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Nucleic Acid Amplification Techniques in Microbiology Dr.T.V.Rao MD
DNA replication Basis of Biological Evolution ,[object Object]
DNA Replication is the Basis of all Technologies ,[object Object],[object Object]
Understanding events in vivo Lead to vitro applications ,[object Object],[object Object]
Har Gobind Khorana, Indian Scientist, Nobel Prize Winner   ,[object Object],[object Object]
Polymerase Chain Reaction Methodology A Mile stone in Medical History ,[object Object]
Dr. Kary Mullis, wins Nobel Prize   in 1993 ,[object Object]
How DNA Works ,[object Object],[object Object]
DNA  – RNA -  DNA ,[object Object],[object Object]
Create primers ,[object Object]
Precise  Oligonucleotide  Matches the Sequences
Thermocycler   is Back bone   of   PCR methodology ,[object Object],[object Object]
Primers ,[object Object],[object Object]
PCR a Chain reaction ,[object Object]
Taq polymerase fuels the Reaction ,[object Object],[object Object]
Bacteria Of Boiling Hot Springs In Yellowstone National Park
Boiling hot springs in Yellowstone National Park. The orange-red coloration is caused by thriving colonies of photosynthetic   cyanobacteria.
Taq polymerase ,[object Object],[object Object]
Drawbacks of Taq polymerase ,[object Object],[object Object]
Disadvantages of Taq Pol ,[object Object],[object Object],[object Object],[object Object],[object Object]
PCR  -  Three basic Steps ,[object Object],[object Object],[object Object]
What does PCR need? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Four Alphabets make what we are
DNA polymerases ,[object Object]
Create primers ,[object Object]
PCR Primers ,[object Object],[object Object],[object Object],[object Object],[object Object]
Cutting, pasting and amplifying is the basis of Reaction
DNA ,[object Object],[object Object],[object Object],[object Object],[object Object]
What does PCR need? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
PCR Requirements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Steps in PCR ,[object Object],[object Object],[object Object]
How does PCR work? ,[object Object],[object Object],[object Object],[object Object],[object Object]
Denaturation of DNA ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],Annealing
Taq polymerase binds …. ,[object Object],[object Object],[object Object],[object Object],[object Object]
Denaturing Template Heat causes DNA strands to separate Denature DNA strands 94 o C 3’ 5’ 5’ 3’ 5’ 3’ 3’ 5’
Annealing Primers ,[object Object],[object Object],3’ 5’ Primers anneal 64 o C 3’ 5’ 3’ 5’ 5’ 3’ 3’ 5’ 5’ 3’
Taq Polymerase Extends 3’ 5’ 3’ 5’ Extend 72 o C 3’ 5’ 3’ 5’ ,[object Object],[object Object],Repeat  denaturing, annealing, and extending  30 cycles 3’ 5’ 3’ 5’ 5’ 3’ 5’ 3’
Taq Polymerase Extends 3’ 5’ 3’ 5’ Extend 72 o C 3’ 5’ 3’ 5’ ,[object Object],[object Object],Repeat  denaturing, annealing, and extending  30 cycles 3’ 5’ 3’ 5’ 5’ 3’ 5’ 3’
The target product is made in the third cycle 3 ’ 5’ 3 ’ 5’ 3’ Cycle 1 Cycle 2 Cycle 3 3’ 5’ 5’ 3’ 5’ 5’ 3’ 5’ 3’ 5’ 3’ 3’ 3’ 3’ 3’ 5’ 5’ 5’ 5’
PCR Cycles Review ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Primers That Form Hairpins ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Applications of PCR differentiates the results can be compared of Individual specimens
Advantages of PCR ,[object Object],[object Object],[object Object],[object Object],[object Object]
Limitations of PCR ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How to overcome Difficulties ? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
REAL TIME ASSAYS
New Technologies – Real Time Assays ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Real-time polymerase chain reaction ,[object Object]
RT - PCR ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
OVERVIEW of RT - PCR tissue extract RNA copy into cDNA (reverse transciptase) do real-time PCR analyze results
Real Time Reporters ,[object Object]
REAL TIME PCR Cyber Green ,[object Object],[object Object],[object Object]
How SYBR Green works ,[object Object],[object Object]
Limitations  of  SYBER®Green ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Reverse transcription polymerase chain reaction ,[object Object]
