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To Codon Optimize or Not: That is the Question

Posted by Alyssa Cecchetelli on Nov 12, 2020 9:15:00 AM

There are 64 different codons that encode 20 amino acids and three stop codons, meaning that the same amino acid can be encoded by more than one codon. Although the genetic code is universal, many different organisms actually prefer certain codons over others for certain amino acids. This is termed codon usage bias. In fact, some species are known to avoid certain codons altogether. 

So what does this mean for a molecular biologist who wants to express genes from one organism in another? Let’s take a look at codon usage and when you might want to optimize codons for expression in a particular organism.

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Topics: Molecular Biology Protocols and Tips, Plasmids

Quantifying DNA? Here are Five DNA Quantification Methods to Consider

Posted by Jennifer Tsang on Jul 21, 2020 9:15:00 AM

You’ve prepped your DNA and you’re ready to get started on the next step of your experiment. But in many cases, you won’t see any signs of DNA in your final tube after purification. How do you know if you actually have DNA in your tube without seeing it?

There are many ways to do this and the method you choose could be based on your downstream application, time, and instrument availability.

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Topics: Molecular Biology Protocols and Tips, Plasmids

What's the Best Way to Elute and Store Your Plasmid DNA?

Posted by Paolo Colombi on Jun 4, 2020 9:22:22 AM

If you use a kit for DNA purification or if you use a DIY purification protocol, you might have noticed that there are many options to elute your DNA prep. You might see protocols that recommend eluting in water, Tris-EDTA (TE), just Tris buffer, or some other variations. Does it make a difference? Short answer: yes. This last step will influence the stability of your sample over time and determine which experiments you can effectively use the DNA.

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Topics: Molecular Biology Protocols and Tips, Plasmids

RNA Extraction Without A Kit

Posted by Leah Schwiesow on Mar 24, 2020 9:15:00 AM

As with DNA isolation, scientists commonly rely on RNA isolation kits to make their life easier. Recently, we published a blog on DNA purification without a kit that outlined several reasons why doing something without a kit has advantages: less plastic waste, less expense, and less of being left with a bunch of random solutions when all the spin columns run out. In this article, we cover the basics of isolating RNA without a kit.

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Topics: Molecular Biology Protocols and Tips, Plasmids

DNA Purification Without a Kit

Posted by Beth Kenkel on Feb 11, 2020 9:15:00 AM

Before you reach for that silica spin column, stop to consider some ways to purify DNA without a kit. DNA purification kits have advantages: they are convenient and provide uniform, consistent results. But they are also less accessible due to their expense and requirement for lab equipment. Plus they create plastic waste. Kits can also have the annoying tendency to runout right when you need them and to accumulate a bunch of unused buffers because you’ve run out of columns.

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Topics: Molecular Biology Protocols and Tips, Plasmids

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