my question related to primer self complementary and its concerning with secondary structure and dimers.
IDT has found that a significant amount of primers with hetero- or homo-dimers with a Delta G value of -9 kcal/mole can cause problems in your PCR reaction. This value is mainly a guideline to use when designing PCR primers. Ideally the Delta G values for your primers are more positive than -9 kca/mole, however it is not guaranteed that you will experience problems for primers with Delta G values more negative than this.
Essentially the more negative the Delta G value of a secondary structure, the more likely it is that you will experience problems with your PCR assay.
IDT has found that a significant amount of primers with hetero- or homo-dimers with a Delta G value of -9 kcal/mole can cause problems in your PCR reaction. This value is mainly a guideline to use when designing PCR primers. Ideally the Delta G values for your primers are more positive than -9 kca/mole, however it is not guaranteed that you will experience problems for primers with Delta G values more negative than this.
Essentially the more negative the Delta G value of a secondary structure, the more likely it is that you will experience problems with your PCR assay.
Better to say the lower Delta G Value, the perfect and non-specific PCR amplicon. In other words, it should be lower.
Raed Ahmad is that only for the total Delta G for both primers? Does it matter how much the broken down Delta G is? I.e. many single or 2 base complimentarities with high Delta G values vs 1 complimentarity with low delta G?
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