DEPENDENCE OF A GAS-PHASE DNA GLOBULE SIZE ON CHAIN LENGTH
Abstract
Modern trends in using DNA in nano- and biotechnologies generated the need for new methods of analyzing DNA molecules with up-to-date equipment. We developed a method of mild nondestructive ablation with terahertz radiation for bringing DNA molecules to aerosol. DNA nanoparticles were measured in the gas phase with a diffusion aerosol spectrometer. Changes that happen to DNA in the gas phase were visualized by atomic force microscopy (AFM). Comparison of diffusion sizes of plasmid pUC18 aerosol particles with those obtained by AFM indicated that DNA molecules experienced condensation in the gas phase. We constructed a model on the base of modern concepts of DNA condensation and globule formation. The predictions matched well the experimental data. The persistence DNA length estimated in the gas phase was about 0.5 nm. This fact points to the absence of distributed charge on the DNA surface in the gas phase and the nonionizing habit of terahertz radiation. Study of DNA conformations in the gas phase will add to the understanding to DNA compactness under natural and artificial conditions.
About the Authors
T. N. GoryachkovskayaRussian Federation
A. S. Kozlov
Russian Federation
V. M. Popik
Russian Federation
N. A. Kolchanov
Russian Federation
S. E. Peltek
Russian Federation
References
1. Анкилов А.Н., Бакланов А.М., Козлов А.С., Малышкин С.Б. Определение концентрации аэрозолеобразующих веществ в атмосфере // Оптика атмосферы и океана. 2000. Т. 13. № 6-7. С. 644–647.
2. Ветошкин А.Г., Таранцева К.Р. Технология защиты окружающей среды (теоретические основы). Пенза, 2004. 249 с.
3. Либенсон М.Н., Шандыбина Г.Д., Шахмин А.Л. Химический анализ продуктов абляции наносекундного диапазона // Журнал технической физики. 2000. Т. 70. Вып. 9. С. 124–127.
4. Пельтек С.Е., Попик В.М., Горячковская Т.Н., Мордвинов В.А., Петров А.К. Способ абляции целевой ДНК с поверхности ДНК-биочипов. Патент РФ № 2410439. 2009.
5. Тейф В.Б., Ландо Д.Ю. Конденсация ДНК, вызванная адсорбцией лигандов // Молекулярная биология. 2001. Т. 35. № 1. С. 117–119.
6. Флори П.Д. Статистическая механика цепных молекул. М., 1971.
7. Хохлов А.Р., Кучанов С.И. Лекции по физической химии полимеров. М., 2000.
8. Barbara A., Shehadeh-Masha’our R., Garzozi H.J. Laser ablation in eyes with congenital nystagmus // J. Refract. Surg. 2007. V. 23 (6). P. 623–625.
9. Baumann C.G., Smith S.B., Bloomfi eld V.A., Bustamante C. Ionic effects on the elasticity of single DNA molecules // Proc. Natl. Acad. Sci. USA. 1997. V. 94. P. 6185– 6190.
10. Bloomfi eld V.A. DNA condensation // Curr. Opin. Struct. Biol. 1996. V. 6 (3). P. 334–341.
11. Conwell C.C., Vilfan I.D., Hud N.V. Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength. // PNAS. 2003. V. 100 (16). P. 9296–9301.
12. Gavrilov N.G., Knyazev B.A., Kolobanov E.I. et al. Status of the Novosibirsk high-power terahertz FEL // Nuclear instruments and methods in physics research. Sec. A. 2007. V. 575 (1/2). P. 54–57.
13. Hagerman P.J. Flexibility of DNA // Ann. Rev. Biophys.Biophys. Chem. 1988. V. 17. P. 265–286.
14. Klimenko S.M., Tikchonenko T.I., Andreev V.M. Packing of DNA in the head of bacteriophage T2 // J. Mol. Biol. 1967. V. 23 (3). P. 523–533.
15. Lyubchenko Y.L., Shlyakhtenko L.S. AFM for analysis of structure and dynamics of DNA and protein-DNA complexes // Methods. 2009. V. 47 (3). P. 206–213.
16. Manning G.S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides // Q. Rev. Biophys. 1978. V. 11. P. 179–246.
17. Mazur A.K. Evaluation of Elastic Properties of Atomistic DNA Models // Biophysical J. 2006. V. 91. P. 4507–4518.
18. Murphy L.D., Zimmerman S.B. Condensation and cohesion of lambda DNA in cell extracts and other media: implications for the structure and function of DNA in prokaryotes // Biophys. Chem. 1995. V. 57 (1). P. 71–92. Neidle S. DNA structure and recognition. Oxford: IRL Press, 1994. 147 p.
19. Piacenza M., Grimme S. Systematic quantum chemical study of DNA-base tautomers // J. Comput Chem. 2004. V. 25 (1). P. 83–99.
20. Post C.B., Zimm B.H. Internal condensation of a single DNA molecule // Biopolymers. 1979. V. 18. P. 1487–1501.
21. Raspaud E., Olvera de la Cruz M., Sikorav J.-L., Livolant F. Precipitation of DNA by Polyamines: A Polyelectrolyte Behavior // Biophysical J. 1998. V. 74. P. 381 393.
22. Rouzina I., Bloomfi eld V. Force-Induced Melting of the DNA Double Helix 1. Thermodynamic Analysis // Biophysical Journal. 2001. V. 80. P. 882–893.
23. Rueda M., Kalko S.G., Luque F.J., Orozco M. The structure and dynamics of DNA in the gas Phase // J. Am. Chem. Soc. 2003. V. 125 (26). P. 8007–8014.
24. Sarkar T., Vitoc I., Mukerji I., Hud N.V. Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines // Nucleic Acids Research. 2007. V. 35 (3). P. 951–961.
25. Schmutz M., Durand D., Debin A. et al. DNA packing in stable lipid complexes designed for gene transfer imitates DNA compaction in bacteriophage // PNAS. 1999. V. 96 (22). P. 12293–12298.
26. Senkan S., Kahn M., Duan S., Ly A., Leidholm C. Highthroughput metal nanoparticle catalysis by pulsed laser ablation // Catalysis Today. 2006. V. 117. P. 291–296.
27. Shotton M.W., Pope L.H., Forsyth T. et al. A high-angle neutron fi bre diffraction study of the hydration of deuterated ADNA // Biophys. Chem. 1997. V. 69. P. 85–96.
28. Wang W., Lin J., Schwartz D. Scanning force microscopy of DNA molecules elongated by convective fluid flow in an evaporating droplet // Biophys J. 1998. V. 75 (1). P. 513–520.
29. Wilson R., Bloomfi eld V. Counterion-induced condensation of deoxyribonucleic acid. A light-scattering study // Biochemistry. 1979. V. 18. P. 2192–2196.
30. Zheng J., Birktoft J.J., Chen Y. et al. From Molecular to Macroscopic via the Rational Design of a Self-Assembled 3D DNA Crystal // Nature. 2009. V. 461. P. 74–77.