Development of a new GMP TAQ polymerase for improved PCR performance. Marie-Claire Beckers, Peter Haima

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1 Development of a new GMP TAQ polymerase for improved PCR performance Marie-Claire Beckers, Peter Haima

2 Contents Context: Eurogentec GMP manufacturing of IVD components PCR performance issues Novel concept: Hot Diamond Taq Mode of action Proof of principle Conclusions

3 Our Activities PRODUCTS & SERVICES for RESEARCH Manufacturing of custom oligos, reagents & enzymes for (Q)PCR, antibodies, proteins, peptides. CMO SOLUTIONS DIAGNOSTICS GMP compliant ISO13485 certified manufacturer of oligonucleotides, Taq polymerases, peptides and antibodies for R&D and commercial IVD products. CMO SOLUTIONS PHARMA cgmp compliant manufacturer of biopharmaceuticals from bacterial/yeast sources:

4 Fremont San Diego Five Manufacturing Sites Belgium Japan

5 CMO for IVD industry EGT is a leading European manufacturer of research grade oligonucleotides since IVD GMP oligos to global IVD industry since 04. GMP manufacturing and ISO certification for IVD oligos in Europe ( 08), Japan ( 09) and USA( 10). GMP (pharma) production of Taq Polymerases in 2009.

6 Polymerase Chain Reaction > fold amplification of a nucleic acid sequence. Revolutionized molecular research and IVD because of unparalleled sensitivity and specificity (HIV, H1N1). Inherent advantages & disadvantages.

7 PCR issues Enzymes contain E. coli & fungal DNA which can lead to false positives. Contamination and off target amplification, which can lead to false positives. Primer-dimer formation reduces yield of specific amplicon, which can lead to false negatives. Royalty stacking is a concern for IVD companies.

8 GMP TAQ Polymerases Diamond Taq

9 Diamond Taq recombinant non hot-start Manufacturing in GMP-Pharma (QMS/clean rooms). Fully compliant ISO & GMP/QSR Customized Fill & Finish. Batch record & CoA. DNA ultralow (<0.01 fg/u). Bioburden ultralow (typically 0; < 10 CFU/ml). Exceptional lot to lot reproducibility.

10 PCR issues Enzymes contain E. coli & fungal DNA which can lead to false positives. Contamination and off target amplification, which can lead to false positives. Primer-dimer formation reduces yield of specific amplicon, which can lead to false negatives. Royalty stacking is a concern for IVD companies.

11 Hot start PCR Most effective strategy to reduce nonspecific amplification during low temperature set-up. Wax-embedded PCR reagents. Modified DNA polymerase, inactive (< 74 C) prior to heat shock (up to C) Hot-start dntps. PCR Hot Start by magnesium sequestration.

12 Hot start DNA Polymerases Activity modified with blocking antibody. Disadvantage: antibody from hybridomas can contaminate PCR with mammalian DNA; enzymes also tend to be leaky. Activity modified chemically. Disadvantage: requires long activation (10 mins), could cause heat-damage to DNA samples.

13 New Hot Start Concept NEW CONCEPT HOT Diamond Taq Not through chemical modification. Not through blocking antibody. Enzyme shows no activity at room temperature. No heat shock is required; 100% enzyme activity appears in 1 st PCR cycle. Very high yield of specific PCR product.

14 HOT Diamond Taq Proprietary agent prevents non-specific polymerization; effectively prevents primerdimer formation, increases specific PCR yield. Hot Diamond TAQ buffer is designed to maximize effect of the proprietary agent. Hot Diamond TAQ protocol is compatible with all existing hot-start protocols.

15 HOT Diamond Taq Universal concept, Hot Diamond Taq can be used to amplify AT and GC rich regions, long and difficult templates. Production under GMP conditions provides enzyme with ultra low bioburden and E.coli/fungal DNA content. Can be used for demanding Research and IVD applications (sensitivity, specificity, GMP). Universal concept, can also be used to improve performance other (hot-start) enzymes.

16 Polymerisation test Elongation Incubation at 25 C HGS GMP TOP HGS GMP TOP Elongated hybrid Oligo lc hybrid Oligo l Without activation Oligo c With activation

17 Polymerisation test Elongation Incubation at 25 C HGS GMP TOP HGS GMP TOP Without With activation activation 1: Oligoc 2: Oligol 3: Hybrid Oligoc-Oligol 4: Double-strand Oligol 5: Hot Start : 6h30 at 25 C 6: Hot Diamond : 6h30 at 25 C 7: Hot Diamond : 6h30 at 25 C 8: Hot Start : 10min at 95 C and 6h30 at 25 C 9: Hot Diamond : 10min at 95 C and 6h30 at 25 C 10: Hot Diamond : 10min at 95 C and 6h30 at 25 C

18 Polymerisation test Elongation Incubation at 40 C : Hybrid Oligoc-Oligol 2: Double-strand Oligol 3: Hot Start 4h at 40 C 4: Hot Diamond 4h at 40 C 5: Hot Diamond 4h at 40 C 7: Hot Start C/4h at 40 C 8: Hot Diamond C/4h at 40 C 9: Hot Diamond C/4h at 40 C Without activation With activation

19 Polymerisation test Elongation Incubation at 60 C HGS GMP TOP HGS GMP TOP Without activation Without activation With activation With activation 1: Oligoc 2: Oligol 3: Hybrid Oligoc-Oligol 4: Double-strand Oligol 5: Hot Start 4h at 60 C 6: Hot Diamond 4h at 60 C 7: Hot Diamond 4h at 60 C 8: Hot Start C/4h 60 C 9: Hot Diamond C/4h 60 C 10: Hot Diamond C/4h 60 C

