Quantcast
Skip to content

DNA / RNA Manipulation and Analysis

Nucleic acids 101: Confirming Their Quality

Nucleic acids 101: Confirming Their Quality Join us in this webinar as Dr. Victoria Doronina helps you determine the quality of your nucleic acids. In this webinar you will learn:In this tutorial, you will find: How to choose the best method to extract your nucleic acids Which method you should chose to determine nucleic acid…

Fluent automated system from TecanRead More

A Beginner’s Guide to Lentiviral Transduction

The use of viral delivery systems to transduce cells for gene and protein investigations has become prominent over the last 20 years. In particular, the use of lentiviral vectors permits stable expression of your gene of interest. This is all possible with a little bit of nucleic acid magic. Lentiviruses (a genus of retrovirus) express reverse…

HIV-buddingRead More

How to Use CRISPR to Accelerate Cancer Therapies

How to Use CRISPR to Accelerate Cancer Therapies Join Theo Roth as he describes his lab’s novel CRISPR-Cas9 genome-targeting system that does not require viral vectors to modify T cell genomes, but instead focuses on HDR. This allows rapid and efficient insertion of large DNA sequences at specific sites in the genomes of primary human…

T lymphocyteRead More

Using CRISPR/Cas9 to detect sequences on single DNA molecules with high-speed AFM

Using CRISPR/Cas9 to detect sequences on single DNA molecules with high-speed AFM Join Dr. Jason Reed as he describes a novel method by which endonuclease-inhibited Cas9 can be employed as a programmable biomarker in high-speed atomic force microscopy (HS-AFM) imaging.In this tutorial, you will find: How CRISPR/Cas9 can be used to “flag” alterations and mutations…

DNA alterationRead More

Old Reliable: Two-Step Allelic Exchange

Manipulating the genes of organisms is crucial for studying their functions. In times before genetic engineering, scientists would shoot bacteria with X-rays or expose them to destructive chemicals until spontaneous mutations would arise. Fortunately, current methods are more sophisticated and less torturous. Researchers now use more directed techniques to introduce mutations. There are several ways…

Old Reliable: Two-Step Allelic ExchangeRead More

4 Important Considerations for Your Cell Lysis

You’ve cultured your cells and completed your treatments, now it’s time to harvest them and proceed to the downstream effects. Cell lysis is the crucial stage that determines if your experiment has a chance of producing the data that you have been waiting for. Part of the starting biological material is inevitably lost on each…

4 Important Considerations for Your Cell LysisRead More

A Start to Finish Guide to Target Gene Validation Using Quantitative RT-PCR

A Start to Finish Guide to Target Gene Validation Using Quantitative RT-PCR Speaker Matthew Mule In this tutorial, you will find: While next generation sequencing enables researchers to unveil expression levels of the entire genome, qRT-PCR remains the gold standard for measuring transcript levels of individual genes for functional studies and for the purposes of…

Read More

The Use of qPCR to Validate Epigenetic Enrichment of Pathogen DNA from Complex Samples and Human DNA from Stool

qPCR is one of the most specific and sensitive tools in molecular biology, allowing the quantification of target DNA molecules present at less than 1 in 106. Next Generation Sequencing (NGS) has similar potential. However, the presence of large amounts of non-target DNA in most clinical or environmental samples precludes easy and inexpensive analysis of…

Read More

RNA Isolation from Drosophila – Don’t Let the Cuticle Scare You!

Isolating RNA from either Drosophila larvae or adult heads can seem a bit daunting, primarily due to the presence of the cuticle. The cuticle is a protective exoskeleton comprised of insoluble collagens, cuticlins, glycoproteins, and lipids. While it may take some force to remove the cuticle, you can do this easily and without compromising your…

Image of a fruit fly (drosophila melanogaster) on a metal rodRead More

A Guide to Harnessing DNA Assembly for Drug Discovery

Current DNA synthesis and assembly technologies give today’s genetic engineers unprecedented freedom to control every aspect of genetic design. In this webinar on DNA assembly, you will learn: Key concepts in DNA assembly The importance of analyzing combinatorial libraries of genetic designs for natural product biosynthesis Emerging areas of research Join Dr. Michael Smanski as…

Read More

Get to Know Your Reference Genome (GRCh37 vs GRCh38)

