Molecular Biology on Michael’s Domain

Restriction Enzyme Calculator

Tue, 29 Apr 2025 00:00:00 +0000

Use our interactive tool to calculate the volume of restriction enzyme required for your digest.

Restriction Digest Calculator

Sometimes, you need to know how much restriction enzyme is required to cut a specific amount of a certain plasmid within a given time. Here is the calculation tool you have been looking for! All data that was used to write the code for this algorithm was obtained from New England Biolabs (NEB). The survival of the enzyme in the reaction was extrapolated from the experiments reported by NEB. Just plug in the numbers into the form and hit the submit button!

Protection from UV light

Fri, 15 Nov 2019 00:00:00 +0000

First, some definitionsUV-C (100/200-280/290nm, short-wave, hard UV)UV-B (290-315nm, medium-wave, intermediate UV)UV-A (315-400nm, long-wave UV, soft UV, “black light”)Especially for UV-C, different wave-lengths cut-offs are occasionally used to define the borders between the different UV types. Some exclude the wavelengths below 200 nm from UV-C and refer to them with the term “vacuum UV (VUV)”. Others subdevide the UV-C spectrum and refer to the wavelengths between 10 and 200 nm as “UV-C-VUV”). “Extreme UV (EUV)” refers to wave lengths between 10-121 nm and at the short end of this range, radiation is considered to be ionizing (similar to X-rays). However, I do not know of any clear wavelength border that is used to define a separation between ionizing and non-ionizing radiation. Molecular biologyMost UV tables for molecular biology are used to detect ethidium bromid-stained DNA in agarose gels. They use a wavelength around 300nm (mostly 302nm), but some have a longer wavelength option (e.g. the Alpha Innotech LM-26E can be operated at 302 or 365 nm). Rule of thumb is that the longer the wave length the less damage is done to the DNA (but the signal from DNA-intercalated ethedium bromide becomes also weaker). There are 254-nm UV lamps, but these are not suitable for DNA since they will mutate your DNA within seconds. This is not surprising since the absorption maximum of DNA itself is at 260 nm and meaning that the maximum amount of radiation is absorbed by the DNA. Hence the 302 is a compromise between sensitivity and DNA-damage. Working with a UV-table is not without danger and I would assume that there is more danger from UV than from the ethidium bromide stain, which some people (scientists!) for one or the other irrational reason are too much afraid of ( https://bitesizebio.com/95/ethidium-bromide-a-reality-check/ , http://rrresearch.fieldofscience.com/2006/10/heresy-about-ethidium-bromide.html , https://blogs.sciencemag.org/pipeline/archives/2016/04/18/the-myth-of-ethidium-bromide ). I have seen “sunburn” in one of my colleagues from too long exposure to UV light from UV-tables. The face mask protects your face, but you can still burn your arms or your décolletage.UV-transmissive and UV-opaque materialsThere is no way of knowning from the (visible) light transparency of a material how efficiently the material absorps UV light. Regular acrylic glass (“Plexiglas”) is transparent to higher wavelength UV radiation (also called UV-A, 315-400 nm) and is therefore not suitable for protecting the eyes ( https://www.gsoptics.com/transmission-curves/ ). Acrylic glass can be rendered UV-opaque by adding UV-absorbing additives. UV-filtering acrylic glass (“museum grade acrylic”) comes in different qualities. If the UV wave length is below ~375nm, any UV-filtering grade acrylic will do. UF-4 acrylic glass protects the least: 80% of 400nm-UV is passed through a 2mm sheet. UF-3 protects better and UF-5 absorps almost all of the very near-visible light UV (>390nm).Polycarbonate (PC) is your friendHowever, when you need protection from UV, polycarbonate is your friend. 3 mm thick polycarbonate is virtually completely opaque to UV from most UV sources used for molecular biology up to 400 nm. Therefore, UV-protecting face masks and sun glasses are made mostly from polycarbonate.2 mm, which is a bit thicker than the typical thickness of polycarbonate sunglasses, is mostly sufficient but the less efficient absorption compared to thicker polycarbonate matters only for UV above ~385nm (hence, good sun-glasses protect your eyes from molecular biology UV lamps, but your face skin still gets exposed). In fact, 2 mm thick polycarbonate sunglasses have less than 2 mm polycarbonate since they have on both sides of the polycarbonate a non-scratch non-UV-absorbing coating, because polycarbonate is very soft and gets scratched very easily. Unfortunately polycarbonate plastics are difficult to recognize as their number is “7” on the resin identification code (RIC) list, which is the mixed bag of “Other”.Interpreting producers’ dataWhen you check the data sheets for the optical properties of transparent materials, you soon realize that they are difficult to interpret. You soon notice that the approach of producers’ web sites is less scientific, but more advertising. They talk about UV-transmission in %, but do nowhere mention the thickness of the material, which is one of the most important aspects of absorption/transmission ( https://en.wikipedia.org/wiki/Beer%E2%80%93Lambert_law ). I strongly suspect that they use a 2 mm lightpath (thickness), the other possibility being 1 cm (which is the other “standard” length). If you have any insider knowledge, please let me know!

