Archive for the ‘DNA’ Category

Transformation of competent cells

In DNA, GFP, molecular biology, plasmid, Resources, Restriction Enzyme, transformation on March 16, 2011 at 4:53 pm

Scientific Background

Transformation is the process of introducing foreign DNA (e.g plasmids, BAC) into a bacterium. Bacterial cells into which foreign DNA can be transformed are called competent. Some bacteria are naturally competent (e.g B. subtilis), whereas others such as E. coli are not naturally competent. Non-competent cells can be made competent and then transformed via one of two main approaches; chemical transformation and electroporation. It is important to note we have tested transformations of the distribution kit with this protocol. We have found that it is the best protocol. This protocol may be particularly useful if you are finding that your transformations are not working or yiedling few colonies.

In nature what happens is shown on the following two videos:


To see this in a nice lab demonstration tutorial about how transformation procedure is used, and why, watch this:


The demonstration of our iGEM protocol realized in summer 2009 is shown below:

Competent cells (we use DH5α)

DNA (this is a sample)


42°C water bath

37°C incubator

SOC (check for contamination!!)

Petri dishes with LB agar and appropriate antibiotic


1. Start thawing the competent cells on crushed ice (we find this cells in the -70°C fridge)

2. Add 200μl competent cells and 2 or 5μl (50ng) DNA on ice

3. Incubate the cells for 30 minutes on ice

4. Heat shock at 42°C for 90 seconds water bath (not shaker)

5. Incubate for 5 minutes on ice

6. Add 200μl SOC broth (but sometimes not)

7. Shaker 2 hours at 37°C

8. (Sometimes centrifuge for 10 minutes at 10000 rpm and a few supernatant take int he dumb and suspendation the pellet)

9. Plate usually 60μl of the transformation or we make distribution 20μl and 200μl Petri dishes with agar and the appropriate antibiotic(s) with the part number, plasmid and antibiotic resistance

10. Incubate the plate at 37°C for 12-14 hours

Notes & troubleshooting

If you think another video demonstration would be needed, please go on to the next video:

More details about the procedure, with excellent links cand resource material can be found in the Molecular Biology Online Notebook.


1. Sambrook, J., E.F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed.,1.25-1.28. Cold Spring Harbor Laboratory Press, Cold Spring harbor, NY, USA.

Sizes in Biology

In animation, cell, Cool stuff, DNA, molecular biology on June 30, 2010 at 6:09 pm

Dear colleagues,

An excellent tool is available to get a feeling about molecular sizes in Biology.

The tool is available here and was developped by “Learn Genetics” program from the University of Utah.

You can have a short movie on it below, but please check the original one from here!!!

Designing a gene or “Gene design”

In animation, DNA, Gene design, iGEM, Polymerase Chain Reaction, Resources, Restriction Enzyme on June 8, 2010 at 9:19 pm

On this tutorial you can see an easy way to design oligos for gene synthesis, or in other words Gene design.

The description is based on the Instructional Videos from the iGEM website!

Gene design in less than 10 minutes!

Good luck!!!

Some usefull tools:

1. Gene design web page
2. Tools at DNA20
3. Tools at DNA Works
4. A Revese-Complement Tool
5. Gene designer a comprehensive tool to artificial gene design from DNA20 described here.

QPCR oligo design

In DNA, PCR, Polymerase Chain Reaction on May 19, 2009 at 4:57 pm

Designing QPCR oligos might seem complicated but there are some rules and softwares that can make it easy. In our lab, majority of data points we generate are probably measured by QPCR, so I think  it is worth to review an algorithm for desiging QPCR assays.

So, today I will describe the way I design QPCR oligos. You can have a basic intro in PCR here.
More than a year ago I switched to the UPL system, the library of probes designed by Exiqon and now marketed by Roche. The concept is quite clear, the LNA modified oligonucleotides bind much stronger to the DNA template than the average oligonucleotides. By this we can decrease the lengths of them by keeping the Tm unchanged. The UPL library consists of 165 individual oligonucleotides that are in general nine basepair long and together cover the entire genome in respect of the coverage needed to design a QPCR oligo set for any gene. You can read more about the LNA nucleotides here and here. A good website where you can calculate the Tm of the LNA oligos here: The UPL system is described here.

