R.; Houssier, C., Different binding modes of spermine to AT and GC base pairs modulate the bending and stiffening of the DNA double helix[J]. Journal of biomolecular structure & dynamics 1988, 6 (2), 235.
104.Gelbart, W. M.; Bruinsma, R. F.; Pincus, P. A.; Parsegian, V. A., DNA‐Inspired Electrostatics[J]. Physics Today 2000, 53, 38.
105.Montesi, A.; Pasquali, M.; MacKintosh, F. C., Collapse of a semiflexible polymer in poor solvent[J]. Physical Review E 2004, 69 (2), 21916.
106.Schnurr, B.; MacKintosh, F. C.; Williams, D. R. M., Dynamical intermediates in the collapse of semiflexible polymers in poor solvents[J]. EPL (Europhysics Letters) 2000, 51, 279.
107.Ishimoto, Y.; Kikuchi, N., Low-energy states of a semiflexible polymer chain with attraction and the whip-toroid transitions[J]. The Journal of Chemical Physics 2006, 125, 074905.
108.Schnurr, B.; Gittes, F.; MacKintosh, F. C., Metastable intermediates in the condensation of semiflexible polymers[J]. Physical Review E 2002, 65 (6), 61904.
109.Holland, P. M.; Abramson, R. D.; Watson, R.; Gelfand, D. H., Detection of specific polymerase chain reaction product by utilizing the 5'----3'exonuclease activity of Thermus aquaticus DNA polymerase[J]. Proceedings of the National Academy of Sciences of the United States of America 1991, 88 (16), 7276.
110.詹姆斯;沃森;刘望夷,双螺旋——发现DNA结构的故事[J].科学出版社1984.
111.Watson, J. D.; Crick, F., The structure of DNA[J]. Cold Spring Harb Symp Quant Biol. 1953,18,123-131.
112.Dulbecco, R., A turning point in cancer research: sequencing the human genome[J]. Science 1986, 231 (4742), 1055.
113.Hamon, L.; Pastré, D.; Dupaigne, P.; Breton, C. L.; Cam, E. L.; Piétrement, O., High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein—DNA complexes[J]. Nucleic acids research 2007, 35 (8), e58.
114.Sorel, I.; Piétrement, O.; Hamon, L.; Baconnais, S.; Le Cam, E.; Pastré, D., The EcoRI-DNA Complex as a Model for Investigating Protein- DNA Interactions by Atomic Force Biochemistry 2006; 45, 14675-14682.
115.Oh, S. J.; Hong, B. J.; Choi, K. Y.; Park, J. W., Surface modification for DNA and protein microarrays[J]. OMICS: A journal of Integrative Biology 2006, 10 (3), 327-343.
116.Liu, Q.; Wang, L.; Frutos, A. G.; Condon, A. E.; Corn, R. M.; Smith, L. M., DNA computing on surfaces[J]. Nature 2000, 403 (6766), 175-179.
117.Pastré, D.; Piétrement, O.; Fusil, S.; Landousy, F.; Jeusset, J.; David, M. O.; Hamon, L.; Le Cam, E.; Zozime, A., Adsorption of DNA to mica mediated by divalent counterions: a theoretical and experimental study[J]. Biophysical journal 2003, 85 (4), 2507-2518.
118.Rivetti, C.; Guthold, M.; Bustamante, C., Scanning Force Microscopy of DNA Deposited onto Mica: EquilibrationversusKinetic Trapping Studied by Statistical Polymer Chain Analysis[J]. Journal of molecular biology 1996, 264 (5), 919-932.
119.Pastré, D.; Hamon, L.; Landousy, F.; Sorel, I.; David, M. O.; Zozime, A.; Le Cam, E.; Piétrement, O., Anionic polyelectrolyte adsorption on mica mediated by multivalent cations: a solution to DNA imaging by atomic force microscopy under high ionic strengths[J]. Langmuir 2006, 22 (15), 6651-6660.
120.Terry, B.; Jack, W.; Rubin, R.; Modrich, P., Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences[J]. Journal of Biological Chemistry 1983, 258 (16), 9820.
121.McClarin, J. A.; Frederick, C. A.; Wang, B. C.; Greene, P.; Boyer, H. W.; Grable, J.; Rosenberg, J. M., Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution[J]. Science 1986, 234 (4783), 1526.
122.Wright, D. J.; Jack, W. E.; Modrich, P., The kinetic mechanism of EcoRI endonuclease[J]. Journal of Biological Chemistry 1999, 274 (45), 31896.
123.Allison, D.; Kerper, P.; Doktycz, M.; Spain, J.; Modrich, P.; Larimer, F.; Thundat, T.; Warmack, R., Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules[J]. Proceedings of the National Academy of Sciences of the United States of America 1996, 93 (17), 8826.
124.皮新春;邹国林,限制性核酸内切酶与DNA相互作用研究进展[J],氨基酸与生物资源1997,19, 44-48.
125.Smith, H. O., Nucleotide sequence specificity of restriction endonucleases. AAAS: 1979,205, 455-462.
126.邝辉;熊轩;游超;陈仲本,限制性酶切pUC18质粒的AFM研究[J]. 2007,24, 210-211.
127.van Gent, D.; Hoeijmakers, J.; Kanaar, R., Chromosomal stability and the DNA double-stranded break connection[J]. Nature Reviews Genetics 2001, 2 (3), 196-206.