Whether your experiment relies upon a reference-based genome assembly or mapping reads to a reference genome to identify variants, you need to choose a human reference genome assembly. But wait! You go to the FTP site of NCBI’s refseq and click on the Homo sapiens folder. There you are presented with two choices. Which one…

reference genomeRead More

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,…

microsatellitesRead More

Extracting Circulating microRNA, Part Two: Isolation Methods

In the second part of this two part series on analyzing extracellular microRNA (miRNA) from blood or serum, we continue with the methods for miRNA extraction. Generally, there are two different approaches for microRNA isolation. The first of these is organic, liquid-liquid. The total RNA extraction method employs phenol/chloroform isolation with guanidine isotiocyanate as a…

microRNARead More

DNA Footprinting

Studying DNA–protein interactions is an important aspect of molecular biology. Researches use a variety of methods to study these like the chromatin immunoprecipitation (ChIP) assay, electrophoretic mobility shift assay (EMSA), DNA pull down assay, luciferase reporter assay, filter binding assay, yeast one hybrid system, etc. Another interesting assay that helps investigate DNA–protein interactions is the…

Image of footprints in sand by a beachRead More

Extracting Circulating microRNA, Part One: The Preanalytical Phase

microRNA (miRNA) is leading the way as circulating biomarkers in disease biomarker discovery. The hype around circulating miRNA is warranted. They meet many criteria for a good biomarker—namely, stability in circulation and varying levels in certain pathological conditions. Recently, studies have shown that miRNAs could be useful markers for cancer, myocardial infarction, atherosclerosis, and neuro-degenerative…

microRNARead More

Bacterial Transformation Troubleshooting for Beginners

The first time I did a transformation was when I worked with site directed mutagenesis. I cloned a protein sequence into the p15TVL vector, created my mutants (but that’s another story), and was finally ready for the next step: transformation and expression of my desired protein. Little did I know that my enthusiasm would fall…

transformationRead More

How UV Radiation Causes DNA Mutations

We all know that we are supposed to put on sunscreen in the summer months to protect ourselves from skin cancer, and the connection between sun exposure and cancer is well documented (Koh et al., 1996; Armstrong and Cust, 2017). UV-A and UV-B rays from the sun interact with the DNA in our skin and…

Read More

Restriction Enzymes: Five Things to Consider Before you Chop!

The use of restriction enzymes to characterize DNA has been popular since the 1970s. Today, this “old school” technique is still one of the easiest and fastest ways to assess DNA sequences. Like most lab reagents, restriction enzymes can be fickle and you should bear a few things in mind when using them. Generally, sticky-ended enzymes have greater…

Read More

DNA Extraction from FFPE Tissues for NextGen Sequencing

Rapid genomic analysis offered by next generation sequencing (NGS) is ideal for personalized medicine approaches to clinical genetics, microbiological profiling, and diagnostic oncology. Many standard clinical samples are preserved as formalin-fixed, paraffin-embedded (FFPE) tissues, which presents obstacles for use in NGS analysis. FFPE tissue preservation has the benefit of keeping samples intact for histological examination…

Read More

Those Site-Specific Recombinases in Your Tool Kit

Most of us are aware of genetic engineering systems like Cre-Lox, TALENs, Zinc finger systems, and of course, CRISPR-Cas9.  These are all examples of CSSR- Conservative Site-Specific Recombination. We use these site specific recombinases routinely, but do we really know about them or what the future hold for these tools? It turns out that CSSR…

Read More

Using Synthetic DNA For Long Term Data Storage

The amount of data requiring long-term storage is growing and accelerating. Current long-term digital storage technology cannot keep up. Imagine roughly 2.5 QUINTILLION bytes of data being created everyday in this world1–2 as more computers and network infrastructure come online. For average users, a long-term storage solution is probably not an issue. However, organizations and…

Read More

FISHing for miRNAs in Archived Tissues? Yes, It Is Possible!

We use fluorescent in situ hybridization (FISH) techniques routinely to detect DNA or RNA sequences in tissues, but what about micro RNAs (miRNAs)? No worries, FISH is now optimized to meet the challenge. To help you get going with the method, here’s what you need to know. The first thing that comes to mind when…

Read More

Transfection Toolkit

Engineering a mutation or overexpressing a recombinant protein to study and characterize its function in mammalian cells is no easy task. Luckily, Chinese hamster ovary (CHO) cells, which have been a mainstay in the lab since the 1950s, represent a relatively easy mammalian model system to engineer. There are several methods to choose choose from…

