Template viruses

Viruses are similar to biomolecular templates because the viral capsid is in fact a complex composed of protein subunits. Viruses coupled with nanoparticles can be used as building blocks to form nanoparticle assemblies or virus assemblies of two and three dimensions can be used as templates. Virus is advantageous as a building block because identical viruses can be produced in large amounts at low cost, and nanoparticles templated by viruses generally have a high monodispersity. Viruses may have inherent self-assembly, for example, nanowires mineralized... 

Fig. 18 Composite micelles consisting of antisense oligonucleotides and (a) viral capsids or (b) synthetic polymers, (a) Micelles of DNA amphiphiles loaded with either small hydrophobic compounds top left) or with hydrophilic compounds by hybridization top right) were used to template virus capsid formation at neutral pH. TEM images show micelles incorporated into virus capsids with T = 1 or 2 geometry and an empty capsid formed at pH 5.0 as control inset). Scale bars 40 nm. (b) Representation of a blend micelle. Diblock DNA copolymer PPO-h-DNA was mixed with a triblock copolymer Pluronic (PEO-h-PPO-h-PEO) composed of the same hydrophobic block, PPO [21] (figure reproduced with permission of Royal Society of Chemistry)...

The viruses responsible for AIDS are human immunodeficiency virus 1 and 2 (HIV 1 and HIV 2) Both are retroviruses, meaning that their genetic material is RNA rather than DNA HI Vs require a host cell to reproduce and the hosts m humans are the T4 lymphocytes which are the cells primarily responsible for inducing the immune system to respond when provoked The HIV penetrates the cell wall of a T4 lymphocyte and deposits both its RNA and an enzyme called reverse transcriptase inside There the reverse transcriptase catalyzes the formation of a DNA strand that is complementary to the viral RNA The transcribed DNA then serves as the template from which the host lymphocyte produces copies of the virus which then leave the host to infect other T4 cells In the course of HIV reproduction the ability of the T4 lymphocyte to reproduce Itself IS compromised As the number of T4 cells decrease so does the body s ability to combat infections... 

Crystal structures of the NS5B polymerase alone and in complexes with nucleotide substrates have been solved and applied to discovery programs (Ago et al. 1999 Bressanelli et al. 2002 Bressanelli et al. 1999 Lesburg et al. 1999 O Farrell et al. 2003). From these studies, HCV polymerase reveals a three-dimensional structure that resembles aright hand with characteristic fingers, palm, and thumb domain, similar to the architectures of the RNA polymerases of other viruses. However, none of these experimental structures contained the ternary initiation complex with nu-cleotide/primer/template, as obtained with HIV RT. Accordingly, HCV initiation models have been built using data from other viral systems in efforts to explain SAR (Kozlov et al. 2006 Yan et al. 2007). 

After the virus has attached to CD4 and chemokine receptors, another viral glycoprotein (gp41) assists with viral fusion to the cell and internalization of the viral contents. The viral contents include single-stranded RNA, an RNA-dependent DNA polymerase (also known as reverse transcriptase), and other enzymes. Using the single-stranded viral RNA as a template, reverse transcriptase synthesizes a complementary strand of DNA. The single-stranded viral RNA is removed from the newly formed DNA strand by ribonuclease H, and reverse transcriptase completes the synthesis of double-stranded DNA. The... 

Since nucleic acids and enzymes play such a large role in chromosome replication during mitosis, a considerable amount of research has been conducted in this area to control viruses. On the molecular level, analogues of nucleic acids are capable of forming complexes with adenine, cytosine, uracil, thymine, and guanine. Through complexation, these nucleic acid analogues are potential inhibitors of biosyntheses that require nucleic acids as templates. 

The antiviral activity spectrum of the ddN analogues should, in principle, extend to all retroviruses as well as hepadnaviruses [i.e., hepatitis B virus (HBV)], since HBV, like retroviruses, replicates through an RNA template-driven RT process. Indeed, various ddN analogues (particularly, the L-enantiomeric forms 3TC, FTC, and L-DDC) have been shown to inhibit HBV replication [36-38]. Consequently, 3TC is, at present, pursued as a potential drug candidate for the treatment of both HIV and HBV infections. 

Virus messenger RNA In order for the new virus-specific proteins to be made from the virus genome, it is necessary for new virus-specific RNA molecules to be made. Exactly how the virus brings about new mRNA synthesis depends upon the type of virus, and especially upon whether its genetic material is RNA or DNA, and whether it is single-stranded or double-stranded. Which copy is read into mRNA depends upon the location of the appropriate promoter, since the promoter points the direction that the RNA polymerase will follow. In cells (uninfected with virus) all mRNA is made on the DNA template, but with RNA viruses the situation is obviously different. 

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. 

As noted, the viral RNA is of the plus (+) sense. Replicase synthesizes RNA of minus (-) sense using the infecting RNA as template. After minus RNA has been synthesized, plus RNA is made from this minus RNA. The newly made plus RNA strands now serve as messengers for virus protein synthesis. The gene for the maturation protein is at the 5 end of the RNA. Translation of the gene coding for the maturation protein (needed in only one copy per virus particle), occurs only from the newly formed plus-strand RNA as... 

Subsequently, similar experiments were done with viral nucleic acids. The pure viral nucleic acid, when added to cells, led to the synthesis of complete virus particles the protein coat was not required. This process is called transfection. More recently, DNA has been used in cell-free extracts to program the synthesis of RNA that functions as the template for the synthesis of proteins characteristic of the DNA... 

This is the enzyme responsible for the synthesis of mitochondrial DNA and the DNA of some viruses, such as adenoviruses. Polymerase -y is very large and consists of a tetramer of identical oligomers, each having a molecular weight of 47,000. Synthetic ribonucleotides are very effective templates in the laboratory, but this mitochondrial enzyme differs from reverse transcriptase in that natural RNAs are poor templates. 

Reverse transcriptase is an enzyme isolated from viruses that contain a genome that is RNA. This viral enzyme makes DNA using RNA as a template. 

Viral DNA is integrated into the chromosomal DNA of male and female wasps. The virus also exists in an episomal form in female tissues and even in male wasps, though to a much reduced level (4). It is not known whether the linear or the episomal forms of the virus are the templates for viral replication. 

Replication of Viral Nucleic Acid. In addition to producing molecules for the formation of new capsids, the virus must replicate its nucleic acid to provide genetic material for packaging into the capsids. The way in which this is done might vary. In positive-sense, single-strand RNA viruses, a polymerase translated from viral mRNA produces negative-sense RNA from the positive-sense template which is then repeatedly transcribed into more positive strands. 

The next stage is to ensure that the recombinant DNA molecule is copied by the enzymes which s)mthesize nucleic acids. These DNA and RNA polymerases synthesize an exact copy of either DNA or RNA from a pre-existing molecule. In this way the DNA polymerase duplicates the chromosome before each cell division such that each daughter cell will have a complete set of genetic instructions which are then passed to the newly formed RNA by RNA polymerase. While both DNA and RNA polymerase require a preformed DNA template, some viruses (such as HIV) have an RNA genome. To duplicate that genome, and incorporate it into a bacterial or mammalian cell, the viruses encode a reverse transcriptase enzyme which produces a DNA copy from an RNA template. 

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