DescriptionThe ssRNA Ladder is a set of 7 RNA molecules produced by in vitro transcription of a mixture of 7 linear DNA templates. The ladder sizes are: 9000, 7000, 5000, 3000, 2000, 1000 and 500 bases. The 3000 base fragment is at double intensity to serve as a reference band. This ladder is suitable for use as an ssRNA size standard on denaturing or native agarose gels.
This marker was not designed for precise quantification of ssRNA mass.
Denaturing vs. Native Agarose Gels
It is common practice to electrophorese RNA on a fully denaturing agarose gel, such as one containing formaldehyde (1). However, in many cases it is possible to run RNA on a native agarose gel and obtain suitable results. In fact, it has been demonstrated that treatment of RNA samples in a denaturing buffer maintains the RNA molecules in a denatured state, during electrophoresis, for at least 3 hours (2,3). The use of native agarose gels eliminates (see other side) problems associated with toxic chemicals and the difficulties encountered when staining and blotting formaldehyde gels.
The ssRNA Ladder is also compatible with formaldehyde-based loading buffers.
The following reagents are supplied with this product:
|Store at (°C)||Concentration|
|RNA Loading Dye, (2X)||2X|
Properties and Usage
20 mM sodium citrate
1 mM EDTA
pH 6.0 @ 25°C
- Minimize repeated freeze-thaw cycles. It is best to aliquot the marker into single use portions.
- To avoid ribonuclease contamination: wear gloves, use RNase-free water for gels and buffers, wash equipment with detergent and rinse thoroughly with RNase-free water.
- Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, (2nd ed.).
- Liu, Y.-C. and Chou, Y.-C. (1990). Biotechniques. 9
- Cook, S. and Marchetti, C. Unpublished observation
To 5 ‘end label with T4 Polynucleotide Kinase, first dephosphorylate to remove 5’ triphosphates that are present as a result of invitro transcription. (for ssRNA, dsRNA,and Low Range ssRNA Ladders)