DNA / RNA References

• A Genomics, Proteomics and Bioinformatics Knowledge Base
• Fluorescence Resonance Energy Transfer (FRET)
• The page describes and summarises all technical aspects involved in quantitative gene
  expression analysis using real-time qPCR & qRT-PCR. It presents a lot of cyclers, kits,
  dyes, chemistries, and services involved.
  
• PCR movie/DNA/RNA/Protein synthesis a common link with a variety of information
• Real time PCR and other related references and web-site
• Duplex Scorpion primers in SNP analysis and FRET applications by Whitcombe,D., Theaker,J., Guy,SP, Brown,T. and Little,S. (1999) (PDF)

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For the exhaustive information on the following subject click here: PCR books RT-PCR and real-time RT-PCR (in general) LightCycler specific technical notes absolute quantification using kinetic PCR relative quantification using kinetic PCR classical block RT-PCR & competitive RT-PCR normalisation  &  housekeeping gene problems in real-time PCR verification of DNA array results quantification software: REST, REST-XL,  Q-Gene, geNorm, RTPrimerDB kinetic  RT-PCR poster board ABI - Essentials of Real Time PCR (153k PDF) real-time PCR in Molecular Immunology

REFERENCES LIST ON TaqMan and Scorpion Oligonucleotides:

1. Tyagi, S.; Kramer, F. R. Nat. Biotechnol. 1996, 14, 303–308.
2. Whitcombe, D.; et al. Nat. Biotechnol. 1999, 17, 804–807.
3. Zhang, P.; Beck, T.; Tan, W. Angew. Chem., Int. Ed. 2001, 40, 402–405.
4. Marras, S. A. E.; Kramer, F. R.; Tyagi, S. Genet. Anal. Biomol. Eng. 1999, 14, 151–156.
5. Smit, M. L.; et al. Clin. Chem. 2001, 47, 739–744.
6. Thelwell, N.;Millington S.; Solinas A.; Booth J.; Brown T. Nucleic Acids Research. 2000, 28, 3752-3761.
7. Ortiz E.; Estrada G.; Lizardi P. M. Molecular and Cellular Probes. 1988, 12, 219-226.

Articles on PCR and RTPCR:

Mackay IM, Arden KE, Nitsche A. Real-time PCR in virology. Nucleic Acids Res. 2002 Mar 15;30(6):1292-305. Review.

Bustin SA. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol. 2002 Aug;29(1):23-39. Review.

Bustin SA, Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000 Oct;25(2):169-93. (PDF)

O’Connell J, ed. RT-PCR Protocols. Methods in Molecular Biology, Vol. 193, Humana Press, 2002. Text Book.

Co-labeling Using In Situ PCR: A Review Journal of Histochemistry and Cytochemistry, 2001, Vol. 49, 1329-1340,

FJ Jenkins Basic methods for the detection of PCR products PCR Methods Appl. 1994 3: 77-82.  

E Fahy, M Biery, M Goulden, SS Ghosh, and TR Gingeras Issues of variability, carryover contamination, and detection in 3SR- based assays PCR Methods Appl. 1994 3: 83-94.  

K Kretz, W Callen, and V Hedden Cycle sequencing PCR Methods Appl. 1994 3: 107-112.  

LE Bockstahler Overview of international PCR standardization efforts PCR Methods Appl. 1994 3: 263-267.

RT-PCR Protocols. Methods in Molecular Biology, Vol. 193. Joe O’Connell, ed. Totowa, NJ: Humana Press, 2002, 378 pp.,

