Pcr troubleshooting
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PCR Troubleshooting. Definition. PCR troubleshooting is a collection of techniques that alter PCR reactions in order to achieve optimum PCR results. http://academic.brooklyn.cuny.edu/biology/bio4fv/page/genetic-engin/pcr.html. Examples. PCR troubleshooting is used to…

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PCR Troubleshooting

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Pcr troubleshooting

PCR Troubleshooting



  • PCR troubleshooting is a collection of techniques that alter PCR reactions in order to achieve optimum PCR results




  • PCR troubleshooting is used to…

    • Increase primer specificity

    • Increase quantity of PCR product

    • Increase quality of PCR product

Non examples


  • PCR Troubleshooting is not used to…

    • Purify extracted DNA

    • Create recombinant DNA

    • Quantify DNA

Factors influencing pcr success

Factors Influencing PCR Success

  • Tissue type used for DNA extraction

  • Quantity and quality of DNA

  • Length of the DNA fragment to be amplified

  • Primer specificity

Troubleshooting strategies

Troubleshooting Strategies

  • Vary temperatures to optimize primer annealing

Troubleshooting strategies1

Troubleshooting Strategies

  • Extend annealing time

    • Allows primers more time to find correct complement on template DNA

    • Can increase quantity of PCR product

    • But decreased primer specificity can lead to smeared bands

Troubleshooting strategies2

Troubleshooting Strategies

  • Ramping: Gradual increase from annealing to extension temperature

    • Taq polymerase has more time to extend amplification before the optimum extension temperature is reached

    • Locks primers into position for the final extension step

Troubleshooting strategies3

Troubleshooting Strategies

  • Other adjustable parameters:

    • Magnesium Chloride (MgCl2) concentration

    • DNA template concentration

    • dNTP concentration

    • Primer concentration

Pcr troubleshooting


California state chemistry standards

California State Chemistry Standards

Grade 8

6c. Living organisms have many different kinds of molecules…

Grades 9-12

6.Solutions are homogenous mixtures of two or more substances

7. Energy is exchanged or transformed in all chemical reactions and physical changes of matter

8. Chemical reaction rates depend on factors that influence the frequency of collision of reactant molecules

California state biology standards

California State Biology Standards

Grade 7

2e. DNA is the genetic material of living organisms and is located in the chromosomes of each cell

3a. Genetic variation and environmental factors are causes of evolution and diversity of organisms

Grades 9-12

2. Mutation and sexual reproduction lead to genetic variation in a population

7. The frequency of an allele in a gene pool of a population depends on many factors and may be stable or unstable over time

California state investigation and experimentation standards

California State Investigation and ExperimentationStandards

Grade 7-8

a. Select and use appropriate tools and technology to perform tests, collect data, analyze relationships, and display data

Grades 9-12

c. Identify possible reasons for inconsistent results, such as sources of error or uncontrolled conditions

d. Formulate explanations by using logic and evidence

k. Recognize the cumulative nature of scientific evidence

l. Analyze situations and solve problems that require combining and applying concepts from more than one area of science

National standards

National Standards

Grades 6-12

Content Standard A: Science as Inquiry

Content Standard C: Life Science

Content Standard E: Science and Technology

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