Template-directed DNA synthesis

Minetti, A. A., Rem eta, D., Miller, H., Gelfand, C.A., Plum, G.E., Grollman, A.P., and Breslauer, K.J. (2003) The thermodynamics of template-directed DNA synthesis base insertion and extension enthalpies. Proc. Natl Acad. 

However, in the case of template-directed DNA synthesis, the situation seems more complicated [33], as is also most likely the case for many other situations. Hence, it is fair to state that combined / and D measurements must be considered critical in order to arrive at a proper interpretation of kinetic data. 

Fig. 3. Replication of telomeric DNA. Telomerase has a bound RNA molecule that is used as template to direct DNA synthesis and hence extension of the ends of chromosomal DNA.

Figure 22.20. Models of two damage tolerance mechanisms. At the lesion site, template switching (the left pathway) uses the newly synthesized daughter strand as the template for DNA synthesis, thus, bypassing the lesion in an error-free manner. In contrast, translesion synthesis (the right pathway) directly copies the damaged site on the template. Consequently, mutations, shown as a square, are often generated opposite the lesion.

Fig, 5. Amplified production of silicatein protein from recombinant DNA cloned in bacteria. DNA coding for the silicatein a protein was integrated enzymically into a double-stranded circular DNA vector molecule to produce a recombinant DNA. When introduced into bacteria, the recombinant DNA is replicated by intracellular enzymes to produce many copies in each cell. These DNA molecules serve as templates, directing the synthesis of the silicatein protein they encode. Rapid reproduction of the bacteria greatly amplifies this synthesis. 

Cellular protein biosynthesis involves the following steps. One strand of double-stranded DNA serves as a template strand for the synthesis of a complementary single-stranded messenger ribonucleic acid (mRNA) in a process called transcription. This mRNA in turn serves as a template to direct the synthesis of the protein in a process called translation. The codons of the mRNA are read sequentially by transfer RNA (tRNA) molecules, which bind specifically to the mRNA via triplets of nucleotides that are complementary to the particular codon, called an anticodon. Protein synthesis occurs on a ribosome, a complex consisting of more than 50 different proteins and several stmctural RNA molecules, which moves along the mRNA and mediates the binding of the tRNA molecules and the formation of the nascent peptide chain. The tRNA molecule carries an activated form of the specific amino acid to the ribosome where it is added to the end of the growing peptide chain. There is at least one tRNA for each amino acid. 

The genetic information within the nucleotide sequence of DNA is transcribed in the nucleus into the specific nucleotide sequence of an RNA molecule. The sequence of nucleotides in the RNA transcript is complementary to the nucleotide sequence of the template strand of its gene in accordance with the base-pairing rules. Several different classes of RNA combine to direct the synthesis of proteins. 

The head-to-tail-coupling reactions described above are potentially useful in the design of dynamic combinatorial libraries. Features of these reactions include the rapid and reversible formation of carbon-carbon bonds, multifunctional ene-imine building blocks, and formation of stereo centers upon ene-imine linkage. Support for template-directed synthesis utilizing ene-imine building blocks is the formation of a poly ene-imine species that could recognize 3 -GGA-5 sequences of DNA.48 It is noteworthy that some polyene-imines are helical and could form a triple helix with DNA. 

A virus-specific RNA RNA polymerase is needed, since the cell RNA polymerase will generally not copy double-stranded RNA (and ribosomes are not able to translate double-stranded RNA either). A wide variety of modes of viral mRNA synthesis are outlined in Figure. By convention, the chemical sense of the mRNA is considered to be of the plus (+) configuration. The sense of the viral genome nucleic acid is then indicated by a plus if it is the same as the mRNA and a minus if it is of oppposite sense. If the virus has double-stranded DNA (ds DNA), then mRNA synthesis can proceed directly as in uninfected cells. However, if the virus has a singlestranded DNA (ss DNA), then it is first converted to ds DNA and the latter serves as the template for mRNA synthesis with the cell RNA polymerase. 

