MP-Methy

MP-Methy: Primer Design for Bisulfite Sequencing and Methylation-Specific PCR #

https://m4.igenetech.com/bisd/

Introduction #

MP-Methy is developed on the basis of MP-Ref and is specifically designed for methylation primer design. It supports primer design for bisulfite sequencing of bisulfite-treated DNA, as well as for methylation-specific PCR.

Bisulfite Sequencing #

Primers should not contain CG dinucleotides, particularly at the 3′ end.

  1. “Validation method”: Set to “Bisulfite Sequencing”, also in default;
  2. “No-CG region at 3’ end”: Length (from the primer’s 3’ end) where CG dinucleotides are not allowed, 6 in default;
  3. “Maximum allowed CG count”: Maximum number of CG dinucleotides allowed in the primer sequence, 2 in default.

Methylation-Specific PCR #

The 3′ end of the primer must terminate at the cytosine (C) of a CG dinucleotide, and the presence of additional CG sites within the sequence is generally advantageous.

  1. “Validation method”: Set to “Methylation-Specific PCR”;
  2. “3’ end region for CG requirement”: Length of the region (from the primer’s 3’ end) where a minimum number of CG sites (defined by “Minimum CG sites in 3’ region”) must be present;
  3. “Minimum CG sites in 3’ region”: Minimum number of CG sites required within the defined 3’ end region (defined by “3’ end region for CG requirement”).