DNA sequencing ladder

Footprinting. A technique that results in a DNA sequence ladder in which part of the ladder is missing due to the binding of protein to the DNA before processing. 

Ml3 DNA sequencing ladder, e.g., Sequenase 2.0 (United States Biochemical, Cleveland, Ohio) for use as a molecular weight marker. 

A complex PMMA-based fluidic device was built by Soper s research group [68], which coupled capillary nanoreactors to microseparation platforms (electrophoresis chips) for the generation of sequencing ladders and PCR products. The nanoreactors consisted of fused silica capillary tubes with a few tens of nanoliters of reaction volume, which can be interfaced wiht the chips via connectors micromachined in PMMA, using deep X-ray etching. A DNA tem-... 

To determine the 5 -ends of an mRNA molecule, a 5 -labeled ss DNA probe is hybridized to the RNA in which a overhang of the 3 -end of the DNA and a hybridized 5 -end of the DNA is obtained. Digestion with SI nuclease (ss specific for both RNA and DNA) removes the 3 -overhang. The SI enzyme is eliminated and the exact size of the SI probe, protected by the mRNA, is determined on a sequencing gel using a sequence ladder as a marker. Similarly, the 3 -ends of an mRNA molecule can be established using a 3 -labeled ss DNA probe. 

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