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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

Plasmids 101: Origin of Replication

Posted by Kendall Morgan on Nov 11, 2020 9:23:38 AM

Originally published Feb 6, 2014 and last updated Nov 10, 2020.

Now that we know all about antibiotic resistance genes, let’s consider another basic element of any plasmid: the origin of replication/replicon. The replicon is comprised of the origin of replication (ori) and all of its control elements. The ori is the place where DNA replication begins, enabling a plasmid to reproduce itself as it must to survive within cells.

The replicons of plasmids are generally different from the those used to replicate the host's chromosomal DNA, but they still rely on the host machinery to make additional copies. ori sequences are generally high in As and Ts. Why, you ask? Well, A-T base pairs are held together with two hydrogen bonds not three as G-C pairs are. As a result, stretches of DNA that are rich in A-T pairs can be separated more readily at lower temperatures and allows the replication machinery room to come in and get busy making copies.

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Topics: Plasmid Elements, Plasmids 101, Plasmids

RNA Interference in Plant Biology: New Tools for an Old Favorite

Posted by Guest Blogger on Oct 27, 2020 9:15:00 AM

This post was contributed by guest blogger, Robert Orr, who recently received a Ph.D. in Biology and Biotechnology from Worcester Polytechnic Institute.

What is RNAi?

The loss-of-function (LOF) experiment functions as the building block of our understanding of complex biological processes. Many tools exist to perturb biological function in a direct or unbiased way at the DNA, RNA, or protein level. The “correct” choice of tool requires careful balancing of the inherent advantages and limitations of any technique in the context of the biological question. For example, while gene knockouts have long been considered the “gold-standard” for LOF studies, the high gene copy number found in plants makes traditional knockouts unattractive from a practical perspective. Therefore, techniques that function downstream of DNA, such as RNA interference, can reversibly exert their effect independent of gene copy number.

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Topics: Plant Biology, Other Plasmid Tools, Plasmids

Hot Plasmids - October 2020

Posted by Various Addgenies on Oct 13, 2020 9:15:00 AM

Every few months we highlight a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and we hope they'll make it easier for you to find and use the plasmids you need. If you'd ever like to write about a recent plasmid deposit please sign up here

Here's what you'll find in this post:

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Topics: Hot Plasmids, Other Plasmid Tools, Plasmids

Plasmids 101: Screening Strategies Used in Plasmid Cloning

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

If you’re cloning a plasmid, you’ll need a way to find the needle in the haystack: the one perfect clone that contains the plasmid you’re looking for out of the many cells that don’t. One way to begin the search is by using selection strategies, where only cells that have gained or lost a specific gene survive (ex: antibiotic resistance marker). In a previous blog post, we covered how to use positive and negative selection in plasmid cloning

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Topics: Plasmids 101, Plasmid Cloning, Plasmids

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