THE UNIVERSITY OF NEWCASTLE- DISCIPLINE OF MEDICAL BIOCHEMISTRY. STANDARD OPERATING PROCEDURE PROCEDURE NO: GLP 017 MOD: 1st Issue Page: 1 of 6

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1 Page: 1 of 6 1. Risk Assessment: This Risk Assessment is to be used as a general guide and as such, cannot accommodate all the varying factors that may be encountered when using this equipment. Therefore, personnel are requested to conduct their own Risk Assessment before using this equipment to include any extra hazards introduced by the task performed. TASK PERFORMED The SuperScript. III First-Strand Synthesis System for RT-PCR is optimized to synthesize firststrand cdna from purified poly(a)+ or total RNA. RNA targets from 100 bp to >12 kb can be detected with this system. The amount of starting material can vary from 1 pg to 5 µg of total RNA. SuperScript. III Reverse Transcriptase is a version of M-MLV RT that has been engineered to reduce RNase H activity and provide increased thermal stability. The enzyme is used to synthesize cdna at a temperature range of C, providing increased specificity, higher yields of cdna, and more full-length product than other reverse transcriptases. 1. MgCl 2 (irritant) 2. Tris-HCl (irritant) 3. KCl (irritant) HAZARDS RISK ASSESSMENT 1. Potential risks are associated with using the SuperScript. III First-Strand Synthesis System for RT-PCR Kit. RISK CONTROL 1. All components should be considered as potentially hazardous. Wear suitable protective clothing such as a lab coat, enclosed shoes, safety glasses and gloves. 2. Purpose: 2.1 SuperScript. III First-Strand Synthesis System for RT-PCR Kit is used to synthesize first-strand cdna from purified poly(a)+ or total RNA. WRITTEN BY CHECKED BY AUTHORIZED BY NAME (signed) Rowan Foster Ellen Byrnes Phillip Dickson DATE 12 th May th June th September 2004 Distributed To: GLP Master File / GLP Lab File

2 Page: 2 of 6 3. Equipment: 3.1 Vortex 3.2 Heating blocks 3.3 Ice 3.4 Bench top centrifuge 3.5 Various pipettes 4. Materials: 4.1 Sterile eppendorf tubes 4.2 Sterile plugged tips 4.3 Gloves 4.4 SuperScript. III First-Strand Synthesis System for RT-PCR Kit System Component Amount Oligo(dT)20 (50 µm) 50 µl Random hexamers (50 ng/µl) 250 µl 10X RT buffer* 1 ml 25 mm MgCl2 500 µl 0.1 M DTT 250 µl 10 mm dntp mix 250 µl SuperScript. III RT (200 U/µl) 50 µl RNaseOUT. (40 U/µl) 100 µl E. coli RNase H (2 U/µl) 50 µl DEPC-treated water 1.2 ml Total HeLa RNA (10 ng/µl) 20 µl Sense Control Primer (10 µm) 25 µl Antisense Control Primer (10 µm) 25 µl *200 mm Tris-HCl (ph 8.4), 500 mm KCl

3 Page: 3 of 6 5. Set Up: 5.1 Photocopy the Batch Record attached to this SOP (Illustration 10.1). Ensure the Batch Record is completed as the procedure is carried out (if required). 5.2 Ensure that you have read and understood the Safety Precautions (Section 6 of this SOP) prior to commencing this procedure. Sign the Batch Record to indicate that this has been done. 6. Safety Precautions: 6.1 Good laboratory techniques are to be used at all times. 7. Method: First-Strand cdna Synthesis The following procedure is designed to convert 1 pg to 5 µg of total RNA or 1 pg to 500 ng of poly(a)+ RNA into first-strand cdna: 7.1. Mix and briefly centrifuge each component before use Combine the following in a 0.2- or 0.5-ml tube: Component Amount up to 5 µg total RNA n µl Primer* 1 µl *50 µm oligo(dt)20, or 2 µm gene-specific primer (GSP), or 50 ng/µl random hexamers 10 mm dntp mix 1 µl DEPC-treated water to 10 µl 7.3. Incubate at 65 C for 5 min, then place on ice for at least 1 min Prepare the following cdna Synthesis Mix, adding each component in the indicated order. Component 1 Rxn 10 Rxns 10X RT buffer 2 µl 20 µl 25 mm MgCl2 4 µl 40 µl

4 Page: 4 of M DTT 2 µl 20 µl RNaseOUT. (40 U/µl) 1 µl 10 µl SuperScript. III RT (200 U/µl) 1 µl 10 µl 7.5. Add 10 µl of cdna Synthesis Mix to each RNA/primer mixture, mix gently, and collect by brief centrifugation. Incubate as follows. Oligo(dT)20 or GSP primed: 50 min at 50 C Random hexamer primed: 10 min at 25 C, followed by 50 min at 50 C 7.6. Terminate the reactions at 85 C for 5 min. Chill on ice Collect the reactions by brief centrifugation. Add 1 µl of RNase H to each tube and incubate for 20 min at 37 C cdna synthesis reaction can be stored at -20 C or used for PCR immediately. 8. Maintenance: 8.1 SuperScript. III First-Strand Synthesis System for RT-PCR Kit must be stored at -20 C. 9. Shutdown: 9.1 Attach gel photo to SOP, note file name and date. 10. Illustrations: See attached 10.1 Batch Record 11. Check List: 11.1 Ensure batch record documentation is complete. 12. References: 12.1 SuperScript. III First-Strand Synthesis System for RT-PCR Kit Instruction manual and references therein: Berger, S.L. and Kimmel, A.R. (1987) Methods Enzymol 152, 316. Bracete, A.M., Mertz, L.M., Fox, D.K. (1999) Focus 21, 38.

5 Page: 5 of 6 Chomczynski, P. (1993) Biotechniques Vol. 15, 532. Chomczynski, P. and Sacchi, N. (1987) Anal. Biochem. 162, 156. Compton, T. (1990) in PCR Protocols: A Guide to Methods and Applications (Innis, M., Gelfand, D., Sninsky, J., and White, T., eds.), p. 39, Academic Press, Inc. Frohman, M.A., Dush, M.K, and Martin, G.R. (1988) Proc. Nat. Acad. Sci USA 85, Gerard, G.F. (1994) Focus 16, 102. Sambrook J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor. Simms, D., Cizdziel, P.E., and Chomczynski, P. (1993) Focus 15, 99. Westfall, B., Sitaraman, K., Solus, J., Hughes, J., and Rashtchian, A. (1997) Focus 19, 46. Westfall, B., Sitaraman, K., Lee, J., Borman, J. and Rashtchian, A. (1999) Focus 21, 49. Takagi, M., Nishioka, M., Kakihara, H., Kitabayashi, M., Inoue, H., Kawakami, B., Oka, M., and Imanaka, T. (1997) Appl. Environ. Microbiol. 63, Sitaraman, K., Darfler, M., and Westfall, B. (1999) Focus 21, 10. Nathan, M., Mertz, L., Fox, D. (1995) Focus 17, 78. Schwabe, W., Lee, J.E., Nathan, M., Xu, R.H., Sitaraman, K., Smith, M., Potter, R.J., Rosenthal, K., Rashtchian, A., Gerard, G.F. (1998) Focus 20, Change History: 13.1 Issue Number: 1st Issue Date Issued: 11th October Issue Number: Date Issued: Reason for Change:

6 Page: 6 of 6 BATCH RECORD Page: 1 of 1 ILLUSTRATION 10.1 DATE: BATCH RECORD Date Requirements Records Comments: Batch Record Completed By: Date: / / Countersigned: