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New England Biolabs

DIY Centrifugation-Based Purification of cfDNA

There are many reasons you may want to study circulating, cell-free DNA (cfDNA) such as non-invasive prenatal testing to generate a molecular karyotype of an unborn fetus or for use in cancer to detect, diagnose and monitor the disease. Qiagen’s QIAamp circulating nucleic acids extraction kit is consistently cited in the scientific literature as the…

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A Beginner’s Guide to How Blunt-End Cloning Works

Blunt and sticky might sound dull and dirty but knowing how these different cloning methods work is important when choosing which method to use. Here we give you a guide to how blunt-end cloning works. Blunt-end cloning is the cloning of DNA fragments containing no unpaired bases at the 5’ and 3’ prime ends (i.e.…

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Top Tips for Troubleshooting In Vitro Transcription 

The Phobia of RNases My first experience of troubleshooting in vitro transcription came when I was synthesizing RNA In-Situ Probes for the first time. A lab mate ominously warned me that I had just returned to lab after a bout of flu and that meant I’m a walking talking factory of RNases. I went ahead…

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Faster Ligations: PEGing down the Secret

Overnight ligations are inconvenient — especially when they fail. Luckily, there’s a straightforward way to faster DNA ligations. This article highlights the secret ingredient to faster ligation reactions and offers some tips and caveats on its use. For a general overview of DNA ligations, see here and here. Buy a Quick Ligation Kit The most…

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How to Set up Your Elution Experiment

What do DNA mini preps and protein immunoprecipitation experiments have in common? They start differently, but they end with the same, critical stage – elution. But what exactly is elution, and what is the point? The Terminology First, let’s start with some basic terminology: Elution – extracting one material from another by washing with a…

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CPEC– a Quick and Inexpensive Cloning Strategy

Cloning Strategies – a Whole Lot of Options to Choose Molecular cloning has come a long way from simple restriction digestion-ligation cloning strategies to a large number of highly efficient alternatives. Broadly classified, cloning techniques can be divided as sequence dependent and sequence independent strategies. Sequence-dependent strategies are based on restriction digestion-ligation techniques or site-specific…

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Multiplex Ligation-dependent Probe Amplification (MLPA)

Multiplex ligation-dependent probe amplification (MLPA) is a molecular technique developed by MRC-Holland back in 2002. In a nutshell, MLPA is a sensitive technique that allows quantification of nucleic acid sequences, quickly and efficiently. It is performed in many laboratories worldwide, and can be applied to detect copy number changes (like deletions or duplications) of a…

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Small Differences that Matter: Detecting Microsatellite Polymorphisms

If you have any training in genetics, chances are that during the course of your education you ran into those funny little sequences called microsatellites. These are repeated tandem motifs 1-6 nucleotides long, scattered all over our genomes. These used to be called “junk DNA,” because researchers thought that the repeats served no purpose. Nowadays,…

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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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Three Important Things to Check After Obtaining Your Plasmid

You have a new plasmid, now what do you do? You are excited to go further with your project. But before you can move on, you have to confirm the presence of your insert as well as the sequence and orientation of the insert. Is the insert the right size? Most people use restriction enzymes…

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Six Facts About Restriction Enzymes

When restrictions come in the form of paperwork and approvals, we detest them. Whereas, when the restrictions come in the form of enzymes, we love them, don’t we? Restriction enzymes play a key role in biotechnology research. Read ahead for six useful facts about restriction enzymes.  1.  Restriction enzymes are helpful to bacteria Restriction enzymes…

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Faster, Even Cooler DNA Gels!

When I began a master’s program in 2008, the lab task I hated more than anything was running agarose gels for DNA. Something so simple, ubiquitous, and necessary gobbled up more hours in the lab than I care to remember. Even though we added the DNA stain directly to the molten agarose and didn’t have…

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Comparing Viral Vector Expression Systems

Some viral vectors are the little black dresses of cloning and expression experiments: They work for almost any occasion and always give you the results you were hoping for. Other vectors are more like ballgowns that only come out of storage for special occasions. Let’s wade through all the information out there and take a…

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How to Fix Your Bad Cloning Ratios

You open the incubator in the morning and to your dismay there are a hundred glorious colonies… on your vector-only control plate. While there are a number of potential causes, I’ll highlight a few of the more likely culprits and their solutions.

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How to Light Up your Life – Tips and Tricks to Troubleshoot your Luciferase Assay.

What is a luciferase assay and what is it useful for? A luciferase assay takes advantage of the innate bioluminescent properties some organisms exhibit, most notably the firefly. The firefly can convert luciferin to oxyluciferin in the presence of the enzyme luciferase to emit light. The most common scientific assays utilizing luciferase are reporter assays…

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Quick reference: Determining DNA Concentration & Purity

The most comprehensive way to evaluate DNA concentration and purity is to use both UV spectrophotometeric measurements and agarose gel eletrophoresis. This quick reference guide gives an overview of the information that can be derived from both. UV spectrophotometric measurement of DNA concentration and purity DNA itself, and most of the common contaminants found in…

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More Than a Clever Name: Northern Blots

You might think Northern Blots are an old-fashioned technique. However, qRT-PCR is prone to false positives and negatives, and reviewers may require Northern Blot confirmation of your qRT-PCR results. So sometimes Northern Blots are a necessary evil.

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Defeat RNAse Contamination Using Bleach in Your RNA Agarose Gel

So, you’ve extracted your precious RNA and want to check its quality on a gel. Conventionally, you would run a formaldehyde gel, which is messy and requires a lot of prep. Plus, it is a huge undertaking in terms of time (and money) if all you want to do is just check the quality of…

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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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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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