New England Biolabs, N0362S, ssRNA Ladder

Related Categories RNA Markers & Ladders,, RNA Markers and Ladders Specification Bases Fragment bp 1 9,000 2 7,000 3 5,000 4 3,000 5 2,000 6 1,000 7 500 Effective Size Range 500bp to 9,000bp Storage Buffer 20 mM sodium citrate 1 mM EDTA pH 6 @ 25°C FAQ Q: What types of gels are recommended for ssRNA and dsRNA ladders? (N0363, N0362, N0364) A: In general, when working with single-stranded RNA molecules, one should use a denaturing gel, a denaturing sample loading buffer/dye containing either formamide or urea, and SYBR Gold for staining. The SYBR Gold stain binds preferentially to single-stranded molecules and therefore it give good visualization of the bands after gel electrophoresis. In some instances, when ssRNA molecules are large in size such as the ssRNA Ladder (N0362S), one can use a native gel and stain the gel with ethidium bromide. But keep in mind that the ssRNA samples must always be prepared using a denaturing sample loading buffer/dye containing either formamide or urea. When dealing with double-stranded RNA molecules, one only needs to use a native gel, a non-denaturing sample loading buffer/dye, and stain the gel with either ethidium bromide, SYBR Green or SYBR Safe. Q: What types of gel and staining dyes can I use for NEB’s ssRNA Ladder (N0362S)? A: Although the ssRNA Ladder (N0362S) is made up of single-stranded molecules, you can run the prepared ladder on a native gel such as 1.0% - 1.2% agarose-TBE and stain the gel using either with SYBR Gold or ethidium bromide. Q: How much of the ssRNA Ladder do I need to load on a FlashGel 1.2% (Lonza)? A: We recommend loading 0.5µL - 1µL of the ssRNA Ladder. For example, mix 1µL of ssRNA Ladder with 9µL of the provided (2X) RNA Loading Dye, incubate at 90˚C for 2 minutes, chill on ice, and load 5µL per well. Q: Can I run the ssRNA Ladder on a formaldehyde gel, and if so, how much of the ladder should I use? A: For running the ssRNA Ladder on a formaldehyde gel, you will need to use 3X-5X more than the recommended amount in the protocol (i.e., 12µg-20µg of the ladder per lane) in order to obtain good visibility. Q: What is the concentration of RNA in the ssRNA Ladder (NEB #N0362) and Low Range ssRNA Ladder (NEB #N0364)? A: Since the RNA ladders are designed to be size standards and not meant for quantitation, we do not publish the concentration of these products. The release criteria for the ladders is visual inspection of the electrophoretic pattern. Even though we try our best to keep the ladder profile and band intensity consistent, the RNA concentration may vary between batches. Due to this we do not recommend these products for quantitation purposes.