Electrophoresis ladder

Endonuclease-catalyzed hydrolysis of DNA at the internucleosomal linker regions into multimers of 180 base pairs which are visualized by electrophoresis as a ladder of nuclear DNA fragments. Access of the endonuclease to DNA is facilitated by depletion of polyamines, and the activity of the enzyme is mcrea.sed by and decreased by ADP-tibosylation. Thus, agents that increase intracellular Ca " or inhibit l>oly(ADP-ribose) polymerase can induce apoptosi.s. ... 

Fig. 6. Apoptotic DNA ladder pattern of eosinophils treated with dexamethasone (Dexa, 2 (xM) for 18 h (Zl). DNA was extracted from cells with ethanol (P4) and electrophoresed on 1% agarose gel in 1 X TAE (Tris acetate-EDTA) buffer (pH 8.0). After electrophoresis, the gel was soaked in 1 x TAE buffer containing 0.5 /tg/ml ethidium bromide, and DNA was visualized by an ultraviolet illuminator. Reproduced with permission from Zhang, J. R, Wong, C. K., Lam, C. W. K., Ho, C. Y., and Hjelm, N. M., Biochemical assessment of apoptosis. Chinese J. Lab. Med. Clin. Sci. 1, 27-28 (2000).

Carbeck, J. D., and Negin, R. S. (2001). Measuring the size and charge of proteins using protein charge ladders, capillary electrophoresis, and electrokinetic models of colloids. J. Am. Chem. Soc. 123,1252-1253. 

If you want to verily that the mRNA is not degraded by trace contamination by RNases, analyze the mRNA by agarose gel electrophoresis using standard protocols (16). Usually, ladder bands or smear bands around lkb-3kb are visible when good mRNA is obtained (see Fig. 4). If RNases are present, some bands smaller than 1 kb are visible. 

Figure 7.12 Agarose gel electrophoresis of the PCR product from the recombinant DNA. Lane 1, PCR product from the recombinant DNA lane 2, PCR product from the mixture without the enzymatic ligation M, 200 base pair ladder.

Biochemically, apoptosis is characterized by the internucleosomal degradation of chromosomal DNA to form a series of double-stranded fragments that are multiples of 180 200 base pairs in length. These fragments give a characteristic DNA ladder pattern on gel electrophoresis [91, 92] and can be detected by several cytochemical methods, the most extensively used being the terminal deoxynucleotidyl transferase (TdT)-mediated biotinylated dUTP nick end labeling (TUNEL) [93-95], The detection of ladder pattern and TUNEL positivity has been adopted as a marker of apoptosis. 

Fig. 4.12. Principle of the dideoxynucleotide chain-termination procedure. Primer ( ) is annealed to the single-stranded template at a site adjacent to the cloned sequence. Chain extension in the presence of the competing dideoxynucleotide results in the random incorporation of that nucleotide at the appropriate sites in the extended product. The mixture of labelled chain-terminated products are fractionated according to size by electrophoresis on a denaturing acrylamide gel and the ladder of products revealed by autoradiography.

Fig. 2 Viral genome sizes of different Phaeocystis globosa virus isolates (PgV) determined by pulsed-field gel electrophoresis (PFGE). Lane M Lambda concatamers ladder, Lane 1 uninfected culture of P. globosa, Lane 2 PgV-04 (genome size of 175 kb), Lane 3 PgV-12 T (genome size of 465 kb). The small-sized band (approximately 45 kb) as seen in lanes 1-3 correspond to bacteriophages since algal cultures were not axenic...

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-... 

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