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User:AjoneWiki/sandbox

< User:AjoneWiki

Welcome to my Sandbox

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Summary of Wikipedia's five pillars

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  • Wikipedia is an undiscriminating information database
  • Wikipedia thrives to be unbiased
  • Wikipedia is opensource to the public 
  • Wikipedia is an editor community
  • Wikipedia is not perfect but flexible and evolving[1]


Summary of characteristics of target article

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  • Topic should be well known but not well covered on Wikipedia yet
  • Article should be in "stub" form, only a few sentences or paragraphs to allow for additional information
  • No other article under different title excists[2]


Practice Citations

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In agricultural biotechnology, desired traits in potential seed product are often verified and quantified by qPCR [3] . Even though a variety of commercially available and in house DNA extraction methods exist, routinely a variety of additives have to be used to purify samples for analysis [3] [4].

On example is cotton tissue, which contains pcr amplification inhibitors, which are known to complicate DNA extraction and increases the overall processing time[3][4]. Alternative tissue sampling methods, such as root tissue sampling, rather than traditional leave tissue, has shown decreased amounts of pcr inhibiting compounds easing DNA extraction and improving overall DNA quality for qPCR[4].

Complementarity

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Article Outline

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Introduction

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Principle of DNA base pair complementarity

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Left: the nucleotide base pairs that can form in double-stranded DNA. Between A and T there are two hydrogen bonds, while there are three between C and G. Right: two complementary strands of DNA.

Four nucleobases are involved in DNA complementarity: adenine, thymine (uracil in RNA), guanine and cytosine[5].

Nucleic Acid Nucleobases Base complement
dsDNA adenine(A), thymine(T), guanine(G), cytosine(C) A:T , G:C
dsRNA adenine(A), uracil(U), guanine(G), cytosine(C) A:U , G:C

The nucleobases are held together by hydrogen bonding, which is the basis of complementarity in DNA. The base complement A:T shares two hydrogen bonds, while the base pair G:C has three hydrogen bonds, respectively[5].

Complementarity in ds DNA/RNA

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A complementary strand of DNA or RNA, respectively, may be constructed based on nucleobase complementarity. The spacial geometry of each base pair, A:T vs. G:C, is equivalent to each other, enabling double helix formation. Hydrogen bonding between the nucleobases stabilizes the double helix.

For example, the complementary strand of the DNA sequence

5' A G T C A T G 3'

is

3' T C A G T A C 5'

Note that the latter is often written as the reverse complement with the 5' end on the left and the 3' end on the right, as below:

5' C A T G A C T 3'

Complementarity of DNA strands in a double helix, makes it possible to use one strand as a template to construct the other. This principle plays an important role in DNA replication.

Nucleic acids strands may also form hybrids in which single stranded DNA may anneal with complementary RNA[5].

Hybridization

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  • DNA - RNA strands

DNA repair functions

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  • Re-annealing

Regulatory functions

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  • Antisense transcript
  • Kissing hairpins

Functions/Principles in Biotech

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  • cDNA Libraries
  • Biomarkers

Images

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Self-complimentary molecule
 
3D binding of complementary DNA bases
 
Double helix of DNA showing base matching and stacking
 
Building a complex structure from complementary DNA strands
 
2D image of base pair binding of DNA
 
Multiple bases bound together showing complementary DNA strands

High Quality References

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[5] Key points: Base pairing, hybridization

