Ethanol precipitation is a commonly used technique for concentrating and de-salting nucleic acid (DNA or RNA) preparations in aqueous solution. The basic procedure is that salt and ethanol are added to the aqueous solution, which forces the nucleic acid to precipitate out of solution. The precipitated nucleic acid can then be separated from the rest [...]

Most available heatmap programs I’ve encountered cost too much, come bundled in a huge application, don’t do what I want, or don’t offer enough flexibility. In the previous article on heatmaps, I showed how you can use ASAP utilities to sort color-coded cells using this useful Excel Add-in. What I didn’t tell you is how [...]

Alkaline lysis was first described by Birnboim and Doly in 1979 (Nucleic Acids Res. 7, 1513-1523) and has, with a few modifications, been the preferred method for plasmid DNA extraction from bacteria ever since. The easiest way to describe how alkaline lysis works is to go through the procedure and explain each step, so here [...]

The cell theory, or cell doctrine, states that all organisms are composed of similar units of organization, called cells. The concept was formally articulated in 1839 by Schleiden & Schwann and has remained as the foundation of modern biology. The idea predates other great paradigms of biology including Darwin’s theory of evolution (1859), Mendel’s laws [...]

Phenol extraction is a commonly used method for removing proteins from a DNA sample, e.g. to remove proteins from cell lysate during genomic DNA preparation. It’s commonly used, but not commonly understood. If you want to know how it works so you can show off to all of your friends… read on. The basic protocol [...]

If you want to isolate plasmid DNA, you crack your cells open and carry out a miniprep, trying very hard not to get any contaminating genomic DNA in your sample. If you want genomic DNA, you crack your cells open in a different way and try to isolate as much of the stuff as possible. [...]

BioEdit is a biological sequence alignment editor supreme. The author of this software calls it an intuitive multiple document interface with convenient features. What an understatement! At the moment I only use a couple of functions of BioEdit. Mainly I use it to view chromatograms of sequencing results, to do sequence alignments, to reverse complement [...]

Lysis of some microbes is easy, but for others its much more difficult – I think due to differences in the make-up of their cell wall. At the moment, one of my colleagues is preparing hundreds of cell-free extracts from microbes isolated from the environment to screen for interesting enzyme activities. Since she is processing [...]

Since our most popular article of all time (“The Basics: How Ethanol Precipitation of DNA and RNA Works”) was published, many of our readers have asked us to further explain the difference between precipitating DNA with ethanol vs. isopropanol and which is the better choice. So today, I’ll meet the challenge and discuss the pros [...]

I once knew a postdoc who was absurdly accurate at guessing the optical density of microbial cultures. I was jealous – imagine how much time I would save if I could spec my cultures just by looking at them! Since I lacked the innate optical talents required to compete with my friend, I developed a [...]