Difference between revisions of "Resource list: DNA melting and PCR"
From Course Wiki
Steven Nagle (Talk | contribs) |
|||
| (8 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
[[Category:20.309]] | [[Category:20.309]] | ||
| − | [[Category:Resource | + | [[Category:Resource list]] |
[[Category:NMR]] | [[Category:NMR]] | ||
{{Template:20.309}} | {{Template:20.309}} | ||
| − | |||
| − | |||
==DNA melting thermodynamics== | ==DNA melting thermodynamics== | ||
| Line 10: | Line 8: | ||
* Ryan T. Koehler and Nicolas Peyret [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/16/3333 Thermodynamic properties of DNA sequences: characteristic values for the human genome] Bioinformatics 2005 21(16):3333-3339; doi:10.1093/bioinformatics/bti530 | * Ryan T. Koehler and Nicolas Peyret [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/16/3333 Thermodynamic properties of DNA sequences: characteristic values for the human genome] Bioinformatics 2005 21(16):3333-3339; doi:10.1093/bioinformatics/bti530 | ||
| − | ==Use of fluorescent | + | ==Use of fluorescent reporters to measure DNA melting curves== |
* Ririe, et al. [http://www.sciencedirect.com/science/article/B6W9V-45MH2GK-G7/2/d2bf78d53a161a9793a248ec388d4659 Product Differentiation by Analysis of DNA Melting Curves during the Polymerase Chain Reaction]. ''Analytical Biochemistry'' 245, 154–160 (1997) | * Ririe, et al. [http://www.sciencedirect.com/science/article/B6W9V-45MH2GK-G7/2/d2bf78d53a161a9793a248ec388d4659 Product Differentiation by Analysis of DNA Melting Curves during the Polymerase Chain Reaction]. ''Analytical Biochemistry'' 245, 154–160 (1997) | ||
| Line 17: | Line 15: | ||
* [http://www.ambion.com/techlib/tn/81/813.html Applied Biosystems discussion of real-time PCR with SYBR Green I vs. TaqMan assays] | * [http://www.ambion.com/techlib/tn/81/813.html Applied Biosystems discussion of real-time PCR with SYBR Green I vs. TaqMan assays] | ||
| + | |||
| + | *Neuzil, et. al. [http://www.rsc.org/Publishing/Journals/LC/article.asp?doi=c005243d Non-contact fluorescent bleaching-independent method for temperature measurement in microfluidic systems based on DNA melting curves]. Lab Chip, 2010, 10, 2818 - 2821, DOI: 10.1039/c005243d | ||
==Applications of DNA melting curves== | ==Applications of DNA melting curves== | ||
| Line 24: | Line 24: | ||
*[http://www.clinchem.org/cgi/content/full/46/3/423?ijkey=61c477a414787cde9c8b650bd108c179ec230248&keytype2=tf_ipsecsha Marziliano, et. al. Melting Temperature Assay for a UGT1A Gene Variant in Gilbert Syndrome.] ''Clinical Chemistry''. 2000;46:423-425.) (Also see: Ahsen, et. al. [http://www.clinchem.org/cgi/content/full/47/7/1331#R1 Limitations of Genotyping Based on Amplicon Melting Temperature.] Clinical Chemistry. 2001;47:1331-1332. | *[http://www.clinchem.org/cgi/content/full/46/3/423?ijkey=61c477a414787cde9c8b650bd108c179ec230248&keytype2=tf_ipsecsha Marziliano, et. al. Melting Temperature Assay for a UGT1A Gene Variant in Gilbert Syndrome.] ''Clinical Chemistry''. 2000;46:423-425.) (Also see: Ahsen, et. al. [http://www.clinchem.org/cgi/content/full/47/7/1331#R1 Limitations of Genotyping Based on Amplicon Melting Temperature.] Clinical Chemistry. 2001;47:1331-1332. | ||
| − | == | + | ==PCR== |
| + | |||
| + | * Saiki, et. al. [http://www.sciencemag.org/cgi/reprint/239/4839/487.pdf?ijkey=06edd3fdcd16b286ed884189fcd203fd9197b18f Primer-Directed Enzymatic Amplification of DNA with a Thermostable DNA Polymerase]. Science 29 January 1988: Vol. 239. no. 4839, pp. 487 - 491 DOI: 10.1126/science.2448875 | ||
| + | |||
| + | * Kubista, et. al. [http://www.tataa.com/files/documents/molecularaspectsofmedicine2006.pdf The real-time polymerase chain reaction]. ''Molecular Aspects of Medicine'' 27 (2006) 95–125. | ||
| + | |||
| + | * [http://www.youtube.com/watch?v=ZmqqRPISg0g PCR animation] | ||
| + | |||
| + | * [http://www.youtube.com/watch?v=4jtmOZaIvS0 Animation] of copying process from PBS series [http://www.pbs.org/wnet/dna/ ''DNA: The Secret of Life''.] | ||
| + | |||
| + | ===Quantitative methods=== | ||
| + | |||
| + | * C A Heid, J Stevens, K J Livak, et al. [http://genome.cshlp.org/content/6/10/986.full.pdf+html Real time quantitative PCR.] Genome Res. 1996 6: 986-994. | ||
| − | + | {{Template:20.309 bottom}} | |
| − | + | ||
Latest revision as of 14:32, 23 August 2013
DNA melting thermodynamics
- Ryan T. Koehler and Nicolas Peyret Thermodynamic properties of DNA sequences: characteristic values for the human genome Bioinformatics 2005 21(16):3333-3339; doi:10.1093/bioinformatics/bti530
Use of fluorescent reporters to measure DNA melting curves
- Ririe, et al. Product Differentiation by Analysis of DNA Melting Curves during the Polymerase Chain Reaction. Analytical Biochemistry 245, 154–160 (1997)
- Michael T. Bjorndal and D. Kuchnir Fygenson. DNA Melting in the Presence of Fluorescent Intercalating Oxazole Yellow Dyes Measured with a Gel-Based Assay. Biopolymers, Vol. 65, 40–44 (2002)
- Neuzil, et. al. Non-contact fluorescent bleaching-independent method for temperature measurement in microfluidic systems based on DNA melting curves. Lab Chip, 2010, 10, 2818 - 2821, DOI: 10.1039/c005243d
Applications of DNA melting curves
- Worm, et. al. In-Tube DNA Methylation Profiling by Fluorescence Melting Curve Analysis Clinical Chemistry 47:7 1183–1189 (2001)
- Marziliano, et. al. Melting Temperature Assay for a UGT1A Gene Variant in Gilbert Syndrome. Clinical Chemistry. 2000;46:423-425.) (Also see: Ahsen, et. al. Limitations of Genotyping Based on Amplicon Melting Temperature. Clinical Chemistry. 2001;47:1331-1332.
PCR
- Saiki, et. al. Primer-Directed Enzymatic Amplification of DNA with a Thermostable DNA Polymerase. Science 29 January 1988: Vol. 239. no. 4839, pp. 487 - 491 DOI: 10.1126/science.2448875
- Kubista, et. al. The real-time polymerase chain reaction. Molecular Aspects of Medicine 27 (2006) 95–125.
- Animation of copying process from PBS series DNA: The Secret of Life.
Quantitative methods
- C A Heid, J Stevens, K J Livak, et al. Real time quantitative PCR. Genome Res. 1996 6: 986-994.
