Energy Transfer in DNA Complexes

DNA molecules, with their double-helix structure, provide the basis of the genetic code. The four different bases (adenine, guanine, cytosine, and thymine). 

Since the use of dye molecules in cells plays an important role in the diagnosis and therapy of cancer (Sect. 15.5) a detailed knowledge of the relevant energy transfer processes and the photoactivity of different dyes is of vital interest. 

The efficiency of the energy transfer depends on the coupling between the dye molecule and its surroundings. Measurements of this energy transfer for different base sequences allow the investigation of the coupling strength and its variation 

Example of energy transfer within a DNA-dye complex with acridine dye molecules inserted between the bases adenine and guanine after laser excitation [15.98] 

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Only a limited number of reliable prediction tools are currently available for photoinduced toxicity. This is not surprising since establishing phototoxic potential is a complex task. Phototoxicity can be the consequence of various mechanisms such as photogeneration of reactive oxygen species, production of toxic photoproducts or sensitization of DNA damage by energy transfer. In addition, so far, there are no available universal descriptors (indicators) to predict the photodynamic potency of chemicals. 

There are some recent application of a mixed quantum classical description to investigate quantum dynamics in large CC. The absorbance of a photosynthetic light harvesting complex caused by electronic Frenkel-exciton formation has been considered in Ref. [23], and Refs. [24,25] focused on excitation energy transfer in a DNA double helix strand. In both cases, however, the considerations have been restricted to an approximate description based on the use of... 

Maliwal, B.P., Kusba, J. and Lakowicz, J. R. (1995). Fluorescence energy transfer in one dimension Frequency-domain fluorescence study of DNA-fluorophore complex. Biopolymers, 35,245-255. 

The interaction of biologically active molecules like dyes with nucleic acids is of great interest because such molecules are used as drugs in chemotherapy (e.g. antibiotics, antitumor substances) other ones can induce mutations and tumors. They form intermolecular complexes with nucleic acids. A special class are dyes interacting with DNA by intercalation. These dye molecules are inserted between two base pairs (Fig. 10). A peculiarity of such complexes are base-sequence-dependent effects, for example, the fluorescence behaviour or the energy transfer inside the complex. These processes can depend on the type of base pairs between which the dye molecules are inserted. The quantum yield of fluorescence for some dyes after intercalation is much higher in AT-AT than in AT-GC or GC-GC sequences. 

The favoured excitation of DNA bases (e.g. only, A, T, G or C) via a one-step electronic excitation was performed by Anders 841 and was tested by the interaction of these bases with intercalated dye molecules. In such DNA-dye-complexes energy is transfered from the bases to the dye and from base to base depending on the base sequence (see Chapter 4.2.2). In order to analyze selective effects the energy transfer in the three possible base pair units (Fig. 10) after the favoured excitation of one kind of bases was compared in different complexes. Two tendencies are found ... 

Itaka K, Harada A, Yamasaki Y, Nakamura K, Kawaguchi H, Kataoka K (2004) In situ single cell observation by fluorescence resonance energy transfer reveals fast intra-cytoplasmic delivery and easy release of plasmid DNA complexed with linear polyethylenimine. J Gene Med 6 76-84... 

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