The system allows the design of an oligo set for any DNA sequence in the UPL Design Centre. You can access the Design Centre directly here.

UPL Assay Design Center

UPL Assay Design Center

Before we design an assay let us first look for the transcripts of a specific gene. It is very important to use annotated data, since in the annotated genomic data we have informations about possible SNP variations. This might be important, since the oligos and especially the probe should bind to an SNP free free region, because an SNP might disturb the binding of the probe to the template.

To make this data available we should use not the sequence but the transcript ID from the Ensembl.



At Ensembl select your species of interest, e.g. mouse and write the name of your gene of interest in the search box:

search box

If you write into the box a gene of interest (e.g. COUP-TF2) we will see the results as it is shown here:

couptf search

Here I have to click on the link of the gene and I will find the following screen: transcript infoThe most important info we are looking for is in the table on the top of the page:


The two transcripts of the gene are:

We will use these ID-s in the UPL Assay Design Centre. First select as organism the “Mouse”, and write into the box the two Ensembl transcript ID-s selected by commas. designIf you follow the steps the results will be like this:

resBelow this data you can see two links as it follows:common assaysTo design an assay that would measure all transcripts select: “common assays”.

The results will be given in a downloadable pdf report. Save this file and name is by the name of the gene you used as input.

The results in the pdf file look like this:


You can see that the amplicon is 95 bp long, there is no SNP in the binding regions of the primers and probes and the probe is closer to one of the primers. There is an SNP in the gene that was avoided by the program. You can have an SNP even in the amplicon, unless is not in the binding site of the primers or the probe.

Before I order the oligos, I usually test them with e-PCR on the UCSC Genome Browser.

UCSC Genome Browser

UCSC Genome Browser

Select the PCR view and paste the oligos into the given locations. Select the genome, the assembly and the target as “UCSC Genes”(If you used a genomic sequence for design use the target: “genome assembly”).

in silico PCRIf you have a hit, click on the link provided and the results will be represented in the genome as seen here:

browser results

The oligos are intron spanning and in the right location. Order the oligos in an HPLC pufied form in the lowest available scale for the first try. Be aware that according to the experience of several groups, and my own experience too,  only 2/3 of the UPL assays work without further optimization. This means, if you want to be sure from the first you better try two, three different assays for the same gene. The UPL Design Centre will generate several primer-probe sets and you can retrive these results too. Since the UPL library is given and one or two of the three ordered assays will work, it this worth trying three from the beginning!

In general the rules for a good QPCR assay:

1. The amplicon should be as short as possible (60-70 bp is ideal, but should be shorter than 100bp).

2. The Tm of the oligos should be around 60C, while the Tm of the probe 10C higher.

3. The distance between the the oligo and the probe should be as small as possible for a better exonuclease activity of the Taq polymerase.

4. The GC content of the two oligos should be as close as possible.

5. The number of GC bases in the last five nucleotides on the 3′ ends of the two primers should be identical (if possible).

6. Select for oligo sets with week internal bonds (less than four H bonds in the same conformation).

7. Avoid primer dimers that could produce artefacts due to the 3′ elongation of one of the primers.  The same for internal conformations.  Test it on the IDT webpage here. See below:conformations

8. Verify the oligos with e-PCR on the UCSC Genome Browser. The test should give one single hit!

9. If possible use annotated sequences to avoid the SNP effect.

10. If you are looking for genes (cDNA measurement) use exons that are common for all transcripts variants (or use the “batch assay-common assays” in the UPL Assay Design Centre)

Good luck!

