Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking

Abstract

This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT AbstractThe conductivity of DNA covalently bonded to a gold surface was studied by means of the STM technique. Various single-and double-stranded 32-nucleotide-long DNA sequences were measured under ambient conditions so as to provide a better understanding of the complex process of chargecarrier transport in natural as well as chemically modified DNA molecules. The investigations focused on the role of several features of DNA structure, namely the role of the negative charge at the backbone phosphate group and the related complex effects of counterions, and of the stacking interactions between the bases in Watson-Crick and other types of base pairs. The measurements have indicated that the best conductor is DNA in its biologically most relevant double-stranded form with Watson-Crick base pairs and charged phosphates equilibrated with counterions and water. All the studied modifications, including DNA with non-Watson-Crick base pairs, the abasic form, and especially the form with phosphate charges eliminated by chemical modifications, lower the conductivity of natural DNA.

DNA and RNA Electronic Properties for Molecular Modifications and Environmental State Diagnostics

“…Studying transport in thick molecular films and devices, such as organic thinfilm transistors or light-emitting diodes (Kratochvílová et al 2008). 2.…”

“…The first electrical transport measurements of micrometer-long DNA ropes, followed by large numbers of DNA molecules, have indicated that DNA behaves as a good linear conductor (Porath et al 2000;Taniguchi and Kawai 2006). The Scanning Tunneling Microscope (STM) has already been proven (Kratochvílová et al 2008) as a very suitable tool for investigating ordered monolayer films, making it possible to contact one or more molecules and obtain images of the structural characteristics of the film. The experiments have also been used to investigate the room-temperature electronic properties of 12 base-pair d(GC) 12 -d (GC) 12 DNA molecules attached to the gold surface by a thiol link (Kratochvílová et al 2008).…”

“…The Scanning Tunneling Microscope (STM) has already been proven (Kratochvílová et al 2008) as a very suitable tool for investigating ordered monolayer films, making it possible to contact one or more molecules and obtain images of the structural characteristics of the film. The experiments have also been used to investigate the room-temperature electronic properties of 12 base-pair d(GC) 12 -d (GC) 12 DNA molecules attached to the gold surface by a thiol link (Kratochvílová et al 2008). The STM experiments offer a novel way of probing the electronic properties of biomolecules on surfaces at the atomic level.…”

“…In previous studies (Kratochvílová et al 2008(Kratochvílová et al , 2010) the STM measurements were performed with the NTEGRA Prima NT MDT system. Both topographic and spectroscopic data were obtained using freshly cut Pt/Ir tips.…”

“…In Kratochvílová et al (2008Kratochvílová et al ( , 2010, three double-stranded 32-mer oligonucleotides were studied: the canonical standard double strands, DNA double strands with three mismatched base pairs, and double strands with three central pairs of nitrogenous bases replaced by methyl groups.…”