Important References

1. Bell, P.A.; Chaturvedi, S.; Gelfand, C.; Huang, C.Y.; Kochersperger, M.; Kopla, R.; Modica, F.; Pohl, M.; Zhao, R.; Zhao, X.; Boyce-Jacino, M.T.: "SNPstream UHT: Ultra-High Throughput SNP Genotyping for Pharmacogenomics and Drug Discovery." 2002, Biotechniques, 70-77.
2. R. T. Pon, N. Usman, and K.K. Ogilvie, Derivatization of controlled pore glass beads for solid phase oligonucleo-tide synthesis, Biotechniques 1988, 6, 768-775.
3. C. McCollum and A. Andrus, An optimized polystyrene support for rapid, efficient oligonucleotide synthesis, Tetrahedron Letters 1991, 32, 4069-4072.
4. Horn, T.; Chaturvedi, S.K.; Bala, T.N.; and Letsinger, R.L.: "Oligonucleotides with Alternating Anionic and Cationic Phosphoramidite Linkages: Synthesis and Hybridization of Stereo-uniform Isomers." Tetrahedron Letters, 1996, 37, 743-746.
5. J. Kaufman, M. Le, G. Ross, P. Hing, M. Budiansky, E. Yu, E. Campbell, V. Yoshimura, V. Fitzpatrick, K. Nadimi, and A. Andrus, Trityl monitoring of automated DNA synthesizer operation by conductivity: A new method of real-time analysis, Biotechniques 1993,14, 834-839.
6. Solid-Phase Synthesis of Oligopurine Deoxynucleic Guanidine (DNG) and Analysis of Binding with DNA Oligomers. Linkletter, B.; Szabo, I.E.; Bruice. T.C. Nucl. Acids Res. Dec. 2001, 29, 2370-2376.
7. Nordhoff, E. et al "Mass Spectrometry of Nucleic Acids" Mass Spec. Rev., 15, pp 67-138 (1996).
8. Solid-Phase Synthesis of Deoxynucleic Guanidine (DNG) Oligomers and Melting Point and Circular Dichroism Analysis of Binding Fidelity of Octameric Thymidyl Oligomers with DNA Oligomers.Barry A. Linkletter, Istvan E. Szabo, and Thomas C. Bruice Journal of the American Chemical Society, 1999, 121, 3888-96
9. Synthesis of Protected Guanidinium Linked Dinucleoside Incorporable Into an Oligonucleotide Using Solid Phase DNA Methodology.Dinesh A. Barawkar, Barry Linkletter, and Thomas C. Bruice Bioorganic & Medicinal Chemistry Letters, 1998, 8, 1517-20.
10. Solid-Phase Synthesis of Oligomeric Deoxynucleic Guanidine (DNG): A Polycationic Analogue of DNA. Barry A. Linkletter and Thomas C. Bruice
    Bioorganic & Medicinal Chemistry Letters, 1998, 8, 1285-90.
11. Solid-phase Synthesis of Positively Charged Deoxynucleic Guanidine (DNG) Modified Oligonucleotides Containing Neutral Urea Linkages. Effect of Charge Deletions on Binding and Fidelity. Linkletter, B.; Bruice, T.C.. Bioorg. Med. Chem. 2000, 1893-1901.
12. W. Lint, E. Vanaja, F. J. Grant, P.G. Lockhart and P.J. O'Hara, 1994, Easier DNA synthesis quality control with a semi-automated dimethoxytrityl cation assay, Biotech-niques 16, 408.
13. B. S. Sproat and W. Bannwarth, Improved synthesis of oligonucleotides on controlled pore glass using phospho-triester chemistry and a flow system, Tetrahedron Letters 1983, 24, 5771-5774.
14. S. P. Adams, K. S. Kavka, E. J. Wykes, S. B. Holder, and G. R. Galluppi, Hindered dialkylamino nucleoside phosphite reagents in the synthesis of two DNA 5l-mers, J. Amer. Chem. Soc. 1983, 105, 661-663.
15. M. H. Caruthers, DNA synthesis for nonchemists: The phosphoramidite method on silica supports, in Synthesis and Applications of DNA and RNA, ed. Saran A. Narang, Academic Press, Orlando, FL. 1987,
16. M. H. Caruthers, Chemical synthesis of DNA and DNA analogues, Acc. Chem. Res. 1991, 24, 278-284.
17. M. H. Caruthers, 1985, Gene synthesis machines: DNA chemistry and its uses, Science 230, 281-285.
18. M. S. Urdea, Design, chemical synthesis, and molecular cloning of a gene for human epidermal growth factor, Methods in Enzymology 1987, 146, 22-41.
19. L. Ferretti, S. S. Karnik, H. G. Khorana, M. Nassal, and D. D. Oprian, Total synthesis of a gene for bovine rhodopsin, Proc. Natl. Acad. Sci. 1986, 83, 599-603.
20. M. S. Urdea, J. P. Merryweather, G. T. Mullenbach, D Coit, U. Heberlein, P. Valenzuela, and P. J. Barr, Chemical synthesis of a gene for human epidermal growth factor urogastrone and its expression in yeast, Proc. Natl. Acad. Sci. 1983, 80, 7461-7465.
21. P. Wright, D. Lloyd, W. Rapp, and A. Andrus, Large scale synthesis of oligonucleotides via phosphoramidite nucleosides and a high loaded polystyrene support, Tetrahedron Letters 1993, 34, 3373-3376.
22. T. Tanaka and R. L. Letsinger, Syringe method for the stepwise chemical synthesis of oligonucleotides. Nucl. Acids. Res. 1982, 10, 3249-3260.
23. G. Zon, K. A. Gallo, C. J. Samson, K.-L. Shao, M. F. Summers, and R. A. Byrd, Analytical studies of "mixed sequence" oligodeoxyribonucleotides synthesized by competitive coupling of either methyl- or b-cyanoethyl-N,N-diisopropylamino phosphoramidite reagents, including 2'-deoxyinosine, Nucl. Acids. Res. 1985, 13, 8181-8196.
24. N. D. Sinha, Large scale oligonucleotide synthesis using the solid-phase approach, in Methods in Molecular Biology 20: Protocols for Oligonucleotides and Analogs, ed. S. Agrawal, Humana Press Inc., Totowa, NJ. 1993.
25. R. B. Ciccarelli, P. Gunyuzlu, J. Huang, C. Scott, and F. T. Oakes, Construction of synthetic genes using PCR after automated DNA synthesis of their entire top and bottom strands, Nucleic Acids Res. 1991, 19, 6007-6013.
26. "DNA Synthesis and DNA Hybridization" S. Ficht, W. Hecker, A. Mattes, O. Seitz, Chemical Biology – A Practical Course (H. Waldmann, P. Janning; Eds.) 2004, Wiley-VCH, Weinheim, 23-34.
    

