Hybridisation of short DNA molecules investigated with in situ atomic force microscopy

• Published in: Ultramicroscopy 2003-10, Vol.97 (1), p.257-261
• Main Authors: Holmberg, M., Kühle, A., Garnæs, J., Boisen, A.
• Format: Article
• Language: English
• Subjects: Atomic force microscopes; Atomic force microscopy; Biological and medical sciences; Biosensing Techniques - methods; DNA molecular layers; DNA, Complementary - chemistry; DNA, Single-Stranded - chemistry; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; General aspects, investigation technics, apparatus; Gold; Hexanols - chemistry; Hybridisation; Instruments, apparatus, components and techniques common to several branches of physics and astronomy; Microscopy, Atomic Force - methods; Nucleic Acid Hybridization - methods; Physics; Scanning probe microscopes, components and techniques; Scanning tunneling and atomic force microscopy; Spacer molecules; Surface Properties; Tissues, organs and organisms biophysics
• ISSN: 0304-3991; 1879-2723
• DOI: 10.1016/S0304-3991(03)00050-0

By introducing the complementary DNA (cDNA) strand to a molecular layer of short single stranded DNA (ssDNA), immobilised on a gold surface, we have investigated hybridisation between the two DNA strands through the technique of in situ atomic force microscopy (AFM). Before introduction of cDNA, the ssDNA molecular layer was modulated with the spacer molecule mercaptohexanol (MCH), which makes the ssDNA molecules more accessible for hybridisation. With in situ AFM, we have monitored the formation of a smooth, mixed molecular layer containing ssDNA and MCH. Furthermore, the hybridisation between the two DNA strands has been studied. Introduction of the cDNA strand resulted in an increase in smoothness and thickness of the molecular layer. Both the increase in order and thickness of the molecular layer can be expected if hybridisation occurs, since double stranded DNA molecules have a more rigid and elongated structure than ssDNA molecules.