Stable Stretched Suspended DNA Molecules

Manola Moretti¹, Tania Limongi^1*, Monica Marini¹, Francesco Gentile², Andrea Giugni¹, Bruno Torre¹, Marco Allione¹, Luca Tirinato¹, Gobind Das¹, Gerardo Perozziello², Patrizio Candeloro² and Enzo Di Fabrizio¹

¹SMILEs Lab, PSE and BESE Divisions, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, E-mail: Manola@Moretti.sa

²University of Magna Graecia, Viale Europa, Germaneto, Italy, E-mail: Manola@Moretti.sa

Introduction

The elastic properties of nucleic acids (DNA and RNA) are strictly related to their biological function and especially in the case of DNA, they control its bending and twisting by ensuring that long molecules can fit into the nucleus of a cell and that, proteins and drugs, can regulate all the cellular processes by means of effective bindings. Accurate measurement of DNA molecules response to chemo/ mechanical stress is usually determined in elastic parameters determination with pulling experiments by investigating secondary structure formation and conformational transitions. There are many techniques for their manipulation: optical and magnetic tweezers measurements, for example, that examined worm-like chain model properties and torsional rigidity of DNA at relatively low forces (torques) determining interesting mechanical phenomena such as a massive forced overstretching of DNA [1] and mechanically-induced strand separation [2]. Flexibility DNA manipulation experiment first requires to anchor the molecules extremities to appropriately treated surfaces; different methods have been developed to achieve specific DNA binding to surfaces [3]. The extremity of the molecule can be functionalized with biotin that can interact specifically with streptavidin bound to a surface [4]. Here we briefly present a new alternative application of the devices presented in [5-11], does not require any modification of the DNA, relies on the reproducible stratification of nucleic acid by its ends on silicon microfabricated super hydrophobic surfaces. DNA was observed to adhere strongly to the surface by its end(s). Once DNA is anchored, it is stretched by letting the solution evaporate. Using the proposed devices for the stratification of the samples by the receding meniscus, the anchored DNA molecules result uniformly stretched on the top of the surface (Figure 1) in a free background manner [12]. It will no longer be necessary to fix DNAs on the substrates and on the tips [7] during molecular stretching by atomic force microscopy (AFM) highresolution imaging, elasticity measurement, cut and other manipulation of DNA. The presented device could represent also a powerful tool for others DNA nanotechnology application including novel single molecule enzyme assay.

Figure 1: Low magnification (left) and high magnification (right) scanning electron microscopy images of DNA suspended on the device surface (scale bar, 10 μm).

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