DMS protection

Introduction

• DMS = dimethyl sulfate (different from DMSO = dimethyl sulfoxide)
• Advantage: In the footprint analysis, DNaseI is used as a probe for the protein binding site. Since DNase I is quite large itself, the protein may protect a region which is larger than the real binding sites. DMS is a small molecule; therefore, it can penetrate into the  protected region and detect the binding site more precisely.
• Disadvantage: DMS is able to methylate not only the DNA, but also the proteins. You need to verify whether you are looking at the protection pattern of the native protein or a methylated protein.

Rationale

• A DNA binding protein will protect the binding site from DMS

Methylation sites

• G: N7  (major groove), methylate faster
• A: N3 (minor groove), methylate slower

http://www.accessexcellence.org/AB/GG/basePair1.html