SnapGene - Simply the best DNA manipulation software

Fri, 01 Jan 2016 00:00:00 +0000

Our lab has been using different software packages to plan, document and visualize DNA constructs. Among those that we liked a lot for a long time were Textco’s GeneConstructionKit (GCK) and Clone Manager (Professional) . The latter runs unfortunately only under Windows. However, since several of our computers run Ubuntu Linux , we did run GCK versions 2.5 and 3 using WINE (a compatibility layer that allows us to run native Windows programs under Linux). However, with the upgrade to version 4, GCK became unusably slow under WINE and we were looking for a replacement. We contacted the developers of GCK, but they apparently were either not willing or able to help us. I suppose that the codebase of GCK is probably more than 20 years old and for that reason nobody dares to touch it. Just around that time, SnapGene was released and it fulfilled almost all of our requirements:

2-week Lab Course

Tue, 30 Dec 2014 00:00:00 +0000

I had no idea how much work it is to organize a practical lab course. Had I known, Pirjo would have had a much harder time to convince me to give this course for the Doctoral Programme in Biomedicine (DPBM)l . Kari had warned me… The accompanying lecture course had been running from September to November. The practical course had been offered with 16 free slots, but that was totally unrealistic given that we were confined to my 23.7 square meters of lab space. Teaching lab space is available, but without equipment and all the other infrastructure that is needed for such an undertaking. 8 people registered to the practical course and - luckily - half of those pulled out in the last moment with insufficient possibility to commit to the heavy workload that the course required. Thus we ended up with four students and three projects. Under no circumstances would we have managed with more.The idea was to offer each participant the possibility to realize his own DNA cloning and protein expression project. Something that would be relevant for his own PhD studies. For that matter, I had meetings with the three groups one month in advance to plan the cloning and to order the necessary materials. We were working in parallel on the following three projects:

Practical Molecular Biology and Genetic Engineering

Mon, 08 Sep 2014 00:00:00 +0000

Collection of the presentation slides for the DPBM course Practical Molecular Biology and Genetic Engineering . There are files in (at least) two different formats for each lecture: PDF and ODP (Open Document Presentation). The ODP file is editable using LibreOffice software. If you want to open it with Microsoft Office, you need to convert it first using either LibreOffice or some online conversion tool (like cloudconvert ). All material is available under the creative commons license . I might add improved versions of the lecture slides later based on participants’ feedback. The slide about restriction enzymes (REs) and how to calculate the necessary RE amounts to digest a certain amount of DNA is in the file of Lecture 1.

Software development projects for Molecular Biology

Thu, 05 Apr 2007 00:00:00 +0000

GCK2.5-related

GCK2.5 debug under wine** There are still some bugs that make using gck2.5 sometimes a pain under wine. Especially the inability to annotate regions, to search for a sequence and to open a new file.
GCK2.5 export** GCK2.5 is not able to export in embl format with the regions converted into features. It can, however, export comments to text file and plain sequence to a text file. It should be trivial to write a perl script that takes these two files and converts them into one embl file, EMBOSS cirdna/lindna or pDRAW32 file.
GCK2.5/wine desktop integration** When clicking on files that are associated with Windows programs (using wine), the Linux file manager (e.g. Konqueror) passes the file as an argument to the associated Windows application and the file is opened under wine. However GCK2.5 refuses to accept the file as an argument. When clicking on a .gcc file, GCK2.5 starts up, but opens an empty window and I have to open the .gcc file from within GCK2.5. Unnecessary clicking, especially when I need to navigate over several folder hierachies. When GCK2.5 is running natively under Windows, is it possible to start GCK2.5 with a construct file as a command line argument? I should check that out.

pDRAW32-related

Molecular Weight and Extinction Coefficient of Oligonucleotides

Wed, 30 Aug 2006 00:00:00 +0000

The formula to calculate the molecular weight of DNA oligonucleotides is:

MW (g/mol) = (nA × 249,08619) + (nG × 265,0811) + (nC × 225,07496) + (nT × 240,07462)

To calculate ε (epsilon, the extinction coefficient) of an oligo, the formula is:

The Genetic Code

Wed, 30 Aug 2006 00:00:00 +0000

Second position of codon

First
position
of
codon

ttt	Phe	F
ttc	Phe	F
tta	Leu	L
ttg	Leu	L

tct	Ser	S
tcc	Ser	S
tca	Ser	S
tcg	Ser	S

tat	Tyr	Y
tac	Tyr	Y
taa	Ochre	Stop
tag	Amber	Stop

tgt	Cys	C
tgc	Cys	C
tga	Opal	Stop
tgg	Trp	W

Third
position
of
codon

ctt	Leu	L
ctc	Leu	L
cta	Leu	L
ctg	Leu	L

cct	Pro	P
ccc	Pro	P
cca	Pro	P
ccg	Pro	P

cat	His	H
cac	His	H
caa	Gln	Q
cag	Gln	Q

cgt	Arg	R
cgc	Arg	R
cga	Arg	R
cgg	Arg	R

att	Ile	I
atc	Ile	I
ata	Ile	I
atg	Met	M

act	Thr	T
acc	Thr	T
aca	Thr	T
acg	Thr	T

aat	Asn	N
aac	Asn	N
aaa	Lys	K
aag	Lys	K

agt	Ser	S
agc	Ser	S
aga	Arg	R
agg	Arg	R

gtt	Val	V
gtc	Val	V
gta	Val	V
gtg	Val	V

gct	Ala	A
gcc	Ala	A
gca	Ala	A
gcg	Ala	A

gat	Asp	D
gac	Asp	D
gaa	Glu	E
gag	Glu	E

ggt	Gly	G
ggc	Gly	G
gga	Gly	G
ggg	Gly	G

Quick reference

Sun, 06 Aug 2006 00:00:00 +0000