DNA/RNA isolation

Every Sample, from plant and animal species to soil and water, requires a specific and optimized DNA/RNA isolation protocol. The same applies for tissue types and sample storage conditions. We not only use the popular DNA or RNA isolation kits but also the more “old school” protocols like 2%CTAB, TES buffers or hot phenol, that we can optimize and tweak for the highest quality of DNA/RNA possible.

For the cell lysis steps we use the Precellys24 or the Qiagen TissueLyser II. Furthermore, the lab is equipped with different centrifuges, cooled and non-cooled, swing-out and fixed-angle rotors, for the centrifugation of all size reactions vails and tubes.

To measure the DNA/RNA quantity and quality we use a wide variety of gel electrophoresis equipment plus two dedicated gel photo-documentation systems, the Syngene GeneGenius and VWR Imager2.  For the more precise measurements we have the Nanodrop-1000, Qubit and Implen NanoPhotometer N60 Touch.

Downstream analysis

For downstream analysis we have 4 Bio-Rad T100 Thermal cyclers. They are used for all possible PCR applications, from amplification of genomic regions of interest to cDNA synthesis and other enzymatic incubations. For gene expression experiment we have several systems

• two Quantitative Real-Time PCR Systems (qPCR)

• the ABI 7500 and the Bio-Rad CFX Connect

We also implemented new techniques like DNA sequencing from Oxford Nanopore Technologies for whole genome and microbiome sequencing, but also genetic modification techniques like CRISPR-Cas.

For CRISPR-cas9 experiments we have an Eppendorf Femtojet-4i that allows us to inject guide RNA in insect eggs. With this technique individual genes can be manipulated to study their effects on physiology and behaviour. There are 2 Biological Safety Cabinets and a large amount of climate chambers, climate cabinets and stoves for our genetic transformation and cell cultures

In the molecular biology we also have a Pamas SVSS-c, a Standard laboratory particle counter and a Partec Ploidy analyser for DAPI based DNA fluorescence used for plant cell ploidy measurements.

Organization

Three technicians are dedicated to molecular genetic analyses: Peter Kuperus, Betsie Voetdijk and Lin Dong. They assist in conducting molecular-genetic experiments using established protocols together with (and provided by) IBED PhD candidates, Postdoc researchers and staff members. Moreover, they regularly assist in a wide range of projects and courses of Bachelor and Master students.

Contact information

Please contact us if you are a permanent IBED staff member and you or your students are planning to undertake a project for which you need help on conducting molecular genetics: IBED-lab-science@uva.nl