Conductivity in DNA

Ever since the discovery of the repetitive structure of DNA, it has been speculated that DNA is conducting. In fact, there have been a number of experiments that 

FIGURE 18.22 Calculated conductivity as a function of temperature in the case with localized charge carriers. 

Furthermore, theories for conductivity in fact require that the system is infinite for all practical purposes, and this may not be the case if conductivity is measured over a few layers of bases. In later and more relevant experiments, J. Barton et al. have attempted to use microscopic electrodes, built into both ends of a DNA string. This experiment is done either in the ground state as an ordinary ET experiment, or by photoinduced electron transfer. All ET is supposed to take place through the x-systems of the bases. 

In the theoretical studies, the DNA strand is treated as an ET systan. The reorganization energy (A.) has to be calculated for each of the bases. The coupling 

FIGURE 18.23 (See color insert) Part of a DNA strand with two adenosine bases. 

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Electrical conduction in DNA has become a highly contentious subfield of its own. The uncertainties here are even greater than those in the chemical measurements of charge transfer in DNA, partly because of the greater strand length generally involved, and partly because of the necessity for making contacts in measurement of DC conduction. 

In sum, then, although fascinating reports of conductivity in DNA structures have been published, and some general structure/function motifs have become clear, difficulties with reproducibility of experimental data and with appropriate interfaces between nanoscale DNA structures and macroscopic electrodes have limited the accuracy with which DNA charge transport can be measured, and the depth in which it can be understood. This remains an active area, and (especially given DNA s very powerful presence as the synthetic component of nanostructures) it is one that will almost certainly be more clearly elucidated in the near future. 

Electronic Structures and Conduction Properties 447 15.3 Electronic Conduction in DNA 15.3.1 Introduction... 

Possible conductivity in DNA could occur vertically in Figure 18.23. A reason for confusing the results may be that immense experimental difficulties cannot be surmounted. A single DNA strand is picked out from its environment and inserted between two electrodes in a vacuum. The DNA chain may not survive that treatment. 

The theoretical results are reasonably accurate and consistent between different calculations. ET takes place in single jumps, although a slight inaccuracy of the calculation is sufficient to allow multiple jumps in some cases. The most concise conclusion is that conductivity in DNA is caused by single leaps between the bases in the DNA strand, approximately, as in graphite, in the perpendicular direction. 

The gap in alternating trans-polyacetylene is described on the basis of its quasi-particle band structure and the question of the Bloch-type conduction in DNA (either through doping or the possibility of intrinsic conduction due to charge transfer from the sugar rings to the nucleotide bases) is discussed. This is followed by a brief discussion of the electronic structure of disordered polypeptide chains. 

In solid state materials, single-step electron transport between dopant species is well known. For example, electron-hole recombination accounts for luminescence in some materials [H]. Multistep hopping is also well known. Models for single and multistep transport are enjoying renewed interest in tlie context of DNA electron transfer [12, 13, 14 and 15]. Indeed, tliere are strong links between tire ET literature and tire literature of hopping conductivity in polymers [16]. 

Ethylene oxide has been shown to produce mutagenic and cytogenic effects in a variety of test systems (226). An increased frequency of chromosomal aberrations in peripheral lymphocytes of monkey exposed to ethylene oxide for 104 weeks has been reported (240). In mice, it is an effective inducer of chromosome breaks leading to dominant-lethal mutations. In addition, ethylene oxide has been shown to induce heritable effects in the heritable translocation test conducted in mice exposed to ethylene oxide by inhalation (241,242). In this study, male mice were exposed to ethylene oxide ranging from 165 to 300 ppm for 6 h per day 5 or 7 days/week for 8.5 weeks. Ethylene oxide has also been shown to bind to proteins (243) as well as to DNA (244). Several studies on ethylene oxide-exposed workers have demonstrated an increased incidence of chromosomal aberrations and sister chromatid exchanges the relevance of such effects to human health evaluation is currendy uncertain. 