PCR or the Polymerase Chain Reaction

In animation, DNA, molecular biology, PCR, plasmid, Polymerase, Polymerase Chain Reaction, Replication, Taq on April 12, 2009 at 6:25 pm

When I first heard about the Polymerase Chain Reaction my first association was with the atomic bomb chain reaction. You know probably from your studies: the labile Uranium if receives a neutron it transformed to a stable Uranium isotope while several new neutrons are released. If these newly release neutrons meet novel labile Uranium atoms the reaction is amplified, more and more neutrons will be released until the system if is lost from control explodes in the form of an atomic bomb. If the reaction is under control we can produce heat and through this electricity in an electric plant, if the critical mass of the labile isotope is ignited with a neutron beam, it will explode.

You can have two excellent representations of the chain reaction below:

The chain reaction

But this is a blog about techniques in the molecular biology lab, so we will not deal with the fission chain reaction but we will see how a similar type of amplified reaction is produced with the DNA by specific enzymes in a reaction tube. The enzymes that can do a chain reaction are the Polymerases.

What is the function of polymerases? We have them in each of our cells. They do the most basic reaction that keeps life going on from the start of the very first organism ever. They are duplicating in a semi-conservative way the DNA in order to allow the transmission of the genetic information during cell division.

You can have an animation about DNA replication below.

What is the Polymerase doing?

The two DNA strands are connected by hydrogen bonds and code for the same information by the A:T and C:G base pairing.  The two strands are anti-parallel if we look to the double strand from one direction one of the strands will be in 5′-3′ direction and the other vice-versa in 3′-5′ direction. As an important rule we have to know that in nature all polymerases are doing the DNA synthesis in the 5′-3′ direction. The strand that can be replicated according to this rule is the leading strand. The other one is called lagging strand. The problem is that both strands have to replicated in by the same protein complex! But how can one single Replication complex produce the leading strand and the lagging strand in the same time ? We arrived to the problem of the the Okazaki fragments.

In the animation below you can find a good representation about how a single Replication complex can do the synthesis of the two different strands.

In order to speak about PCR we have to go out to trip to check some Geysers.

So let us check first the big Steamboat Geyser.

Yellowstone Steamboat Geyser

If we go closer to one of the hot springs we might see that the water is “living”, there are some algae, micro-organisms in this water. Let’s have a look:

The Yellowstone Hot Springs

These micro-organisms are living in really hot water. But if they are living, they should replicate, and if they replicate, they should have DNA polymerases!

These micro-organisms were isolated and one of them, called Thermo aquaticus (sometimes named Thermophilus aquaticus) became really famous. It has a polymerase that is used in vast majority of the in vitro DNA replication processes and in PCR.

I am sure you all have an idea already about PCR. We put all reagents needed for a DNA replication in a tube and reproduce the normal DNA replication process. So what do we need? We need a DNA template an oligonucleotide as a primer, the building blocks of the DNA (dATP, dTTP, dCTP, dGTP or in general dNTP -deoxi nucleotide tri phosphate), Mg and the Polymerase. If possible from Thermo aquaticus, which is called Taq.

There is one trick! This one trick was invented by Kary Mullis and he received Noble Prize for this single idea. The trick is, that we will not reproduce completely the natural reaction. We do not want to bother with leading strand and lagging strand and with all kind of Okazaki fragments and helicases and ligases.

The idea of Kary Mllis was that if you separate the double strand and design two oligos that will bind the two different strands but will look towards each other, than the product will be doubled. If you separate the strands by heating the solution to 95C you can repeat the reaction, and now you will have 4 copies. In the next run 8 copies and so on in each reaction you will have 2 on the power of the “cycle number” copies in a chain reaction fashion!!!

Let us have a really simple and good introduction to the whole procedure in the next two animations:

Below you can find a more fancy animation of the same procedure:

For this idea Mullis got the Noble Prize. His work changed completely the history of molecular biology. Let us check an interview with him about how he discovered PCR:

What is the practical use of this whole method?

Amplifying DNA by PCR became one of the most widely used method in a molecular biology lab. You can use it for transferring DNA from one plasmid to a different one, to introduce mutations and even to measure the amount of a specific gene in a sample. By combining it with a Reverse Transcription reaction we can measure copy numbers of RNA molecules.

