Product Class: Nucleic Acid Marker

ssRNA Ladder

Catalog #SizeConcentrationGel Lanes
N0362S25 gel lanes2,000 μg/ml25

Description

The 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.

Usage Recommendation
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.

Sample Preparation
The ssRNA Ladder is also compatible with formaldehyde-based loading buffers.

N0362

4 μg of ssRNA Ladder (denatured) on a 1.2% agarose-TBE gel.

Reagents Supplied

The following reagents are supplied with this product:

Store at (°C)Concentration
RNA Loading Dye, (2X)2X

Properties and Usage

Bases

Fragmentbp
19,000 bases
27,000 bases
35,000 bases
43,000 bases
52,000 bases
61,000 bases
7500 bases

Storage Temperature

-20°C

Storage Conditions

20 mM sodium citrate
1 mM EDTA
pH 6.0 @ 25°C

Supporting Documents

The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.
The Product Summary Sheet, or Data Card, includes details for how to use the product, as well as details of its formulation and quality controls. The following file naming structure is used to name the majority of these document files: [Catalog Number]Datasheet-Lot[Lot Number]. For those product lots not listed below, please contact NEB at info@neb.com or fill out the Technical Support Form for appropriate document.

Notes

  1. Minimize repeated freeze-thaw cycles. It is best to aliquot the marker into single use portions.
  2. 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.

References

  1. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, (2nd ed.).
  2. Liu, Y.-C. and Chou, Y.-C. (1990). Biotechniques. 9
  3. Cook, S. and Marchetti, C. Unpublished observation
  1. I need to know what types of gel to use to run RNA ladders?
  2. What types of gel and staining dyes can I use for NEB’s ssRNA Ladder (N0362S)?
  3. How much of the ssRNA Ladder do I need to load on a FlashGel 1.2% (Lonza)?
  1. Sample preparation using provided RNA Loading Dye (2X) (N0362)

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)