- Course Introduction
- 01: Evidence & DNA
- 02: Forensic Biology
- 03: DNA Extraction & Quantitation
- 04: DNA Amplification
- Overview
- Introduction
- Amplification
- Primer Design
- Primer Length
- Primer Melting Temperature
- Primer Annealing Temperature
- Values for Tm
- Maximum 3′ Stability
- GC Content Percentage
- No Secondary Structures
- No Self-complementarity
- No Complementarity To Other Primers
- No Long Runs With The Same Base
- Distance Between Two Primers On Target Sequence
- Plateau Effect
- Thermal Cyclers
- Thermal Cycling Parameter and Optimization
- Works Cited & Online Links
- Locus Selection
- Multiplexing
- Contamination
- Overview
- 05: Amplified DNA Product Separation
- 06: STR Data Analysis & Interpretation
- 07: Population Genetics & Statistics
- 08: Communicating Results
- 09: Other DNA Markers & Technologies
- Course Resources
- Laboratory Training Manual
President's DNA Initiative
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Advancing Justice Through DNA Technology
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Advancing Justice Through DNA Technology
DNA Analyst Training
No complementarity to other primers
Home > DNA Amplification > Overview > Primer Design > No complementarity to other primers
Primers should contain fewer than 4 complementary bases especially at the 3′ end. Complementarity between two primers, especially at the 3′ ends, can lead to the formation of product artifacts arising from amplified primer-dimers and primer-oligomers. The concentration of primers is much higher than that of target DNA in PCR. Therefore, if the primers exhibit self-complementarity they may hybridize to each other and form homo-dimers or hetero-dimers.
Avoiding primers with 3′ overlaps is extremely important in multiplex reactions.
- A self-dimer is formed due to intermolecular interactions of the same primer.
- A cross dimer is formed due to intermolecular interaction between sense and antisense primers.
In order to detect cross dimers, the sense primer in 5′ - 3′ direction is compared with the antisense primer in 3′ - 5′ direction for homology.