Below we can see an example of how it is used in criminal justice!

In the next video you can see the workflow of DNA sequencing with a New Generation sequencing machine. What is remarkable here is that the designers of the instrument are skipping the cloning of the DNA fragments into plasmids and amplification of the plasmids by bacteria. They use micro reactors in the form of an emulsion PCR. One oligo is on a bead and the DNA binds the oligo. Each bead is fused with a small droplet that contains all the other reagents for the PCR. By this trick you will have a clonal amplification of the DNA fragments. One bead will contain on  type of DNA and you skipped all bacterial work. The result is that you can sequence the whole human genome in a couple of weeks for less the 100k USD. Or you can sequence a bacteria in a day…

Emulsion PCR in the FLX sequencer workflow

At the end of this lesson, lets have some fun and see the celebration of the PCR!

Restriction Enzyme Resources

In DNA, plasmid, Resources, Restriction Enzyme, Uncategorized on April 6, 2009 at 8:46 pm

Dear Colleagues,

Sometimes it is good to have links that cover a topic. This is why I have collected here a bunch of links that might be useful for you in your work.

You can have a good description of the methods used in restriction enzyme analysis here:

If you would like to use restriction enzymes for your work, you can find a list of links of the best known restriction enzyme providers below.

New England Biolabs


Roche Applied Science: Benchmate



If you want to start your work with these enzymes, please consult the protocol provided with the enzyme or check it at the website of the manufacturer.

Be sure you know what an isoschizomer is, what star activity is, or how you can make double digestion (details here and here).

Hunting Viruses

In cell culture, DNA, molecular biology, RNA, virus on March 30, 2009 at 6:02 pm

If it comes to speak about the future possibilities of molecular biology, it is worth keeping an eye on the medical applications. And if you think about the most peculiar infection agents you should for sure think of viruses also. What is a virus? Of course we all know what a virus might cause to us, like a simple respiratory infection. These are usually caused by viral infections that later are super infected with bacteria. I had a professor who tried to explain us what a virus is. It skips almost any definitions. We can not be sure if we could consider a living thing at all!!! At the end he told us in a laconic way: a virus is a VIRUS! Nothing more.

If we try to find them it is good to know, that they were discovered through the observation that you can transfer an infection from one cell culture to the other even after filtrating the solution through a filter with 0.4 micrometer holes. That means that no bacteria can bypass this filter, but infections can be transferred with this solution. The firs experiments were done in order to monitor these infections, to see that after infection there was a “clean window period”, a period when the infections agent disappeared from the cell culture. After this window the virus reappeared and the supernatant solution had infections properties again.

Today we know plenty of details about viruses. There are basically two flavours of them DNA and RNA viruses. So that is an important point! because we have plenty of molecular biology tools that allow us to characterize nucleic acids. One of the most complex tool from this series is the DNA microarray. As one of my students pointed out last week, in the next video from TED, we can have a wonderful presentation about how these tools can be used in a fast and relatively easy way to get a deeper insight in the world of viruses. As a perspective the video shows us some excellent diagnostic applications that will be probably used to develop state of the art diagnostic tools in the next couple of years.

So, let us see how it works!

More info about the viruses and vaccination, here.

Restriction Enzymes

In DNA, molecular biology, plasmid, transfection, Water on March 15, 2009 at 9:22 pm

Restriction enzymes are used to cut plasmids. We have tackled the plasmids in the previous lecture. You can have a full description about the restriction enzymes here.

As a most basic introduction I would say that restriction enzymes are enzymes of the bacteria representing a kind of immune function of the bacteria. They are present in pairs in bacteria: a DNA methylase and a restriction enzyme. They both recognize the same sequence. The bacteria is methylating its own DNA in a sequence specific manner. By this its own DNA is protected against any foreign DNA. Since horizontal gene transfer is quite common in bacteria, the bacterial cell can protect its own genetic material with the help of the restriction enzymes. The foreign DNA entering into the cell will present a different DNA methylation pattern. The unmethylated recognition sites will be cut  by the restriction enzymes and by this destroyed.