Articles on Fluorescent Probes::

"Forced Intercalation Probes (FIT-Probes) - Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous SNP Detection" O. Köhler, D. V. Jarikote, O. Seitz*, ChemBioChem 2005, 6, 69-77.

"Forced Intercalation as Tool in Gene Diagnostics and in Studying DNA-Protein Interactions" O. Köhler, D. V. Jarikote, I. Singh, V.S. Parmar, E. Weinhold, O. Seitz*, Pure & Appl. Chem 2005, 77, 327-338.

"Doubly-labeled Peptide Nucleic Acids (PNAs) as Probes for the Detection of DNA Point Mutations" O. Köhler, S. Röttger, O. Seitz, Chemical Biology – A Practical Course (H. Waldmann, P. Janning; Eds.) 2004, Wiley-VCH, Weinheim, 35-44.

"Solid Phase Synthesis of Doubly Labelled Peptide Nucleic Acids as Probes for the Real Time Detection of Hybridisation" O. Seitz, Angew. Chem. 2000, 112, 3389-3392; Angew. Chem. Int. Ed. 2000, 39, 3249-3252.

"Convergent Strategies for the Attachment of Fluorescing Reporter Groups to Peptide Nucleic Acids in Solution and on Solid Phase" O. Seitz*, O. Köhler, Chem. Eur. J. 2001, 7, 3911-3925.

Literature on PNA Oligomers:

"Mass-spectrometrical Monitoring of a PNA-based Ligation Reaction for the Multiplex Detection of DNA Single Base Mutations" A. Mattes, O. Seitz*, Angew. Chem., 2001, 113, 3277-3280.

"Single-Nucleotide-Specific PNA-Peptide Ligation on Synthetic and PCR DNA Templates" S. Ficht, A. Mattes, O. Seitz*, J. Am. Chem. Soc. 2004, 126, 9970-9981.

"Chemically Modified Antisense Oligonucleotides - Recent Improvements of RNA Binding and Ribonuclease H Recruitment" (Highlight) O. Seitz, Angew. Chem. 1999, 111, 3674-3677; Angew. Chem. Int. Ed. 1999, 38, 3466-3469.

"Solid Phase Synthesis of Protected Peptide Nucleic Acids" O. Seitz, Tetrahedron Lett. 1999, 40, 4161-4164

"A Convergent Strategy for the Modification of Peptide Nucleic Acids (PNA). Novel Mismatch-Specific PNA-Hybridisation Probes." O. Seitz*, F. Bergmann, D. Heindl, Angew. Chem. 1999, 111, 2340-2343; Angew. Chem. Int. Ed. 1999, 38, 2203-2206.

"New Protecting Group Strategies for the Solid Phase Synthesis and Modification of Peptides, Oligonucleotides and Oligosaccharides" (Highlight) O. Seitz, Angew. Chem. 1998, 110, 3289-3291; Angew. Chem. Int. Ed. 1998, 37, 3109-3111.