Northern Hybridization

sRNA expedites polycistronic mRNA decay in Escherichia coli

In bacteria, most small RNA (sRNA) elicits RNase E-mediated target mRNA degradation by binding near the translation initiation site at the 5' end of the target mRNA. Spot 42 is an sRNA that binds in the middle of the gal operon near the translation initiation site of galK, the third gene of four, but it is not clear whether this binding causes degradation of gal mRNA. In this study, we measured the decay rate of gal mRNA using Northern blot and found that Spot 42 binding caused degradation of only a specific group of gal mRNA that shares their 3' end with full-length mRNA. The results showed that in the MG1655Δspf strain in which the Spot 42 gene was removed, the half-life of each gal mRNA in the group increased by about 200% compared to the wild type. Since these mRNA species are intermediate mRNA molecules created by the decay process of the full-length gal mRNA, these results suggest that sRNA accelerates the mRNA decaying processes that normally operate, thus revealing an unprecedented role of sRNA in mRNA biology.

Transfer and Fixation of Denatured RNA in Agarose Gels to Membranes by Capillary Transfer

In most cases, fractionation of RNA by agarose gel electrophoresis is but a prelude to hybridization of the fractionated population to specific labeled probes that detect particular target mRNAs. RNA is first transferred from an agarose gel to a 2D support, usually a nylon membrane. This protocol presents the steps involved in the transfer of RNA from an agarose gel to a membranous support, facilitated by the upward flow of buffer, followed by various methods for fixation of the RNA to the membrane in preparation for hybridization. An alternative method for transfer by downward capillary flow is also given.

Dot and Slot Hybridization of Purified RNA

Dot blotting and slot blotting are techniques for immobilizing several preparations of nucleic acids on the same solid support, usually a charged nylon membrane. The concentrations of the target sequence of interest can be estimated by hybridizing the immobilized samples to an appropriate probe. The amounts of target sequence are estimated by comparing the intensity of signals emitted by dots containing the test samples with standards containing known concentrations of the target sequence. This protocol describes the blotting and subsequent hybridization of RNA that has been purified from cells or tissues.

Analysis of RNA by Northern Blotting

Northern hybridization is used to measure the amount and size of RNAs transcribed from eukaryotic genes and to estimate their abundance. No other method is capable of obtaining these pieces of information simultaneously from a large number of RNA preparations; northern analysis is therefore fundamental to studies of gene expression in eukaryotic cells. To prepare a northern blot for hybridization, RNA must be separated according to size through a denaturing agarose or polyacrylamide gel and transferred to a solid support in a way that preserves its topological distribution within the gel. These important steps in northern analysis are discussed here.

Separation of RNA according to Size: Electrophoresis of RNA through Denaturing Urea Polyacrylamide Gels

Thin (0.4-1.5 mm) polyacrylamide-urea gels provide high resolution of RNAs up to 1000 nt in size and are capable of resolving single-stranded fragments of RNA that differ in length by as little as 1 nt. The polyacrylamide gel is cast between two glass plates that are separated by two thin Teflon or nylon spacers. A so-called shark's tooth comb or, less frequently, a standard slotted comb forms the sample wells into which the RNA samples are loaded before electrophoresis. In contrast to electrophoresis using agarose gels, which occurs while the gel is horizontal, polyacrylamide gels are run while in the vertical position. Gels are also typically run at 45°C-55°C, which is the melting temperature of RNA, and in the presence of 6-8 m urea. The gel recipe and protocol presented here for 8 m urea/TBE polyacrylamide gels can be used for a variety of applications including mapping RNA with nuclease S1, ribonuclease protection assay, or analysis of RNA by primer extension.

Transfer and Fixation of Denatured RNA in Polyacrylamide Gels to Membranes by Electrophoretic Transfer

Polyacrylamide gels, unlike agarose gels, have a highly cross-linked matrix that does not permit efficient, quantitative, or reproducible transfer by passive diffusion. Polyacrylamide gels should therefore be transferred by electroblotting (also known as "electrophoretic transfer"). Because this approach requires the use of a transfer buffer of low ionic strength, nylon membranes are generally used. The membrane is placed directly on the gel, and the gel together with its membrane is then sandwiched between layers of filter paper and placed in a special cassette that, in turn, is placed in a tank of buffer; the cassette is oriented such that the membrane side of the gel faces the positively charged anode. A voltage gradient is applied perpendicular to the direction of the initial electrophoresis of the gel, forcing the sample to migrate out of the gel and onto the membrane.