PCR Primer Design

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PCR Primer Design
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Definition

• PCR primer design is the creation of short
  nucleotide sequences for use in amplifying a
  specific region of DNA.

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Examples

• PCR primers are designed to
• Highly conserved DNA regions
• Protein-coding regions with low degeneracy
• More conserved regions that flank variable regions

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Non-examples

• PCR primers are not designed to
• Repeat regions
• Regions with secondary structure
• Regions that can form primer-dimers
• Regions with low G/C content

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Applications

• Primer design is used for
• Finding new genes
• Developing new identification tools
• Optimizing PCRs

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Primer Design Criteria

• Target Conserved nucleotide or protein regions
• Length Usually 18 - 24 bases
• Purinepyrimidine content of around 11
• End with 1-2 GC pairs, if possible
• No inter- or intra-primer interactions
• Check with databases for specificity
• Cycling conditions and buffer concentrations
  should be adjusted for each primer pair (see
  PCR troubleshooting)

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Resource
http//www.swbic.org/education/bioinfo/pcrprimer.h
tml
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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

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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

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California State Investigation and
ExperimentationStandards

• Grades 7, 9-12
• a/b. Select and use appropriate tools and
  technology to perform tests, collect data,
  analyze relationships, and display data
• Grade 8
• a. Plan and conduct a scientific investigation
  to test a hypothesis

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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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