PCR Primer DesignPCR Primer Design

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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

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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

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