AFM images of short oligonucleotides on a surface of supported lipid films

Humeník, Drahoslav; Chorvát, Dušan; Novotný, Ivan; Tvarožek, Vladimír; Oretskaya, Tanya S.; Hianik, Tibor

doi:10.1016/j.medengphy.2006.05.005

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Volume 28, Issue 10 , Pages 956-962, December 2006

AFM images of short oligonucleotides on a surface of supported lipid films

Drahoslav Humeník
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovak Republic
Dušan Chorvát Jr.
- International Laser Center, Ikovičova 3, 812 19 Bratislava, Slovak Republic
Ivan Novotný
- Department of Microelectronic, Slovak University of Technology, Ikovičova 3, 812 19 Bratislava, Slovak Republic
Vladimír Tvarožek
- Department of Microelectronic, Slovak University of Technology, Ikovičova 3, 812 19 Bratislava, Slovak Republic
Tanya S. Oretskaya
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
Tibor Hianik
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovak Republic
- Corresponding author. Tel.: +421 2 60295683; fax: +421 2 65426774.

Received 28 April 2006; accepted 4 May 2006. published online 11 July 2006.

Abstract

Atomic force microscopy (AFM) was used to study the topography of lipid films on a gold support with immobilized 19mer single stranded DNA (ssDNA) chemically modified by oleylamine and after hybridization with complementary DNA. The topography of various surfaces was analyzed, including alkanethiol layer chemisorbed on a gold support, lipid films formed on alkanethiol layer without and with immobilized single or double stranded DNA (dsDNA). The value of root means square roughness (RMS) for each surface was determined. RMS value for sBLM with immobilized ssDNA was 2.98nm, while slightly higher value of 3.37nm was typical for dsDNA. The analysis of AFM images revealed that both ssDNA and dsDNA form clusters. The clusters formed by ssDNA are not uniform, but that formed by dsDNA are almost of circular shape with diameter of 13.6±0.5nm. Formation of the clusters could be consequence of lower hydration of lipids and DNA at an air. The water deficit and hence increased ion concentration probably facilitate the attraction between oligonucleotides.