New England Biolabs, N2102S, microRNA Marker

Related Categories RNA Markers & Ladders,, RNA Markers and Ladders FAQ Q: Can I use the microRNA Marker on a non-denaturing gel? A: This product is not recommended for use on non-denaturing gels. The microRNA marker is intended for measuring the size of small ssRNA molecules on a denaturing gel. It is supplied in a denaturing buffer for that purpose. Q: Should I denature the microRNA Marker before loading on my gel? A: Yes. The microRNA marker is supplied in a denaturing loading buffer. It can be heated at 95°C for 5 minutes then chilled on ice before loading. Q: What is the difference between the siRNA marker and the microRNA marker (discontinued)? A: The siRNA marker (discontinued) is consisted of three synthetic non-phosphorylated RNA duplexes. This marker is used for measuring the size of small dsRNA molecules such as siRNA. The siRNA Marker should not be denatured prior to electrophoresis on a native gel. The microRNA marker (NEB #N2102S) is composed of three synthetic non-phosphorylated single-stranded RNA molecules supplied a denaturing buffer. This marker is used for measuring the size of small ssRNA such as microRNA molecules. The microRNA Marker is used in denaturing gels and stained with SYBR® Gold (Invitrogen) for visualization. This marker can also be detected via hybridization using the provided biotinylated probe. In addition, this biotinylated probe can be labeled with γ32P-ATP using T4 Polynucleotide Kinase (NEB #M0201S), since the probe has a free 5’-end. Q: Can I use EtBr for staining the microRNA Marker after gel electrophoresis? A: No. We do not recommend using ethidium bromide (EtBr) for staining the microRNA Marker, since EtBr does not chelate single-stranded RNA molecules well. In general, in order to have good visualization of single-stranded RNA molecules after gel electrophoresis, the gel must be stained using SYBR Gold (available at Life Technologies). In addition, the staining step should be brief, i.e., 1-2 minutes, otherwise the small sized single-stranded RNA molecules of the microRNA Marker will diffuse out of the gel. Q: Should I load more of the microRNA Marker so I can get better visibility of the bands after staining the gel with EtBr? A: No. Loading more than the recommended amount does not improve the visibility of the bands when the gel is stained using EtBr. In order to visualize the bands of the microRNA Marker, the gel must be stained with SYBR Gold (available at Life Technologies).