- 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
Maximum 3′ Stability
Home > DNA Amplification > Overview > Primer Design > Maximum 3′ Stability
Free energy, ∆G, can be used to measure the thermodynamic stability of the primer-binding site. The maximum ∆G value for the five bases from the 3′ end is used for this calculation.
For primers shorter than 30 base pairs, ∆G is computed using the following equation:
∆G = ∆H – T · ∆S
∆H = enthalpy
∆S = entropy
T = the user-defined melting temperature or Tm
When ∆G is negative, the reaction is spontaneous. When choosing between various primer pairs, a lower ∆G value is favorable.10, 13, 14