Different bacterial species have different restriction enzymes with different recognition sites (certainly each has a DNA methyltransferase, too). The nomenclature of the restriction enzyme reflects their origin. In the most trivial case the name Eco RI enzyme is informing us that it has been isolated from Escherichia coli strain R and it has been the first to have been isolated from this strain.

In the molecular biology lab we use them to cut and manipulate plasmids. They are like scissors that can be directed to specific sites in the plasmid to cleave it. With an appropriate collection of site specific cutting enzymes we can step into the very exciting field of genetic engineering.

Let us have a look to some basic usage of restriction enzymes:

You can check a good introductory video here.

In any case when working with enzymes, please use latex gloves, and keep enzymes on ice!

The unit of a restriction enzyme “U” stands for the amount of enzyme needed to cut 1microgram of plasmid with a single cutting site, in one hour, in ideal environment.

The environment of the reaction is provided by buffers. The enzymes are usually provided in a concentration of 10U/ul (10 units per microliter). The enzymes are supplied in glicerol solution and always stored at -20 C. The buffer may as well come in a 10 fold concentrated solution (10X) and it should also be kept frozen.

A typical restriction enzyme reaction is set up in the following way:

1. Check the map of the plasmid for the distribution of the cutting sites.

2. Measure the concentration of the plasmid solution by spectrophotometer. Your plasmid concentration should be in the range of 1 microgram per microliter.

3. Calculate the volume of the plasmid needed to have the required amount of product at the end. The volume of the reaction should be kept as low as possible, and should not exceed 100 ul/ reaction tube. Use sterile, DNAse free microcentrifuge (so called) “Eppendorf” tubes.

4. Plan the reaction. You should have approx 1 to 10 U of enzyme per microgram of plasmid. In the final volume of the reaction the total volume of the enzyme should be less the 1/10, because higher glicerol concentration might alter the specificity of the reaction. The buffer will be 1/10 of the final volume. Keep the final volume low (less then 100 microliters). If needed, adjust the reaction volume to the planned final volume with nuclease free water. Check the optimal temperature for the reaction. It is usually 37C, but it might differ. Check for possible star activity of the enzyme in its data sheet.


Mix the following components (ul stands for microliter):

16ul Nuclease Free Water+

1ul Plasmid solution (concentration 1ug/ul)+

2ul 10X Buffer+

1ul Restriction Enzyme (10U/ul)

Total:     20ul

5. Once the reaction is planned, start to do it: bring ice, prepare tubes, melt the buffer in your hands.

6. Pipette the required volumes of water, plasmid and buffer into the tube.

7. Add the enzyme to the tube and mix gently. Do not vortex!

8. Put the reaction into the thermostat set to the required temperature.

9. Put the enzyme and the buffer back to -20C and clean up you bench!

10. After the allocated time has  passed, stop the reaction. We are usually keeping the reaction in the thermostat for 4 hours. You can stop the reaction in several ways: by adding EDTA; by heat inactivating the enzyme at 85C for 10 minutes, or simply by freezing the tube and keeping it frozen until you purify it.

You can have a look on the applications in the video below.

Good luck!

Green Fluorescent Protein or GFP

In animation, cell, DNA, GFP, molecular biology, plasmid, RNA, transfection on March 7, 2009 at 7:00 pm

Green lights in the dark

When someone first shows up in our lab, the prime goal I set up for him or her is to make “green cells” – I mean to introduce a Green Fluorescent Protein into a mammalian cell culture. In order to be able to perform this one has to know some basic molecular biology. One has to know what a cell is, what the difference is between a prokaryote and an eukaryote cell; what the central dogma is namelly that the information flows from DNA to RNA and from here to proteins is, or as it has been formulated originally and still correctly, the information flows from nucleic acids towards proteins (albeit I assume we will see exceptions for this rule, too). (You can reach a very good lecture on this topic here.)  One has to know what the difference between DNA and RNA is, in most basic approach the chemical difference is minuscule (there is a deoxyribose in the backbone of the DNA and a ribose in the RNA, there are other differences but this is the most prominent), while the results are spectacular. DNA is a quite stable molecule that can be degraded by DNAses. DNases require divalent metal ions for their activity ( usually Mg, but other divalent ions can be used too), and we can remove these ions from solutions with so called chelating agents. Most commonly we use EDTA for this task.