The natural conductivity of DNA and the potential means for its improvement have recently been re-evaluated [54,55]. Use of DNA bridges for nano-wiring appears very attractive in view of the recent great achievements in the design, control, and fabrication of DNA-made nanostructures [5]. It appears, however, that the conversion of DNA wires into effective nano-conductors is still a major problem. 

Norden, B Elvingson, C Jonsson, M Akerman, B, Microscopic Behavior of DNA Duing Electrophoresis Electrophoretic Orientation, Quarterly Reviews of Biophysics 24, 103,1991. Nozad, I Carbonell, RG Whitaker, S, Heat Conduction in Multiphase Systems—I Theory and Experiment for Two-Phase Systems, Chemical Engineering Science 40, 843, 1985. 

Because the PCR exponentially copies the target molecule or molecules, amplicon contamination in the laboratory is a serious concern. It is recommended that the mastermix is prepared in an isolated area, such as a PCR station equipped with a UV light. This work area should be exposed to UV radiation after use to destroy any DNA contaminants. The use of dedicated pipets and Altered pipet tips is also recommended. The template DNA should be prepared and added to the reaction in an area that is isolated from the mastermix preparation hood. The thermal cycling and gel electrophoresis should be conducted in a third work area and care should be taken not to introduce amplified PCR products into the mastermix or template preparation work areas. 

Extended solid state n systems facilitate CT, particularly when doped [4-6]. The analogy between DNA and conductive solid state -stacks therefore establishes that a requisite condition for CT may exist in DNA. DNA contains an array of heterocyclic aromatic base pairs, stacked at a distance of 3.4 A, wrapped within a negatively charged sugar phosphate backbone [7] (Fig. 1). The interactions between the n electrons of the DNA base pairs provide the electronic coupling necessary for CT to occur. 

As with conductivity measurements, methods and results of theoretical treatments of CT in DNA have varied significantly. Mechanisms invoking hopping, tunneling, superexchange, or even band delocalization have been proposed to explain CT processes in DNA (please refer to other reviews in this text). Significantly, many calculations predicted that the distance dependence of CT in DNA should be comparable to that observed in the a-systems of proteins [26]. This prediction has not been realized experimentally. The dichotomy between theory and experiment may be related to the fact that many early studies gave insufficient consideration to the unique properties of the DNA molecule. Consequently, CT models derived for typical conductors, or even those based on other biomolecules such as proteins, were not adequate for DNA. 

We performed a study to apply the a-CGH technique to test the quality of DNA extracted from FFPE tissues by different methods, using a nonheating protocol, a heat-induced extraction protocol, based on AR as applied to IHC, and comparing the findings to extracts from paired fresh frozen tissue samples (unpublished data). The study was conducted in two stages. 

Receptor sites. The intercalation and kinked sites in DNA used in this study are listed in Table V. Three theoretically determined intercalation sites (I, II and III) permit the study to be conducted with the DNA unwound by 7°-12°, lU-l8° and 25°-32° with parallel base pairs separated by 6.76 A and with alternating (a) sugar puckers (67,68) Attention will be confined to site I because it was found to be the most favorable in the present studies. Several kink (K) sites have been identified (66). The constraint that proper hybridization exists about N2(g) and CIO of BPDEs stimulated an investigation in kinked DNA. In an idealized structure the pyrene moiety is approximately parallel to one of the base pairs as shown... 

The involvement of carbenes has been excluded in the DNA cleavage reactions activated by cupric acetate as these experiments were conducted in the dark. However, the contribution of metal-carbenoids [79] could not be ruled out. In a series of studies dealing with the metal-catalyzed... 

Many sites of exposure to bile in the body are associated with the development of cancer, e.g. the oesophagus, gallbladder and bile duct, pancreas, small intestine and colon (reviewed in ref. 2). One explanation for increased cancer at these sites could be that bile acids stimulate carcinogenesis via DNA-damaging effects. This chapter provides an overview of research conducted in relation to establishing the genotoxic and carcinogenic effects of bile acids. 

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