DNA, single- or double-stranded

A multitude of nucleases cleave DNA, single- or double-stranded. They range from the pancreatic digestive enzyme DNase I through specialized nucleases that function during DNA repair and the hundreds of restriction endonucleases that have become so valuable in modern laboratory work. Some nucleases leave a 3 -phosphate ester at a cut end in a DNA chain, while others leave a 5 -phosphate end.824 Many nucleases are dealt with in later chapters. Only a few will be mentioned here. 

DNA-cellulose columns are used to separate DNA-bindlng proteins from non-binding proteins. Preparation of DNA-cellulose consists of mixing cellulose powder with a solution of DNA (single- or double-stranded) and drying the mixture under vacuum. The dried powder is washed to remove unbormd DNA. To couple the DNA more tenaciously to cellulose, the dried powder is resuspended in ethanol and irradiated with ultraviolet light. The procedure chemically couples the two substances. 

PARP binds to DNA surrounding single- or double-strand breaks and attaches polymers of ADP-ribose to itself and other proteins. This increases the negative charge in this area, thus facilitating DNA repair. Payne et al. reported increased poly(ADP-ribose) polymerase (PARP) activity in Jurkat cells treated with sodium deoxycholate. Activation of PARP in colonic cells was similarly reported by Glinghammer et al " following treatment with this bile acid. 

You have been given a sample of nucleic acid, describe two ways you could determine whether it is RNA or DNA and two ways to determine whether it is single- or double-stranded. 

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. 

As we have already mentioned, various methods of immobilization of aptamers onto a solid support are used. In principle these methods are similar to those applied previously for immobilization of single- or double-stranded DNA in genosensors or DNA biosensors for detection of DNA damage (see Pividori et al. [33] for review). The methods of... 

The mobility of DNA, either single or double stranded, through a gel matrix is determined by a number of factors. By comparing the mobility of a test DNA sample to that of a normal control sample it is possible to determine the presence of a sequence alteration in the test sample. The major factors that affect DNA mobility are listed below ... 

Viral genomes consist of RNA or DNA, which can be single- or double-stranded, and may consist of one or more fragments. During viral replication, both DNA and RNA viruses synthesize protein by translation of messenger RNA. The mRNA is then translated by the cell into the viral proteins that will constitute the viral particles. 

Aptamers are single- or double-stranded pieces of DNA or RNA, usually 15-40 bases long. They work by binding target molecules such as proteins with high affinity and specificity. Researchers recognized the medical and pharmaceutical potential of the interaction years ago, which led to the... 

Radiosensitizing effect in hypoxic cells [84, 91, 123—126], in normal tissue [123] toxicity to hypoxic cells [112, 113, 115, 116, 124, 125, 127], toxicity in vivo [128] antimicrobial drugs (effect on single- or double-stranded DNA Escherichia coli) [112] antiprotozoan, antibacterial (Salmonella typhimurium cells [123] and antitrichomonal activity [128, 129]) inhibition of ribonucleotide-reductase [130] structure—activity [115, 116, 127]... 

Poly(ADP-ribose) polymerases are a family of enzymes that catalyze transfer ofmultiple ADP-ribose units onto target proteins, as shown in Figure 8.6. They are DNA-binding proteins with a zinc-finger motif and require nicked DNA (with single- or double-strand breaks) for activity. They are present in the ceU in high concentrations about one molecule of enzyme for each kilobase of DNA (Hayaishi and Ueda, 1977 D Amours et al., 1999). 

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