Nucleic acid polymerases

Short replication cycles that may be completed within a few hours, a large amount of viral progeny from one infected host-cell, as well as the general inaccuracy of viral nucleic acid polymerases result in an evolution occurring in fast motion, allowing rapid adaptation of viruses to selective pressures (see chapter by Boucher and Nijhius, this volume). Generalizing, it can be stated that any effective antiviral therapy will lead to the occurrence of resistance mutations. A well studied example... 

The nonnucleoside reverse transcriptase inhibitors (NNRTIs), used in the treatment of AIDS, provide interesting examples of clinically relevant noncompetitive inhibitors. The causative agent of AIDS, HIV, belongs to a virus family that relies on an RNA-based genetic system. Replication of the vims requires reverse transcription of the viral genomic RNA into DNA, which is then incorporated into the genome of the infected host cell. Reverse transcription is catalyzed by a virally encoded nucleic acid polymerase, known as reverse transcriptase (RT). This enzyme is critical for viral replication inhibition of HIV RT is therefore an effective mechanism for abrogating infection in patients. 

Enzymes in viruses We have stated that virus particles do not carry out metabolic processes. Outside of a host cell, a virus particle is metabolically inert. However, some viruses do contain enzymes which play roles in the infectious process. For instance, many viruses contain their own nucleic acid polymerases which transcribe the viral nucleic acid into messenger RNA once the infection process has begun. The retroviruses are RNA viruses which replicate inside the cell as DNA intermediates. These viruses possess an enzyme, an RNA-dependent DNA popo called reverse transcriptase, which transcribes the information in the incoming RNA into a DNA intermediate. It should be noted that reverse transcriptase is unique to the retroviruses and is not found in any other viruses or in cells. 

The enzymes that synthesise RNA and DNA are known as nucleic acid polymerases. They are classified as nucleotidyl transferases (Chapter 3). The basic reaction can be represented as follows ... 

Although some depolymerases act processively in cleaving their polymeric substrates, others act by what can be described as multiple attack which results in nonselective scission or random scission. The analysis of cleavage products during the course of enzyme-catalyzed depolymerization can provide important clues about the nature of the reaction. With random scission, the rate of bond scission must be proportional to the total number of unbroken bonds present in the solution. Thomas measured the rate of base addition in a pH-Stat (a device with an automated feedback servomotor that expels ti-trant from a syringe to maintain pH) to follow the kinetics of DNA bond scission by DNase. The number of bonds cleaved was linear with time, and this was indicative of random scission. In other cases, one may apply the template challenge method to assess the processivity of nucleic acid polymerases. See Processivity... 

A procedure used to assess the processivity of nucleic acid polymerases In this method, the investigator perturbs the polymerization reaction proceeding on one template by the addition of a new template. See Processivity... 

Sethi, V. S. 1976. Inhibition of mammalian and oncornavirus nucleic acid polymerase activities by alkoxybenzophenantridine alkaloids. Cancer Research, 36 2390-2395. 

Synthesis of early regulatory proteins (nucleic acid polymerases) used to aid nucleic acid synthesis... 

Several other major classes of enzymes, among them the nucleic acid polymerases, activate ATP (and other NTPs) in a completely different manner. Similar to transphos-phoiylation enzymes, they utilize two metal ions for catalysis. However, steric interactions are purposely employed in order to reverse the preferred binding situation. A MaMp y motif is generated which weakens the P —O—P,5 linkage This allows a nucleoside monophosphate group to be transferred (under liberation of PPi), a process which is essential in the biosynthesis of DNA and RNA sequences. 

Viral replication consists of several steps (Figure 49-1) (1) attachment of the vims to receptors on the host cell surface (2) entry of the virus through the host cell membrane (3) uncoating of viral nucleic acid (4) synthesis of early regulatory proteins, eg, nucleic acid polymerases (5) synthesis of new viral RNA or DNA (6) synthesis of late, structural proteins (7) assembly (maturation) of viral particles and (8) release from the cell. Antiviral agents can potentially target any of these steps. 

In many cases nucleic acid polymerases are zinc-dependent enzymes. Hutchinson et al.45 have drawn upon the use of phosphonoacetic acid and phosphonoformic acid and introduced mono- and bis-thiopyrophosphate. They propose that the inhibition of influenza virus occurs by inhibition of RNA transcriptase45. By using 31P-NMR they... 

Ono T, Scalf M, Smith LM. 2 -Fluoro modified nucleic acids polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionizationmass spectrometry. Nucleic Acids Res 1997 25 4581-4588. 

Exploring the Capabilities of Nucleic Acid Polymerases by Use of Directed Evolution... 

This book, Highlights in Bioorganic Chemistry, describes exciting recent advances in all the aspects of the field. Part 1 deals with Biomolecules and their Conformations. Chapters on the natural chemistry of RNA, of / -amino acids, on binding to DNA, on nucleic acid polymerases, on ribozymes and proteases, are concerned with using chemistry tools to help us understand biological chemistry. Part 2 deals with Non-Covalent Intermolecular Interactions. Here there is work on... 

Riva, S., Fietta, A. Silvestri, L.G. Mechanism of action of a rifamycin dervative (AF/013) which is active on the nucleic acid polymerases insensitive to rifampicin. Biochim. Biophys. Acta 49, 1263 (1972)... 

Some typical biological interactions, frequently used in affinity chromatography are enzyme to substrate analogue, inhibitor, or cofactor antibody to antigen, virus, or cell lectin to polysaccharide, glycoprotein, cell surface receptor, or cell nucleic acid to complementary base sequence, histones, or nucleic acid polymerase hormone or vitamin to receptor, or carrier protein glutathione to glutathione-S-transferase (GST) or GST fusion proteins and metal ions to poly (His) fusion proteins, or native proteins with histidine, cysteine and/or tryptophan residues on their surfaces. 

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