Read More

Get Your Polymerase Cycling Assembly Oligos Together

The polymerase chain reaction (PCR) is the backbone of many lab techniques. In short, it allows for the exponential amplification of a specific segment of DNA. Through the use of primers encoding restriction enzyme sites, these amplified fragments are used in downstream cloning procedures, usually leading to the insertion of one, maybe two, PCR fragments…

polymerase cycling assemblyRead More

How to Perform DNA Extraction from Dried Blood Spots Using Chelex Resin

Every bio- scientist who wants to analyze DNA knows that the process begins with the extraction of DNA from cells of interest. These cells could be RBCs, parasites, or bacteria to name a few. Furthermore, there are various DNA extraction methods1  to choose from depending on sample type, downstream analysis, and so forth. Many scientists…

Read More

Benzyl Isoamyl Alcohol: a Novel, Bizarre, and Effective DNA Purification Tool

DNA Purification We all use our favorite techniques for DNA cloning, such as Gibson assembly, TOPO cloning, ligation independent cloning (LIC), and TA cloning. However, DNA purification methods themselves, haven’t changed all that much since the 90’s. Historically, the introduction of phenol extraction in 1956, to purify nucleic acids from rat liver, rapidly replaced previous…

Read More

Guide to CRISPR/Cas9 Delivery: How to Maximize Your Editing Efficiency

In this webinar, you will learn how to maximize your genome editing efficiency using CRISPR/Cas9 and how to apply this technique in your research. The main points in the webinar will include: How to design guide RNAs using online tools specific to the genome and application of interest. Tips and practical advice to assist you…

Read More

Quantifying & Assessing RNA: TE or not TE?

Red Pill or Blue? Carrying out science often involves many difficult decisions! I see it all the time in RNA protocols – the “gracious” option of using purified water or Tris-EDTA (TE) buffer to dissolve (or elute, if you are using column purification) RNA. When I was trained in assessing RNA using UV spectrophotometry, graduate…

Read More

Cloning Large or Complex DNA Fragments

Sometimes you know a project is going to be a pain before you even start it. For me, that is whenever I need to clone large (> 3 kb) or complex (e.g., a sequence with repeats) DNA fragments. Long and complex DNA fragments are more likely to create challenges during cloning. Such projects require extra care in just about…

Read More

How DNA Extraction Is Different in Plants

I know what you are thinking, everything is made of cells, so how different can DNA extractions be in plants? The answer is… sort-of different. The overall concept is the same. Cell membranes are lysed, DNA is separated from other cell materials, washed a few times, and then resuspended in water or Tris-EDTA buffer (aka…

Read More

The Three Ts of Introducing Foreign DNA: Transfection, Transduction, and Transformation

Introducing foreign DNA into bacterial or eukaryotic cells is a common molecular biology technique. Some of the terminology involved can be confusing: transformation, transfection and transduction. What do these words actually mean? To make matters worse, sometimes people use these terms interchangeably, resulting in confusion between colleagues and collaborating labs. Here then is your definitive guide…

introducing foreign dnaRead More

Viral Vector Production: Myths & Misconceptions

Viral vector production is a worthwhile skill that can be made even easier with a few tips and tricks. In general, transfection of multiple plasmids into a producer cell line results in infectious, non-replicative virus. However, it is important to ensure that your vector preparation is efficient, giving your experiments the best chance of success.…

Virus mythsRead More

AAV Production Part II: Virus Purification

In Part I of AAV Production, I described how to produce crude (non-purified) AAV. In this article, I am going to tell you how to purify that crude prep. Virus purification is usually done by gradient ultracentrifugation. Two common methods involve gradients made from increasing concentrations of cesium chloride or iodixanol. A cesium chloride prep…

virus purificationRead More

Acid Phenol Chloroform Extraction of DNA, RNA and protein: 3 in 1

In austerity times, nothing is in excess. Apart from saving reagents, which can be refilled with extra financial injections, there is a commodity that cannot be easily resupplied – tissue samples! If, like me, you have experienced the fear of not having enough sample for performing a qPCR, western blot, and conventional PCR from the…

acid phenol chloroformRead More

Pulsed Field Gel Electrophoresis: Tips and Tricks

Running a pulsed field gel can be exciting. It isn’t often that you get to visualize such large pieces of DNA. However, it can also be extremely frustrating. It isn’t uncommon to wait 24 hours only to find out that your DNA was degraded before you started the run. Then, you have to start all…

pulsed field gel electrophoresisRead More

7 Tips for using Magnetic Beads for DNA Cleanup

Whatever molecular biology techniques you use, at some point you will have to clean up your DNA samples to remove things like buffers, contaminants and nucleotides from you precious sample, so that you have perfectly pure DNA for your downstream experiments. Magnetic beads are one DNA cleanup option. They are simple and effective—and their reassuringly…

Read More
Scroll To Top