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PCR Primer DesignPCR Primer Design
http://www.modares.ac.ir/elearning/mnaderi/Genetic%20Engineering%20course%20II/images/2a.jpg
DefinitionDefinition
PCR primer design is the creation of short nucleotide sequences for use in amplifying a specific region of DNA.
ExamplesExamples
PCR primers are designed to:
Highly conserved DNA regionsProtein-coding regions with low
degeneracyMore conserved regions that flank variable
regions
Non-examplesNon-examples
PCR primers are not designed to:
Repeat regionsRegions with secondary structureRegions that can form primer-dimersRegions with low G/C content
ApplicationsApplications
Primer design is used for:
Finding new genesDeveloping new identification toolsOptimizing PCRs
Primer Design CriteriaPrimer Design Criteria
Target: Conserved nucleotide or protein regions Length: Usually 18 - 24 bases Purine:pyrimidine content of around 1:1 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)
ResourceResource
http://www.swbic.org/education/bioinfo/pcrprimer.html
END
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 StandardsCalifornia 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 California State Investigation and Experimentationand Experimentation
StandardsStandards
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
National StandardsNational Standards
Grades 6-12
Content Standard A: Science as Inquiry
Content Standard C: Life Science
Content Standard E: Science and Technology
ENDEND
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