20 Performance Test Lambda DNA Amplification SmartLadder 2.Lambda DNA 100 pg 3. Lambda DNA 10 pg 4. Lambda DNA 1 pg 5. Lambda DNA 0.1 pg Thermal cycling conditions: 94 C 3' 25 cycle 94 C 30'' 60 C 1' 72 C 2' 72 7' 4 C end temperature

21 Hot Diamond Taq 1: SmartLadder 2: NTC 3: 0,1ng DNA 4: NTC 5: 0,1ng DNA 6: SmartLadder 7: NTC, 8: 0,1ng DNA 9: NTC 10: 0,1ng DNA 11: SmartLadder Non-Hot Start Taq 1: SmartLadder 2: NTC 3: 0,1ng DNA 4: NTC 5: 0,1ng DNA 6: SmartLadder 7: NTC 8: 0,1ng DNA 9: NTC 10: 0,1ng DNA 11: SmartLadder AT rich gene from H.Pylori GC rich gene from S. Coelicolor Setup Incubation: 4h at 25 C Thermal cycling conditions: 3 min 95 C 40 cycles 30 sec at 95 C 30 sec at 50 C for AT rich sequence or 30 sec at 60 C for GC rich sequence 1 min at 72 C/ 5 min at 72 C Performance Test Multiple Targets

22 Performance Test Different Taq Polymerases Numb gene Amplification 1. SmartLadder 2. Hot Diamond 3. Competitor A Hotstart Taq 4. Competitor B Hotstart Taq 5. Competitor C Hotstart Taq 6. Competitor D Hotstart Taq 7. Diamond Taq GC rich gene Amplification 8. SmartLadder 9. Hot Diamond 10. Competitor A Hotstart Taq 11. Competitor B Hotstart Taq 12. Competitor C Hotstart Taq 13. Competitor D Hotstart Taq 14. Diamond Taq

23 Performance Test Multiple Targets & Different Taq Polymerases λ DNA /8. SmartLadder 2/9. Hot Diamond Taq 3/10. Competitor A Hotstart Taq 4/11. Competitor B Hotstart Taq 5/12. Competitor C Hotstart Taq 6/13. Competitor D Hotstart Taq 7/14. Diamond Taq Gluco3203 (3.2 Kb) Thermal cycling conditions (Gluco3203): 1 min 94 C First 10 cycles: 10 sec at 94 C 60 sec at 60 C 5 min at 68 C Next 20 cycles: 10 sec at 94 C 60 sec at 60 C 5 min at 68 C + 10sec each cycle 5 min at 72 C 4 C

24 Lambda DNA Amplification Different Times of Heat Activation Hot Diamond Taq Hot Start Taq Thermal cycling conditions: 94 C 10 min, 5 min or 20 seconds 25 cycles 94 C 30'' 60 C 1' 72 C 2' 72 7' 4 C end temperature 1. SmartLadder 2. λ DNA 5 pg - 20 sec 3.λDNA 1 pg - 20 sec 4. NTC - 20 sec 5. λ DNA 5 pg - 5 min 6. λ DNA 1 pg - 5 min 7. NTC - 5 min 8. λ DNA 5 pg - 10 min 9. λ DNA 1 pg - 10 min 10. NTC - 10 min

25 Real-Time PCR Performance Probe Assay : TATA box binding protein gene Relative low expression level Hot Diamond Taq Hot Start Taq Samples Hot Start Hot Diamond Ct Ct 100ng cdna 30,07 30,15 50ng cdna 31,4 31,28 25ng cdna 32,42 32,28 12,5ng cdna 33,46 33,44 6,25ng cdna 34,78 34,23 3,13ng cdna 34,9 36,58 NTC x x Thermal cycling conditions: 2 min at 50 C 10min at 95 C 40 cycles: 15sec at 95 C 1 min at 60 C

26 Quantification of residual gdna from E. coli qpcr qpcr qpcr

27 Quantification of residual gdna from E. coli Hot Diamond Taq Hot Start other fg DNA/ Taq unit Genome copies/ Taq unit

28 Hot Diamond TAQ concept applied to other enzymes Numb gene 1. gdna 10 ng 2. gdna 1 ng 3. gdna 0.1 ng 4. NTC HS TAQ 1 Modified HS TAQ 2 Modified PCR conditions 3 min 95 C 35 cycles: 30 sec at 95 C 10 sec at 60 C 30 sec at 72 C 5 min at 72 C 4 C

29 Conclusions Hot Diamond Taq demonstrated equal to better performance in direct comparison with other HotStart DNA polymerases in PCR and qpcr applications without the «Hot start» issues. Complete enzyme activation provides maximal enzymatic activity during PCR to generate higher yields. Universal concept, can also be used to improve performance other (hot-start) enzymes.

30 Conclusions Hot Diamond Taq improves PCR efficiency and specificity to amplify AT and GC rich regions, long and difficult templates. Hot Diamond Production under strict GMP conditions provides an ultrapure bioburden-free enzyme and extremely low in residual E.coli DNA. Hot Diamond Taq is highly suited for all IVD and demanding research applications and bacterial and fungal PCR assays. (sensitivity, specificity, GMP). Hot Diamond Taq may also be suitable for isothermal amplification.

31 Arigatou gozaimasu Thank you very much!

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