Not to be confused with RT- PCR ,[object Object]
Other Emerging Alternatives ,[object Object],[object Object]
TaqMAN ®
TaqMAN ® Sequencing
TaqMAN ®  probes
Documentation of Amplification ,[object Object]
Molecular Beacons ,[object Object],[object Object],[object Object],[object Object]
Molecular Beacons – RT PCR ,[object Object]
Loop Mediated Isothermal Amplification (LAMP) ,[object Object],[object Object],[object Object]
LAMP ,[object Object]
LAMP ,[object Object],[object Object]
Advantages of LAMP ,[object Object],[object Object],[object Object],[object Object]
Lesser False Positives in LAMP ,[object Object],[object Object]
Loop Mediated Isothermal Amplification in Clinical Diagnosis ,[object Object],[object Object],[object Object],[object Object]
LAMP proving an efficient Technology ,[object Object],[object Object]
Multiplex PCR ,[object Object]
Uses of Automated RT - PCR ,[object Object],[object Object],[object Object]
Multiplex PCR in Real Time ,[object Object],[object Object]
Real-Time PCR Method Molecular Beacons ,[object Object]
Molecular methods are necessary if the traditional methods provide poor results ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
How are you going to measure the PCR product ,[object Object],[object Object],[object Object],[object Object],[object Object]
Importance of controls ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Standards   ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Real-time PCR applications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Emerging Technologies in Molecular Diagnosis
QIAGEN One Step RT-PCR Kit   ,[object Object]
RT-PCR in one step  The Robus™ T I Kit is base   ,[object Object]
Uses and Advantages in Testing by PCR Methods ,[object Object],[object Object],[object Object],[object Object]
Advantages Molecular methods ,[object Object],[object Object],[object Object],[object Object],In-house (home-brew) PCR methods ,[object Object],[object Object],[object Object],[object Object],[object Object],R&D is absolutely necessary
Advantages Molecular methods ,[object Object],[object Object],[object Object],[object Object],In-house (home-brew) PCR methods ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],R&D is absolutely necessary
ESTABLISHMENT OF A PCR LABORATORY ,[object Object]
Prevention of Contamination in PCR Laboratory ,[object Object]
Avoiding contamination ,[object Object],[object Object]
PCR laboratory Sample handling DNA preparation Clean room Stock solutions   Laboratory Mixing site Thermocycler Amplification Detection Documentation QC & QA Quality control & assurance R & D ( Research and development) Alternatives: - commercial kits   - robots + kits No alternative
Aseptic Handling of  Specimen a Top Priority
Machines can be Operated in limited Space
Contamination ,[object Object],[object Object]
C an we do better  ? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
A Drop of Blood decides Human Destiny
Conclusion ,[object Object],[object Object]
Dr. Kary Banks Mullis on Wisdom of Creative Nature   ,[object Object],[object Object],[object Object],[object Object]
Playing well with Genes Can Change Life ?
Created for Awareness in Developing World on Emerging Technologies in Microbiology Dr.T.V.Rao MD Email [email_address]

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PCR Technique Amplification Nucleic Acids Microbiology

Editor's Notes

  1. In this presentation, we will be using Sybr green to monitor DNA synthesis. Sybr green is a dye which binds to double stranded DNA but not to single-stranded DNA and is frequently used to monitor the synthesis of DNA during real-time PCR reactions. When it is bound to double stranded DNA it fluoresces very brightly (much more brightly than ethidium bromide does, which is why we use Sybr Green rather than ethidium bromide; we also use Sybr green because the ratio of fluorescence in the presence of double-stranded DNA to the fluorescence in the presence of single-stranded DNA is much higher that the ratio for ethidium bromide). Other methods can also be used to detect the product during real-time PCR, but will not be discussed here. However, many of the principles discussed below apply to any real-time PCR reaction.