rRNA Probe Design Service
For Diagnostics and Environmental Microbiology
Background:
If literature and public repositories do not provide appropriate sequence signatures for the rRNA-based identification of selected microorganisms, own molecular probes must be designed. The initial calculation of a list of potential molecular probes targeting a number of selected rRNA sequences can be done easily if corresponding software tools and sequence databases are available. But handling of these tools and selection of adequate probes from the list of candidates for later experimental success requires expert knowledge.
Solution:
We offer custom-made oligonucleotide probes for rRNA FISH (fluorescence in situ hybridization) based on more than 10 years of experience in the field, including additional support for your experiments to maximize specificity and sensitivity of your hybridization. A service for projects which rely on high-quality FISH experiments.
- maximum transparency for later easy citation
- highest scientific standards - manual interaction and validation
- the complete procedure for a single target sequence/group (see below) is done for a fixed price (reductions for multiple targets)
Please contact 
probes(at)ribocon.com
The procedure ...
is based on 4 steps:
- Just define your single target sequence or group of interest by sending us sequences (if not yet published), accession numbers (if already submitted), or a combination of both. You can also define a group according to a taxonomy such as EMBL or RDP.
- Probe candidates are calculated based on a publicly available, up-to-date rRNA data set comprising more than 300,000 full length rRNA sequences. If no suitable probes in terms of discriminatory power are available based on the current data sets, this will become clear, immediately. You will get informed and you don't have to pay for this service!
- From the list of candidate probes we will manually search for adequate probes for FISH application including manual adjustment of probe sequences, if required. During this procedure we will take into account various parameters affecting a hybridization reaction such as location and quality of mismatches, secondary structures, and in situ accessibility. Finally, probe binding sites will also be checked on the alignment level where potential sequencing errors leading to artificial discriminatory power can be identified.
- Probe sequences plus a quality sheet will be provided. The latter characterizes your probes including their specificity in detail. If more than one suitable probe is found matching the quality criteria (different binding sites but same "phylogenetic specificity"), all of them will be reported. The parallel application of these multiple redundant probes in your experiments dramatically increases the quality of your analysis.
Probe synthesis by our partner biomers.net
For synthesis and labelling of probes, we recommend our partner 
biomers.net.
Based on the sequence signatures received from us, you can directly order at biomers.net (biomers.net order). There, you will also find a detailed price list.
If you prefer an all-in-one solution, we can also arrange direct delivery of the ready-to-use FISH probes for you, without extra charge.