If the virus has double-stranded RNA (ds RNA), this RNA serves as a template in a manner analogous to DNA. There are three classes of viruses with ss RNA and they differ in the mechanism by which mRNA is synthesized. In the simplest case, the incoming viral RNA is the plus sense and hence serves directly as mRNA, and copies of this viral RNA are also copied to make further mRNA molecules. In another class, the viral RNA has a minus (-) sense. In such viruses a copy is made (plus sense) and this copy becomes the mRNA. In the case of the retroviruses (causal agents of certain kinds of cancers and AIDS), a new phenomenon called reverse transcription is seen, in which virion ss RNA is copied to a double-stranded DNA (through a ss DNA intermediate) and the ds DNA then serves as the template for mRNA synthesis (thus ss RNA ss DNA ds DNA). Retrovirus replication is of unusual interest and complexity. 

Reverse transcriptase is an RNA-dependent DNA polymerase that requires an RNA template to direct the synthesis of new DNA. Retroviruses, most notably HIV, use this enzyme to repHcate their RNA genomes. DNA synthesis by reverse transcriptase in retroviruses can be inhibited by AZT. ddC, and ddl. 

DNA-directed DNA polymerases [EC 2.7.7.7], also called DNA nucleotidyltransferases (DNA-directed), are enzymes that catalyze the DNA template-directed extension of the 3 -end of a nucleic acid strand one nucleotide at a time. Thus, n deoxynucleoside triphosphates produce n pyrophosphate (or, diphosphate) ions and DNA . This enzyme cannot initiate the synthesis of a polymeric chain de novo it requires a primer which may be DNA or RNA. RNA-directed DNA polymerases [EC 2.7.7.49], also referred to as reverse transcriptases, DNA nucleotidyltransferases (RNA-directed), and revertases, are enzymes that catalyze the RNA template-directed extension of the 3 -end of a nucleic acid strand one nucleotide at a time. Thus, n deoxynucleoside triphosphates produce n pyrophosphate (or, diphosphate) ions and DNA . As was the case above, this enzyme cannot initiate the synthesis of a polymeric chain de novo it requires a primer which may be DNA or RNA. 

Prokaryotic genes encode protein sequences directly with no intervening noncoding DNA, so that mRNA transcripts serve as direct templates for protein synthesis. 

Our discussion of RNA synthesis begins with a comparison between transcription and DNA replication (Chapter 25). Transcription resembles replication in its fundamental chemical mechanism, its polarity (direction of synthesis), and its use of a template. And like replication, transcription has initiation, elongation, and termination phases—though in the literature on transcription, initiation is further divided into discrete phases of DNA binding and initiation of RNA synthesis. Transcription differs from replication in that it does not require a primer and, generally, involves only limited segments of a DNA molecule. Additionally, within transcribed segments only one DNA strand serves as a template. 

Although the existence of this enzyme may not be surprising, the mechanism by which it acts is remarkable and unprecedented. Telomerase, like some other enzymes described in this chapter, contains both RNA and protein components. The RNA component is about 150 nucleotides long and contains about 1.5 copies of the appropriate CyKx telomere repeat. This region of the RNA acts as a template for synthesis of the T -G strand of the telomere. Telomerase thereby acts as a cellular reverse transcriptase that provides the active site for RNA-dependent DNA synthesis. Unlike retroviral reverse transcriptases, telomerase copies only a small segment of RNA that it carries within itself. Telomere synthesis requires the 3 end of a chromosome as primer and proceeds in the usual 5 —>3 direction. Having syn-... 

A sample of double-stranded DNA is denatured. One of the resulting single strands is used as a template to direct the synthesis of a complementary strand of radioactive DNA using a suitable DNA polymerase. The "Klenow fragment" of E. coli, DNA polymerase I, reverse transcriptase from a retrovirus, bacteriophage T7 DNA polymerase, Taq polymerase, and specially engineered enzymes produced from cloned genes have all been used. 

Several antibiotics are also cytotoxic and combine with DNA. blocking its template activity in directing the synthesis of messenger RNA. 

The DNA does not transfer its genetic information directly to protein. Rather, this information passes through an intermediary, the messenger RNA (mRNA). The mRNA is made on a DNA template in the nucleus of a eukaryotic cell and then passes into the cytoplasm, where it serves in turn as a template for the synthesis of the polypeptide chain. The overall process of information transfer from DNA to mRNA (transcription) and from mRNA to protein (translation) is depicted in figure 1.22. 

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