Transcript PCR Primer Design - Marinebiotech.net

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.
Examples
PCR primers are designed to:
Highly conserved DNA regions
Protein-coding regions with low
degeneracy
More conserved regions that flank variable
regions
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
Applications
Primer design is used for:
Finding new genes
Developing new identification tools
Optimizing PCRs
Primer 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)
Resource
http://www.swbic.org/education/bioinfo/pcrprimer.html
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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
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
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 Standards
Grades 6-12
Content Standard A: Science as Inquiry
Content Standard C: Life Science
Content Standard E: Science and Technology
END