From practical point of view, one needs to have some backgrounds in order not to be lost in a molecular biology lab as it follows:

One has to be able to use pipettes (as seen in the previous posts), to make buffers, to know about pH, know what molarity is, and have a good basic background in maths (just enough to calculate the compositions of the buffers).

But you can perform the most basic experiment of DNA isolation even in the kitchen! At the end of this experiment you will be able to even SEE the DNA!

You can extract DNA from any cell, but the easiest way is to use some germs, like wheat or bean germs, soya germs and so on… In the following video you can see the procedure. If you do not have isopropyl alcohol (I don’t have at home for example) use regular ethanol or a strong spirit with at least 70% alcohol content!

Regarding RNA, the world of RNA is a transient world.  RNA is degraded by enzymes that can be found everywhere. RNAses can not be blocked by removing metal ions with EDTA. This makes the half life of RNA very short. Let us take the analology of the computer: DNA is like the information on the hard disk, one might have a software on the computer without using it- this is the information in the DNA. If one double clicks on its icon, the program starts, this corresponds to the transcription: information is transcribed from DNA to RNA, or the software is running, even if it is not yet in use, it is ready to get an input and process it into the output. The RNA is similarly translated by ribosome into proteins: these are the products that have been coded in the DNA. Or according to the computer analogy you create a document with the word processor software. The document is an entity by itself.  You can print it and have it. If you turn off your computer, the temporary files are destroyed, all unsaved files are deleted. So is with the RNA. RNA is carrying an information for a short period of time, it has a short half life, but can be regenerated from the DNA. These processes are explained in the following video:

Ok, so how do we make green cells? Green flourescent protein is encoded in the genome of the Jelly fish. The protein once identified can be introduced into other organisms if we isolate the DNA sequence that is encoding the GFP protein. So let’s have a look to these wonderful organisms!

Beautiful Jelly fish

The discovery of GFP protein and their mode of action changed plenty of studies in biology. The Nobel Prize for Chemistry in 2008 was given for the identification of the GFP protein and its way of action. You can see below two videos about the topic. A detailed, in depth one or below a short overview of the topic. You choose!

Giving green light to biology

Nobel Prize for GFP

After this overview I think it is time to have an experiment. We will see how you can introduce the GFP encoding DNA into a bacteria. For this we use so called plasmids as a vector. We call vector in biology a tool that is able to carry genetic information, like a plasmid, cosmid, or a virus. A plasmid is a small circular DNA that is able to self-replicate into a bacteria and to express a protein. They are responsible for lateral gene transfer in bacteria, e.g. transfering antibiotic resistance gene from one bacteria to a different one.

In the following experiment we will see the introduction of a GFP encoding DNA into a so called Agrobacterium, a bacteria that is infecting plants.

Introducing the GFP into a bacteria

Cool, isn’t it?

We can make even more complicated investigations with the help of the GFP. In the following animation it is shown the transfection process in a mammalian cell where the addressed question is if two proteins interact or not? For this they use the so called FRET or fluorescence resonance energy transfer. In order to see if the two proteins are close to each other or not, we have to use two GFP like tagged proteins with their excitation and emission wave lengths close to each other. See how it works:

Investigating protein-protein interactions with fluorescent proteins

GFP has several other applications, like tracing of migrating neurons, as seen in the following video:

Or full GFP organisms like in the following one:

If you would like to know even more about the GFP protein, please visit the best site in this topic I have ever seen, the page of Marc Zimmer, here.

I think we had even too much of GFP now, so in the next posts we will go back to plasmids…

See you!