128.Shin, D.; Chahwan, C.; Huffman, J.; Tainer, J., Structure and function of the double-strand break repair machinery[J]. DNA repair 2004, 3 (8-9), 863-873.
129.Gemmen, G.; Millin, R.; Smith, D., DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force[J]. Nucleic acids research 2006, 34 (10), 2864.
130.Topal, M.; Thresher, R.; Conrad, M.; Griffith, J., NaeI endonuclease binding to pBR322 DNA induces looping[J]. Biochemistry 1991, 30 (7), 2006-2010.
131.Siksnys, V.; Skirgaila, R.; Sasnauskas, G.; Urbanke, C.; Cherny, D.; Grazulis, S.; Huber, R., The Cfr10I restriction enzyme is functional as a tetramer1[J]. Journal of molecular biology 1999, 291 (5), 1105-1118.
132.M¨1cke, M.; Lurz, R.; Mackeldanz, P.; Behlke, J.; Kr¨1ger, D.; Reuter, M., Imaging DNA Loops Induced by Restriction EndonucleaseEcoRII[J]. Journal of Biological Chemistry 2000, 275 (39), 30631.
133.Friedhoff, P.; Lurz, R.; L¨1der, G.; Pingoud, A., Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops[J]. Journal of Biological Chemistry 2001, 276 (26), 23581.
134.Pastre , D.; Hamon, L.; Sorel, I.; Le Cam, E.; Curmi, P.; Pie trement, O., Specific DNA- Protein Interactions on Mica Investigated by Atomic Force Microscopy[J]. Langmuir 2009, 26 (4), 2618-2623.
135.Sorel, I.; Pi¨|trement, O.; Hamon, L.; Baconnais, S.; Le Cam, E.; Pastr¨|, D., The EcoRI- DNA Complex as a Model for Investigating Protein- DNA Interactions by Atomic Force Microscopy[J]. Biochemistry 2006, 45 (49), 14675-14682.
136.Reich, S.; G ssl, I.; Reuter, M.; Rabe, J.; Kr¨1ger, D., Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I[J]. Journal of molecular biology 2004,341 (2), 337-343.
137.Lushnikov, A.; Potaman, V.; Lyubchenko, Y., Site-specific labeling of supercoiled DNA[J]. Nucleic Acids Research 2006,34,e111.
138.Crampton, N.; Yokokawa, M.; Dryden, D.; Edwardson, J.; Rao, D.; Takeyasu, K.; Yoshimura, S.; Henderson, R., Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping[J]. Proceedings of the National Academy of Sciences 2007, 104 (31), 12755.
139.Neaves, K.; Cooper, L.; White, J.; Carnally, S.; Dryden, D.; Edwardson, J.; Henderson, R., Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping[J]. Nucleic Acids Research 2009,6,2053-2063.
140.Berge, T.; Ellis, D.; Dryden, D.; Edwardson, J.; Henderson, R., Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy[J]. Biophysical Journal 2000, 79 (1), 479-484.
141.Harada, Y.; Ohara, O.; Takatsuki, A.; Itoh, H.; Shimamoto, N.; Kinosita, K., Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase[J]. Nature 2001, 409 (6816), 113-115.
142.Lushnikov, A.; Potaman, V.; Oussatcheva, E.; Sinden, R.; Lyubchenko, Y., DNA Strand Arrangement within the SfiI- DNA Complex: Atomic Force Microscopy Analysis[J]. Biochemistry 2006, 45 (1), 152-158.
143.Halford, S.; Welsh, A.; Szczelkun, M., Enzyme-mediated DNA looping[J]. Biophysics 2004, 33.1-24
144.Deibert, M.; Grazulis, S.; Sasnauskas, G.; Siksnys, V.; Huber, R., Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA[J]. Nature Structural & Molecular Biology 2000, 7 (9), 792-799.
145.Gormley, N.; Hillberg, A.; Halford, S., The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence[J]. Journal of Biological Chemistry 2002, 277 (6), 4034.
146.Wentzell, L.; Nobbs, T.; Halford, S., TheSfiI Restriction Endonuclease Makes a Four-strand DNA Break at Two Copies of its Recognition Sequence[J]. Journal of molecular biology 1995, 248 (3), 581-595.
147.Bilcock, D.; Daniels, L.; Bath, A.; Halford, S., Reactions of type II restriction endonucleases with 8-base pair recognition sites[J]. Journal of Biological Chemistry 1999, 274 (51), 36379.
148.Embleton, M.; Siksnys, V.; Halford, S., DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites1[J]. Journal of molecular biology 2001, 311 (3), 503-514.
149.Bath, A.; Milsom, S.; Gormley, N.; Halford, S., Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA[J]. Journal of Biological Chemistry 2002, 277 (6), 4024.
150.Schneider, S.; L rmer, J.; Henderson, R.; Oberleithner, H., Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy[J]. Pflugers Archiv European Journal of Physiology 1998, 435 (3), 362-367.
151.Edstrom, R.; Meinke, M.; Yang, X.; Yang, R.; Elings, V.; Evans, D., Direct visualization of phosphorylase-phosphorylase kinase complexes by scanning tunneling and atomic force microscopy[J]. Biophysical Journal 1990, 58 (6), 1437-1448.
152.Powell, L.; Dryden, D.; Murray, N., Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme 1[J]. Journal of molecular biology 1998, 283 (5), 963-976.
153.Vanamee, S.; Santagata, S.; Aggarwal, A., FokI requires two specific DNA sites for cleavage1[J]. Journal of molecular biology 2001, 309 (1), 69-78.