Документ взят из кэша поисковой машины. Адрес оригинального документа : http://poly.phys.msu.ru/~glm/lds1.pdf Дата изменения: Tue Jul 23 15:23:46 2013 Дата индексирования: Sun Apr 10 22:58:22 2016 Кодировка:

Phys. Low-Dim. Struct., 5/6(2002)pp.7­12

7

Micromechanics of Nucleic Acids
M.O.Gallyamov, E.V.Dubrovin, and I.V.Yaminsky Physical and Chemical Departments, Moscow Sate University, 119899 Moscow, Russia (Received 3 March 2002, accepted for publication 6 March 2002)
Brief review of scanning probe microscopy visualization of RNA and DNA molecules is presented. Nucleic acids molecules were absorbed on clear and modified surfaces of mica. The relaxation process of nucleic acids molecules is observed on the support substrate. The influence of hydrodynamic flow and electrostatic repulsion on the adsorbed molecule orientation is found. The adhesion energy and the rigidity of the molecules are estimated. The difference in the RNA adsorption on surfaces of modified mica and modified graphite is discussed. The observed formation of various forms of adsorbed nucleic acids in the presence of different chemical reagents is interpreted in the terms of micromechanics.

1. Intro duction Recently, the use of the atomic force microscopy for studying molecular and biological ob jects has b ecome more and more extensive [1­3]. Atomic force microscopy gives a lot of advantages in comparison with other metho ds, b ecause it do es not need sp ecial conditions, such as vacuum or sp ecial pre-dep osition pro cessing. However, the preparation of the samples for AFM study plays a large role. Differently prepared samples of the same ob ject sometimes provide us different visual data. The dep osition pro cess of DNA molecules onto a mica surface for imaging using the atomic force microscopy was describ ed in Ref. [4]. In the present work we have obtained the images of the RNA molecules, which were rinsed with water after their adsorption on the substrate. So, this hydro dynamic flow stretched chains of the RNA molecules and determined their orientation. As a rule, the molecules are fixed to the substrate in their middle part or at the edges. Therefore on the AFM images there are two kinds of the lo ops: (1) lo ops that are fastened in the middle and (2) those fastened at the edges (Fig. 1). Two c VSV Co.Ltd, 2002


The parameters of the absorbed loops were estimated. The angle in between the parts of the RNA mo lecules as a funct ion of their charge was calculated for the model of charged rigid

8

chain. For the typical angles that were obM.O.Gallyamoimentsal.is model gives us tained in the exper v et th charges from several to several tens of electrons.

Fig 1. T typical images of RNA Two t Tw f oop a of own: ( ) loosho at Figure. 1. The ypicalimages of RNA loops.loops.ypes oo ltypsesre shloops1are ps thwn:

(1) floed to that are tfixed to the(black arrows) and (2) ones fixed to the substrate by ws) and are ix ops the substra e in the middle substrate in the middle (black arro (2) edges (white arrows)the esubstrate tat flow isedges w ith dottearrows). The flow the those fixed to . Th dir ection of he the shown (white d arrow. direction is shown with dotted arrow.

crucial factors, hydro dynamic pressure and electrostatic repulsion, determined This work was supported by Russian Foundat ion for Basic Research (Grant N 00-04the conformation of the absorb ed molecules during dep osition from solution. 55020) Russian M The parameters inistrabsorb ed and Techwo logyestimated. .99, Programme "Atoween the of y of Science lo ops n ere (Grant N 1.11 The angle b et mic su face structu es"), NAT parts of rthe RNA rmolecules O Saience Prograof theiro llaborativewasnkage Grant Nfor the as c function mme (C charge Li calculated S CLG.975161), IN cS projec 01-0045. mo del LofT.charged rigidTAhain. t For typical angles obtained in the exp eriments, this mo del gives us charges from several to several tens of electrons.
References [ del . Bol akova, O. 2. Mo1] A.VandshresultsI. Kiselyo va, A.S. Filonov, O.Yu. Frolova, Y.L. Lyubchenko, I.V.

Acknowledgement

Yaminskiy, Ultramicroscopy, 86 (2001) 121.

In the .theoretical.E. Ladel, it. wezanassumedinthat ethere issical Jcharge at the p oint [2] H G. Hansma, D mo ney M B as illa, R.L. S sheim r, Biophy no ournal, 68 (1995) of adhesion of the RNA molecule to the massive (compared with the molecule) 1672. substrate. ansma HcG., Laneyis .assigned . to 7the1996) 1933. discretely and equidistantly The . harge D E., Biophys J., 0 , ( molecule [3] H so that the sum of these elementary charges is the full charge of the molecule [4] C.Rivetti, M. Guthold, C. Bustamante, J. Mol. Bio l. 264 (1996) 919. and is the main parameter of the mo del. In order to describ e the influence of the hydro dynamic flow, the RNA chain was presented as a chain of balls and the Sto ck's law was applied to them: F = 6 r v , where F is the force acting on the ball, r is the ball radius, is the viscosity of water, and v is the sp eed of the flow.


Micromechanics of Nucleic Acids

9

Figure 2. The model of an RNA molecule used to calculate its shape. Freact is the elasticity force, FC oul is the total electrostatic force, f res is the resistance force, vf low is the hydrodynamic flow velocity.

Figure 3. Calculated shape of the RNA molecule. (The flow velocity is
10 cm/s).

The mo del is shown in Fig. 2. It can b e used for any other extensive charged molecules. This mo del yields the following results: (1) the shap e of the molecule is shown in Fig. 3, (2) the total charge of the molecule with the length of 1 µm is


10

M.O.Gallyamov et al.

Figure 4. Full charge of the molecule as a function of the flow velocity
for three different values of parameter k (see the text).

18 electrons. Full charge of the molecule as a function of the hydro dynamic flow velo city for different values of the parameter k is shown in Fig. 4. Parameter k = ye /xe is the ratio b etween the ordinate and abscissa of the edge of the molecule (see Fig. 3) or, in other words, it characterizes the angle at the b ottom of the lo op. We obtained that the full charge is prop ortional to the square ro ot of the flow velo city: Q v (see Fig. 4). 3. Conclusion Atomic force microscopy yields direct information on the conformation of RNA molecules allowing to define various characteristics of the molecule. We have estimated the charge of adsorb ed RNA molecules aligned by the hydrodynamic flow. Acknowledgements This work was supp orted by the Russian Foundation for Basic Research (Grant N 00-04-55020), Russian Ministry of Science and Technology (Grant N 1.11.99, Programme "Surface Atomic Structures"), NATO Science Programme (Collab orative Linkage Grant N LST.CLG.975161), and INTAS pro ject 01-0045.


Micromechanics of Nucleic Acids References

11

[1] A.V.Bolshakova, O.I.Kiselyova, A.S.Filonov, O.Yu.Frolova, Y.L.Lyubchenko, and I.V.Yaminskiy, Ultramicroscopy, 86 (2001) 121. [2] H.G.Hansma, D.E.Laney, M.Bezanilla, and R.L.Sinsheimer, Biophysical Journal, 68 (1995) 1672. [3] H.G.Hansma, D.E.Laney, Biophys. J., 70 (1996) 1933. [4] C.Rivetti, M.Guthold, and C.Bustamante, J. Mol. Biol., 264 (1996) 919.


12