DNA-Based Sensing

Probe ssDNA base length Conc.a (pg mE1) Complementary target ssDNA base length Detection range (g mE1) 

There are some interesting advances in the design and fabrication of OECTs. The most promising one is the use of microfluidic-based OECTs reported by Malliaras et al. [33], They have successfully integrated microfluidic channels 

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In addition to that, DNA-based sensing adds a possibility to conduct a more extensive genetic analysis of a given pathogen, following areal-time PCR detection, similar to what was done for B. anthracis, Y. pestis, and F. tularensis [72]. Recent reviews examine in detail the applications of DNA array methodology and a variety of PCR-based techniques to biodefense [73-75]. 

Detection of the dA N1 and dC N3 adducts may not in one sense be particularly important for DNA based on their central position within the helical conformation and hydrogen bonding network.37,38 Still, the deoxynucleoside studies helped to focus attention on the reversibility of alkylation by QM and provided insight into the reactions of duplex DNA described below in Section 9.3. Reaction at the deoxynucleoside level also provided an essential system for developing a theoretical treatment of QM reaction.50-52 Computations based on density functional theory well rationalized the published results on d A and correctly anticipated the results on dG and dC reviewed above and described in more detail in Chapter 2 (Freccero). 

The labeling can also be done by fluorescence lifetime differences, e.g., introduced by quenching pathways connected with different surroundings. This can be used for lifetime imaging methods (Chapter 1, this volume) or for distinguishing complexes of one and the same fluorescence label with, e.g., different DNA-bases. In this case, the fluorescence label is not only a label but incorporates a function which senses the environment and can therefore be regarded as a sensing fluorescence probe. 

F ig U re 1 3.1 A schematic view of RNA chain elongation catalyzed by an RNApolymerase. In the region being transcribed, the DNA double helix is unwound by about a turn to permit the DNAs sense strand to form a short segment of DNA-RNA hybrid double helix. That forms the transcription bubble. Note that the DNA bases in the bubble on the antisense strand are now exposed to the enzyme and are useable as a template for chain elongation. The RNApolymerase works its way down the DNA molecule until it encounters a stop signal. (Reproduced from D. Voet and J. G. Voet, Biochemistry, 3rd, edn, 2004 Donald and Judith G Voet. Reprinted with permission of John Wiley and Sons, Inc.)... 

The reported strategies utilized in DNA sensing include (1) sequence-specific hybridization processes based on the oxidation signal of most electroactive DNA bases, guanine and adenine [13,24] or (2) quasi-specific detection of small molecules capable of binding by intercalation or complexation with DNA, such as metal coordination complexes, antibiotics, pesticides, pollutants, etc. [17,18] or in the presence of some metal tags such as gold, silver nanoparticles, etc. [23,50,51]. 

Recently, an impressive number of inventive designs of DNA-based electrochemical sensing are emerging. These types of sensors combine nucleic acid layers with electrochemical transducers to produce a biosensor and promise to provide a simple, accurate and inexpensive platform for patient diagnosis. 

From spectroscopic and biochemical studies it has become clear that DNA-mediated CT is extremely sensitive to the re-stacking of the intervening DNA bases and to disruption and perturbation of the DNA structure or conformation. This indicates that sensing of DNA damage could be accomplished, at least in part, on the basis of CT chemistry. In considering these possibilities, it is important to discover whether DNA-mediated CT does occur within the cell. Charge transfer in HeLa cell nuclei has recently been probed by use of a rhodium photooxidant [15]. 

DNA duplex. Naegeli et al. have previously advanced a bipartite model of NER substrate discrimination that is initiated by the detection of disrupted Watson-Crick base-pairing followed by a lesion-sensing step that verifies the presence of a chemically altered nucleotide [29, 33]. The nature of the critically important verification step that leads to the dual incision is still not well understood [24]. The bipartite model is consistent with previous observatisons of Sugasawa et al. who found that XPC/HR23B binds to DNA that contains bubbles of several mismatched DNA bases in the absence of lesions or chemically modified nucleotides, but incisions occur only when a chemically modified base is also present [13, 35]. 

In QCM-based sensing, the recognition is displaced as a measurable shift in the resonant frequency. Ideally, the frequency shift is maximum with the fully complementary sequence and it is absent with non-complementary DNA. 

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