Difference between revisions of "Virus"

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==Definition==
 
==Definition==
  
Polymerase chain reaction (PCR) is a technique to massively replicate short sequences of DNA. Developed in 1983, it has become extremely valuable in molecular biology, especially in terms of being able to detect small amount of a gene of interest by amplifying it to detectable quantities. This technique is based on thermal cycling and takes advantage of DNA replication machinery already found in the cell. This work resulted in the 1993 Nobel Prize in Chemistry.
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Viruses are very small biological constructs which contain either DNA or RNA. As they lack cellular machinery and rely on an infected cell to actually replicate their viral genomes, there is debate as to whether viruses should be considered "living." A virus consists of three main parts.
  
The figure below is a schematic of how PCR works.
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1) Genetic Material - This can be either DNA or RNA. Upon a viral infection, the virus inserts its genome into the host cell, where it is processed by various polymerases.
  
[[image:800px-Phage injecting its genome into bacterial cell.jpg|thumb|500px|right|Image Courtesy Graham Colm, Sept 20, 2008]]
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2) Protein capsid - this is a simple protein "shell" which envelops the genetic material and gives the virus structure.
  
There are six main steps in PCR:
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3) Coat -  there may exist certain proteins or lipids on the surface of the virus that identify the virus and aid in receptor binding to the cell surface. These surface modifications to the virus can induce an immune response in the host organism.
  
1) Initializing - This step may or may not be included, depending on the types of enzymes, but it involves heating the DNA of interest to just under 100 C.
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The figure below is a schematic of a bacteriophage (virus that infects bacteria) inserting its DNA .
  
2) Denaturation - This step heats the DNA to the extent that the two complementary strands dissociate, leaving only single-stranded DNA.
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[[image:800px-Phage injecting its genome into bacterial cell.jpg|thumb|500px|right|Image Courtesy Graham Colm, Sept 20, 2008]]
  
3) Annealing - This step attaches the primers to the single-stranded DNA. Primers are the short DNA sequences that will act as the building blocks for the new complementary strand of DNA. These are pre-made and are heated to just under their melting temperature.
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==Applications/Connections to Soft Matter==
  
4) Elongation - In this step, the temperature is set to the optimum for the activity of DNA polymerase, which builds off of the primer and attaches free nucleotides to the growing complementary DNA strand.  
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In medicine, viruses are modified and then used as vaccines, where they elicit an immune response and confer immunological "memory" without being infectious. In molecular biology, viruses are used as a means of delivery for genetic material. There are currently a number of clinical trials using viruses as the delivery vehicle for gene therapy.
  
5) Secondary elongation - This step is similar to the previous and just ensures that all of the complementary strands have been completed.
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There is growing interest, however, in viruses as a nanotechnology building block.  
 
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6) Repeat - Now that the amount of DNA has been doubled, the process can be repeated, breaking apart the strands and again producing complementary strands.
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==Applications/Connections to Soft Matter==
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Not only have PCR thermal cyclers become common in molecular biology labs, but they now have an increasing commercial importance. PCR can be used in a host of genetic tests and will only become more important as the function of specific genes is further elucidated from the sequencing revolution. There is significant effor to create lab-on-a-chip versions of PCR, that can perform massively-parallel replication of various genes. This problem is mainly one of microfluidic large-scale-integration, which has been revolutionized by Stephen Quake at Stanford.  
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==References==
 
==References==
  
Bartlett, J. M. S.; Stirling, D. (2003). "A Short History of the Polymerase Chain Reaction". PCR Protocols. 226. pp. 3–6.
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Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & And Walter, P. (2008). Molecular Biology of the Cell. (Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, & P. Walter, Eds.) Garland Press.  
 
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Saiki, R.; Gelfand, D.; Stoffel, S.; Scharf, S.; Higuchi, R.; Horn, G.; Mullis, K.; Erlich, H. (1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science 239 (4839): 487–491.
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White, R. A., Blainey, P. C., Fan, H. C., & Quake, S. R. (2008). Digital PCR provides sensitive and absolute calibration for high throughput sequencing. BMC Genomics, 10(1), 116.
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Blum AS, Soto CM, Wilson CD et al. (2005). "An Engineered Virus as a Scaffold for Three-Dimensional Self-Assembly on the Nanoscale". Small 7: 702.
  
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Neltner, B., Peddie, B., Xu, A., Doenlen, W., Durand, K., Yun, D. S., Speakman, S., et al. (2010). Production of hydrogen using nanocrystalline protein-templated catalysts on m13 phage. ACS nano, 4(6), 3227-3235.
  
  

Revision as of 18:54, 6 December 2011

Prepared by Max Darnell - AP225 Fall 2011

Definition

Viruses are very small biological constructs which contain either DNA or RNA. As they lack cellular machinery and rely on an infected cell to actually replicate their viral genomes, there is debate as to whether viruses should be considered "living." A virus consists of three main parts.

1) Genetic Material - This can be either DNA or RNA. Upon a viral infection, the virus inserts its genome into the host cell, where it is processed by various polymerases.

2) Protein capsid - this is a simple protein "shell" which envelops the genetic material and gives the virus structure.

3) Coat - there may exist certain proteins or lipids on the surface of the virus that identify the virus and aid in receptor binding to the cell surface. These surface modifications to the virus can induce an immune response in the host organism.

The figure below is a schematic of a bacteriophage (virus that infects bacteria) inserting its DNA .

Image Courtesy Graham Colm, Sept 20, 2008

Applications/Connections to Soft Matter

In medicine, viruses are modified and then used as vaccines, where they elicit an immune response and confer immunological "memory" without being infectious. In molecular biology, viruses are used as a means of delivery for genetic material. There are currently a number of clinical trials using viruses as the delivery vehicle for gene therapy.

There is growing interest, however, in viruses as a nanotechnology building block.

References

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & And Walter, P. (2008). Molecular Biology of the Cell. (Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, & P. Walter, Eds.) Garland Press.

Blum AS, Soto CM, Wilson CD et al. (2005). "An Engineered Virus as a Scaffold for Three-Dimensional Self-Assembly on the Nanoscale". Small 7: 702.

Neltner, B., Peddie, B., Xu, A., Doenlen, W., Durand, K., Yun, D. S., Speakman, S., et al. (2010). Production of hydrogen using nanocrystalline protein-templated catalysts on m13 phage. ACS nano, 4(6), 3227-3235.


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