Laboratory
Primers Go to basic parts page
A primer, within the realm of genomics, serves as a fundamental component in various laboratory techniques, such as the polymerase chain reaction (PCR), DNA sequencing, and diverse experimental processes. These short single-stranded DNA fragments play a pivotal role in DNA replication by providing a starting point for the synthesis of new DNA strands, a task facilitated by DNA polymerases. Primers are synthesized in laboratories with specific sequences designed to bind to complementary sequences within single-stranded DNA. The design of effective primers involves careful consideration of factors such as length, GC content, melting temperature (Tm), and the avoidance of internal secondary structures or primer-primer annealing. Ideal primers typically possess a length of 18-24 bases, a GC content between 40-60%, and a Tm ranging from 50-60°C. To ensure accuracy, primer pairs should have similar Tm values and no complementary regions. Additionally, it's crucial to prevent G/C repeats at the 3' end of the primer and to limit amplicon length to around 200-1000 base pairs.
Primers are chemically synthesized by joining nucleotides together through a process that involves selectively blocking and unblocking reactive groups on nucleotides while adding them one at a time. These synthetic primers must be carefully designed to be complementary to the template DNA strand, particularly at their 3' ends, to enable efficient elongation during DNA replication.
We, iGEM Bonn Rheinbach utilized these concepts in our project. We designed 4 pairs of primers selective to genes coding for denitrifying enzymes in the bacterium Paracoccus denitrificans (strain: DMS104981). The primers identified the genes napA, nirS, norB, and nosZ. They have restriction sites that help selection and annealing into plasmids for bacterial transformation as well. Few of these primers are unique, (enter gene name) as they are his-tagged for later protein purification.
Calc-O-Matic Download document
Although each team may have its own unique projects, there are always some similarities when it comes to the type of reagents or buffers used. With this comes calculations. We created a simple tool that could revolutionize your biology lab's operations by simplifying reagent calculations. This document automatically calculates the often time-consuming and error-prone process of determining the quantities of reagents required for various experiments. By using this tool, you can save valuable research time, reduce the risk of errors, ensure consistency in your calculations, and optimize the use of resources, ultimately cutting costs and minimizing waste.
Its user-friendly interface means that anyone in the lab can quickly learn to use it effectively, and it can be easily customized to suit different experiment protocols and reagent concentrations. Furthermore, this tool provides clear documentation of all reagent calculations, which can be invaluable for audit trails, research publications, and collaboration with other labs. It's a versatile solution that can adapt to your evolving research needs, ensuring your lab remains at the forefront of scientific advancements.
Management
"Price and Seek" Download document
In the context of iGEM, where teams often operate independently with limited institutional support, the challenges can be overwhelming, particularly when it comes to sourcing essential lab products and reagents. iGEM teams are frequently required to start from scratch, which can be a daunting task. However, imagine the immense benefit a well-curated document listing trusted vendors for various products could provide to iGEM teams. Such a resource would serve as a lifeline, helping new teams embark on their experiments without compromising on quality or wasting valuable time searching for reliable suppliers. This document would not only alleviate the burden of sourcing but also promote consistency and efficiency across iGEM projects, ultimately fostering a more collaborative and successful iGEM community. It's a practical solution that could significantly enhance the experience and outcomes for iGEM teams, empowering them to focus on their innovative research and scientific advancements.
The document has an extensive list of vendors providing kits for DNA, RNA, Plasmid isolation, PCR, His-Tag Isolation, and Nitrate testing. It is accompanied by the catalog number for easy searching and prices for comparison. The list can be filtered based on price or company. These companies are most often known to sponsor various iGEM teams.