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New England Biolabs

What’s The Problem With Ampicillin Selection?

Ever wonder what those small colonies, like satellites, surrounding a larger E. coli colony on your LB with ampicillin plates were? Or why, when you picked that colony, it never had the plasmid you just transformed? Well, it’s because those satellite colonies are “protected” from the ampicillin by the big colony. Read on for more… Ampicillin…

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Strengths and limitations of your Nanodrop

Quantifying a DNA, RNA or protein sample concentration is now as easy as a click of the pipette, a push of a button and a dab of tissue to clean up. Here’s what you need to know about a few of the strengths and limitations of your Nanodrop – before you set up. Take a…

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The BOOM Method for Nucleic Acid Purification: The Ultimate Chick Flick?

The Boom method, or Boom nucleic acid extraction method, is a solid phase extraction technique for isolating nucleic acids from a solution of biological matter. This is just a fancy way of saying you use this technique to expose and remove the nucleic acids from a cell. First developed by William R. Boom, the Boom…

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Southern (blot) exposure remains a useful technique

At a meeting recently, I asked two PhD molecular biologists about the last time they used a Southern blot. After nearly a minute of unrestrained laughter, they asked “Who on earth still does that?” “Maybe for a very, very specific use,” conjectured one of the scientists. When I asked the scientist who taught me the…

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Get Ready, Get Set, Retro – How to Get Started With Retroviral Transduction

Retroviral transduction is becoming a popular choice for gene delivery into mammalian cells and has multiple advantages over other techniques. If you decide to start work on this useful technique, here is how you can go about it: Step 0: Obtain permission First and foremost, do you have the permission, authorization, and training to work…

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How to Cheat QuikChange™

Generating a DNA vector library of single and/or compound mutants for a target protein can be a daunting task. If you’re lucky and work in a well-funded lab, you might outsource this process via gene synthesis. Most of us though, need to do it the old-fashioned way. Traditional QuikChange™ Traditionally, there are many steps you…

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Retroviruses – Friends or Foes?

The word ‘retrovirus’ evokes images of HIV, the AIDS pandemic and a desperate worldwide effort to defeat this mighty adversary. But on the flip side, scientific research has managed to tame the virus and use it as a tool for advancement. Retroviruses are commonly used to introduce genes into mammalian cells to express or knockdown…

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Don’t Clone Alone: A Comparison Between SnapGene and Genome Compiler

There are several software platforms that exist today to help molecular biologists and genetic engineers think about and execute their research for grander hypotheses, more immediate results and the production of masses of data. After recently reading the article “Vector NTI Vs Genome Compiler,” I’ve continued this comparison with another conventional, widely adopted DNA design…

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4 Tips for Extracting RNA from Unfriendly Tissues

Some tissues are tricky to work with. This truth was lost on me in the early years of grad school because I worked with liver samples. If you’re extracting RNA from liver samples, you’re likely not losing sleep over your massive RNA yields. But for the folks doing RNA extractions with less willing donors, such…

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How DNA Extraction Kits Work in the Lab

We give a lot of troubleshooting help on RNA and DNA extraction here at Bitesize Bio because almost everything we do in molecular biology requires DNA or RNA at the very first step.  These days, most labs use commercial DNA extraction kits, which employ spin columns, for the isolation of DNA and RNA. The spin columns…

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Baby Got BAC – Working with Bacterial Artificial Chromosomes

While they may not be as in demand as when they were the basis of sequencing projects, bacterial artificial chromosomes (BACs) are still used for a wide variety of projects. Based off of the F origin of replication, BAC vectors can stably maintain up to 300 kb of sequence in a single plasmid, lending themselves…

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Cloning Round Up

Cloning can be the bane of a scientist’s existence. Rarely is cloning the end goal of an experiment. Generally it is the means to an end for studying something interesting that piece of DNA does, such as expressing a protein. That’s where we come in. We have tips and tricks for all sorts of cloning.…

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Seamless Ligation Cloning Extract (SLiCE) Explored and Explained

Traditionally, if you’re hoping to clone a DNA/RNA fragment (or insert) into a vector, such as a BAC you would need: Expensive exonucleases, called restriction enzymes: pacman-like enzymes that chomp at specific sequences in your destination vector or fragments to be inserted (often just “inserts”). Sequence homologies between your inserts and your destination vector, called…

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Banish the Background with Toxin–antitoxin Cloning Systems

One of the most annoying traits of “classical cloning” is an imperfect system of discriminating between the clones containing an empty vector and vector with insert after cloning. Even when your self-ligation control plate is empty, you can have a lot of colonies containing an empty vector on the “vector + insert” plate. Even the blue-white…

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BioBricks: Lego for Scientists!

Lego bricks are used, mostly by children, to construct vehicles, buildings, and even working robots. Surely the idea of bringing Lego to the lab is childish, but think just for a second… since the human genome has been fully characterized, can we use a Lego-like approach to “build” entire living organisms from scratch? This may…

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Choosing the right plasmid vector: A Guide for beginners

If you’re picking up a list of available plasmid vectors for the first time, it can be mind-blowing to decide on the best one for your experiment. What cloning sites do you need? What restriction enzyme sites? What insert size is possible? Let me help you with some pointers about what factors to look out…

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DIY Phase Separating Gel: Clean and Cheap!

Phenol/chloroform extractions are a common lab technique to remove proteins from aqueous solutions containing DNA and RNA.  They can be tedious and a bit time consuming if you are working with a lot of samples.  And accidental carryover of phenol/chloroform can inhibit downstream applications. Over time, I thought I had achieved some level of competency…

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5 Ways to Really Screw Up Your RNA Prep

Unlike DNA, which can last for eons, RNA is a fragile and degradation-prone cousin. After working with RNA for a while, one becomes quite paranoid about handling RNA because even a single sneeze or drop of saliva can potentially affect your results. The reason is that there are enzymes called RNases that specifically target and…

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