[6] Key points: DNA regulation, antisense transcript

[7] Key points: RNA kissing

[8] Key points: cDNA library creation: background and new methods

[9] Key points: DNA repair, mismatch repair

[10] Key points: DNA repair

[11] Key points: Kissing hairpins, complementary loop

[12] Key points: RNA structure, kissing hairpins

[13] Key points: Complementarity background and overview

References

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  1. ^ https://en.wiki.x.io/wiki/Wikipedia:Five_pillars
  2. ^ https://en.wiki.x.io/wiki/Wikipedia:Training/For_students/Choosing_articles_3
  3. ^ a b c Demeke, T.; Jenkins, G. R. (2010 Mar). "Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits". Analytical and Bioanalytical Chemistry. 396 (6): 1977–90. doi:10.1007/s00216-009-3150-9. PMID 19789856. Retrieved 8 October 2013. {{cite journal}}: Check date values in: |date= and |year= / |date= mismatch (help); Unknown parameter |month= ignored (help)
  4. ^ a b c Rao, P. S.; Kumar, P. S.; Sonti, R. V. (2013 Mar). "Excised radicle tips as a source of genomic DNA for PCR-based genotyping and melting curve analysis in cotton". Journal of Biosciences. 38 (1): 167–72. doi:10.1007/s12038-012-9285-4. PMID 23385824. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |month= ignored (help)CS1 maint: date and year (link)
  5. ^ a b c d School, James D. Watson, Cold Spring Harbor Laboratory, Tania A. Baker, Massachusetts Institute of Technology, Stephen P. Bell, Massachusetts Institute of Technology, Alexander Gann, Cold Spring Harbor Laboratory, Michael Levine, University of California, Berkeley, Richard Losik, Harvard University ; with Stephen C. Harrison, Harvard Medical (2014). Molecular biology of the gene (Seventh ed.). Boston: Benjamin-Cummings Publishing Company. ISBN 978-0-321-76243-6.{{cite book}}: CS1 maint: multiple names: authors list (link)
  6. ^ Xie, ZH (2010 Feb). "[Natural antisense transcript and its mechanism of gene regulation]". Yi Chuan = Hereditas / Zhongguo Yi Chuan Xue Hui Bian Ji. 32 (2): 122–8. doi:10.3724/sp.j.1005.2010.00122. PMID 20176555. Retrieved 8 October 2013. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |month= ignored (help)CS1 maint: date and year (link)
  7. ^ Salim, N.; Lamichhane, R.; Zhao, R.; Banerjee, T.; Philip, J.; Rueda, D.; Feig, A. L. (2012 Mar 7). "Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex". Biophysical Journal. 102 (5): 1097–107. doi:10.1016/j.bpj.2011.12.052. PMC 3296049. PMID 22404932. {{cite journal}}: Check date values in: |date= (help); Unknown parameter |month= ignored (help)CS1 maint: date and year (link)
  8. ^ Naimuddin, M.; Ohtsuka, I.; Kitamura, K.; Kudou, M.; Kimura, S. (2013 Jul 15). "Role of messenger RNA-ribosome complex in complementary DNA display". Analytical Biochemistry. 438 (2): 97–103. doi:10.1016/j.ab.2013.03.022. PMID 23558165. {{cite journal}}: Check date values in: |date= (help)
  9. ^ Spies, M (2013 Feb). "There and back again: new single-molecule insights in the motion of DNA repair proteins". Current Opinion in Structural Biology. 23 (1): 154–60. doi:10.1016/j.sbi.2012.11.008. PMID 23260129. Retrieved 22 October 2013. {{cite journal}}: Check date values in: |date= (help)
  10. ^ Kanaar, R.; Hoeijmakers, J. H.; Van Gent, D. C. (1998 Dec). "Molecular mechanisms of DNA double strand break repair". Trends in Cell Biology. 8 (12): 483–9. doi:10.1016/s0962-8924(98)01383-x. PMID 9861670. Retrieved 22 October 2013. {{cite journal}}: Check date values in: |date= (help)
  11. ^ Chang, K. Y.; Tinoco Jr, I. (1997 May 30). "The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement". Journal of Molecular Biology. 269 (1): 52–66. doi:10.1006/jmbi.1997.1021. PMID 9193000. Retrieved 22 October 2013. {{cite journal}}: Check date values in: |date= (help)
  12. ^ Marino, J. P.; Gregorian Jr, R. S.; Csankovszki, G.; Crothers, D. M. (1995 Jun 9). "Bent helix formation between RNA hairpins with complementary loops". Science (New York, N.Y.). 268 (5216): 1448–54. doi:10.1126/science.7539549. PMID 7539549. Retrieved 22 October 2013. {{cite journal}}: Check date values in: |date= (help)
  13. ^ Mazzocchi, Fulvio (April 2010). "Complementarity in biology". EMBO. 11 (5): 334–339. doi:10.1038/embor.2010.56. PMC 2868532. PMID 20395955.{{cite journal}}: CS1 maint: date and year (link)
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