Psoralen-DNA

Pearlman et al. (196) built a model of a psoralen-DNA covalently crosslinked complex based on the crystal structure of a thymidine-psoralen-thymine complex, using computer graphics and molecular mechanics calcu-... 

The psoralen-DNA photoreaction. Characterization of the monoaddition products from 8-methoxypsoralen and 4,5 ,8-trimethylpsoralen. Biochemistry 21 861-871. 

Modified oligonucleotides can be used to cross-link DNA sequences via a reactive group tethered to an oligonucleotide. When irradiated with uv light, psoralens (31) reacts with thymine bases, and the reaction yields a cross-link if the thymine residues are adjacent to each other on opposite strands. Psoralen linked to oligonucleotides have been shown to induce site-specific cross-links in vitro (51). 

Psoralens can react by two different routes upon photoactivation (Parsons, 1980 Pathak, 1984). The first route is through the well-known photoreaction mechanism that principally involves intercalation within double-stranded DNA or RNA with the formation of adducts with adjacent thymine bases. The furan-side and pyrone-side rings in psoralen both can form cycloaddition products with the 5,6-double bond of thymine to create a crosslink between two DNA strands (Reaction 57) or to a lesser extent, within double-strand regions of RNA. 

Psoralen-PEOj-Biotin has been used to label double-stranded DNA for detection using (strept)avidin reagents (Henriksen et al., 1991 Wygrecka et al., 2007). The psoralen photoreactive group provides better insertion yields than typical phenyl azide-based systems, such as the standard photobiotin probe discussed previously in this section. 

Add a quantity of the Psoralen-PE03-biotin solution to the DNA solution to result in a final concentration of 200 pM. Mix well. 

Figure 11.15 The photoreactive compound psoralen-PEC>3-biotin can intercalate into double stranded DNA or RNA segments and covalently link to thymine bases via a photoreaction process.

Oser, A., Roth, W.K., and Valet, G. (1988) Sensitive non-radioactive dot-blot hybridization using DNA probes labeled with chelate group substituted psoralen and quantitative detection by europium ion fluorescence. Nucleic Acids Res. 16, 1181-1196. 

In this review, we present an introduction to the theory, and exemplify the wide range of problems that can be addressed with some illustrative results from our work in the field of ah initio drug design. The problems addressed are those of activation and DNA binding of the antitumor drug cis-platin (PtCl2(NH3)2), and basic spectrometric data from a family of drugs known as psoralens. 

In the oxygen-independent Type III reactions the excited/sensi-tized psoralen donates its excitation energy directly to, or reacts with, the target compound. This occurs if the substrate and the target compound (e.g., DNA) are already in close proximity or intercalated. The reactions will proceed very rapidly via the excited singlet state, and are, typically, cyclization reactions or electron-transfer between the sensitizer and the target. In addition, the psoralen can be ionized, either directly or via the excited state, and react with the target compound in the form of a radical cation. Furocoumarins are also employed in treatment of cutaneous T-cell lymphoma and some infections connected with AIDS, by so-called photopheresis processes [71, 74-76]. In this case, peripheral blood is exposed to, e.g., photoactivated (sensitized) 8-methoxypsoralen (8-MOP) in an extracorporeal flow system. This... 

Oxygen-free reactions of psoralens, when in close proximity to the target, proceed via the first excited states in which the 3,4-and the 4, 5 7r-bonds of the pyrone and furan moieties, respectively, can undergo C4-cyclization reactions with, e.g., unsaturated bonds of lipids, or the C5=C6 double bonds of thymine in DNA. In reactions with DNA the psoralen is believed to intercalate with DNA in the dark. Subsequent irradiation at 400 nm usually leads to furan-side 4, 5 -monoadduct formation, whereas irradiation at 350 nm increases the formation of crosslinks in which the furan and pyrone rings form C4 cycloadducts to thymines on opposite strands [95], Subsequent irradiation of the 4, 5 -monoadducts at 350 nm leads to formation of crosslinks and conversion into pyrone-side 3,4-monoadducts. Shorter wave-... 

Psoralens must be photoactivated by long-wavelength ultraviolet light in the range of 320-400 nm (ultraviolet A [UVA]) to produce a beneficial effect. Psoralens intercalate with DNA and, with subsequent UVA irradiation, cyclobutane adducts are formed with pyrimidine bases. Both monofunctional and bifunctional adducts may be formed, the latter causing interstrand cross-links. These DNA photoproducts may inhibit DNA synthesis. The major long-term risks of psoralen photochemotherapy are cataracts and skin cancer. 

Photochemically reactive molecules have often been used as labels for specific sites in proteins and nucleic acids. Psoralen derivatives serve as relatively nonspecific photochemically activated crosslinking agents for DNA and double-stranded RNA.195 Aryl azides are converted by light to aryl nitrenes, which react in a variety of ways including insertion into C-H bonds (Eq. 23-27).200 201 In some cases UV irradiation can be used to join natural substrates to enzymes or hormones to receptors. For example, progesterone, testosterone, and other steroids have been used for direct photoaffinity labeling of their receptors.202 Synthetic benzophenones have also been used widely as photoactivated probes.203... 

Chemically modified DNAs can also be used as hybridization probes, provided that the modification does not interfere with the formation of hybrid DNA molecules. A psoralen biotin label has also been developed. Psoralen is a photoactivable agent that can intercalates into single- or double-stranded nucleic acids. On irradiation at 365 nm, it will covalently bind to the probes. This labeling reaction is simple and straightforward. However, the reagents for labeling and detection are only available in a kit format. 

The facility of these reactions was attributed to the favorable geometry of the allenyl ether for intramolecular Diels-Alder reactions, compared with that of the propargyl ether. These methodologies were used in a new synthesis of a naturally occurring furocoumarin, psoralen 308, which is of interest because of its unique photoreactions with DNA and its utility as a phototherapeutic agent. 

For discussion of chromosome sorting by optical zapping, see Roslaniec MC, Reynolds RJ, Martin JC, et al. (1996). Advances in flow cytogenetics Progress in the development of a high speed optical chromosome sorter based on photochemical adduct formation between psoralens and chromosomal DNA. NATO Advanced Studies Series, Flow and Image Cytometry 95 104-114. 

The last major group of reagents are the psoralens which have earlier been exploited to form crosslinks in double-stranded DNA and RNA (Song and Tapley, 1979 Parsons, 1980 Hearst, 1981). Reaction occurs primarily by 2 + 2 addition to pyrimidines but also with purines (Fig. 2.9). 

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