Enzymes acting on DNA

FRET probes based on DNA are strong potential tools to investigate cellular processes where nucleases and a set of enzymes acting on DNA play a role. Most probes of this class are not particularly... 

Figure 7.2 Enzymes acting on DNA breaks. FEN-1, 3 -exonuclease (3 -Exo.), DNA polymerases (DNA pol.) and DNA ligases act on single-strand DNA breaks (SSB). Double-strand DNA breaks (DSB) are also susceptible to FEN-1 and 3 -Exo. PARP-1 is capable of binding to SSB and DSB. In addition, PARP-1 has a binding affinity for RNA stem-loops.

The in vivo characteristics of DNA are important not only to rationalize the existence of functional DNA at high temperature, but also for studying hyper-thermophilic enzymes acting on DNA substrates in vitro. When using a topologically open DNA substrate, the upper temperature of the reaction with a... 

A number of other enzymes that act on DNA and RNA are an important part of recombinant DNA tech-nology. Many of these are referred to in this and subsequent chapters (Table 40-3). 

Fig. 4.14. The polymers (X) acting on DNA are transcription factors activated frequently by small molecules or ions with a wide variety of time constants. E is an enzyme. Instructions are passed to a polymer (X) or directly to DNA. Energy requirements not shown (see also Fig. 3.13). Note. All these cycles are element neutral, non-polluting.

Deoxyribonuclease (pyrimidine dimer) [EC 3.1.25.1] catalyzes the endonucleolytic hydrolysis of a bond in DNA near pyrimidine dimers to generate products with 5 -phosphates. The enzyme acts on damaged strands of DNA, 5 from the damaged site. 

A host of enzymes, which are described elsewhere in the book, act on DNA and RNA. They include hydrolytic nucleases, methyltransferases, polymerases, topoisomerases, and enzymes involved in repair of damaged DNA and in modifications of either DNA or RNA. While most of these enzymes are apparently proteins, a surprising number are ribozymes, which consist of RNA or are RNA-protein complexes in which the RNA has catalytic activity. 

Bacterial Reverse Transcriptase Catalyzes Synthesis of a DNA-RNA Molecule Telomerase Facilitates Replication at the Ends of Eukaryotic Chromosomes Other Enzymes That Act on DNA... 

Many enzymes that act on DNA are involved in processes other than DNA synthesis. They include DNA repair enzymes, DNA degradation enzymes, and DNA recombination enzymes. 

DNA repair is one of the fundamental processes essential for the survival of cells. In fact, disruption of DNA repair often leaves damaged DNA bases on DNA strands, leading to cytotoxicity or carcinogenesis, and consequently cancer. Repair of such damaged DNA bases often occurs through the induction of DNA breaks, and thus, most of the DNA repair enzymes act at DNA breaks. Therefore, it is of the utmost importance to unravel the mechanisms involved in DNA repair enzymes in the stability of oligonucleic acids, which often contain DNA break ends. 

Clearly, designing biologically stable oligonucleic acids that would be resistant to these repair enzymes would improve the therapeutic effect of oligonucleic acids. This chapter focuses on the characteristics of these enzymes which act on DNA breaks. 

Synthetic DNA molecules as substrates for enzymes acting on tRNAs 90CRV1327. 

Synthesis of Thymidine nucleotides first requires deoxyribonucleotide synthesis. The enzyme responsible for this step is Ribonucleotide Reductase. This enzyme acts on oxynucleotides in their diphosphate form. Thioredoxin, a small protein, is oxidized as the 2 hydroxyl group on the ribose ring is reduced. Oxidized Thioredoxin (S-S) is then reduced by FADH2 and NADPH. The products are the respective deoxynucleotide diphosphates which are further phosphorylated and then used for DNA synthesis. 

Although complexes of DNA and histones form the nucleosomal substructures of chromatin, other types of proteins are also associated with DNA in the nucleus. These proteins were given the unimaginative name of non-histone chromosomal proteins. The cells of different tissues contain different amounts and types of these proteins, which include enzymes that act on DNA and factors that regulate transcription. 

---