Descriptions, online bioinformatic tools and applications of cloning are presented in this blog
Cloning genes are necessary for basic research, but also crucial for biomedical, agricultural and pharmaceutical applications. For example, talking about the emerging new technology of CRISPR/CAS, where scientists can specifically target a sequence and further manipulate it by fix mutations and/or add, delete, upregulate, or even downregulate specific gene expression. In that regards, cloning is the primary domain to start such technology and supply the components needed to apply the technology.
Therefore, for a biology student, it is crucial to understand the central dogma and the basic knowledge of their components. Traditionally, as Watson and Crick's model was created, the DNA structure was manually manipulated for cloning designs until last two-decades. Nowadays, with the advancements of digital resources, this has been substituted by online web-based and program-based tools that easily show the components and their sequences and functional information. Engaging digital learning to teach this subject will help to enhance teaching practice and help to evaluate the optimal online tools employed for better learning and student engagement. So, we will briefly review the basics needed for cloning design, and we will discover variable online tools, which can facilitate the cloning design. **
Online websites and bioinformatics reources, which can be used in the process of lab-based cloning design
1- https://www.ncbi.nlm.nih.gov/ for searching and blasting biological components
2- https://web.expasy.org/translate/ for translating DNA into proteins (this is important for checking before and after cloning
3- http://www.labtools.us/nebcutter-v2-0/ for checking restriction digestion sites in your DNA
4- https://www.bioinformatics.org/sms/rev_comp.html for reverse complementation
5- https://www.bioinformatics.org/sms/rev_comp.html for reverse complement
6- https://www.ncbi.nlm.nih.gov/tools/primer-blast/ for Primer design
7- https://www.eurofinsgenomics.eu/en/ecom/tools/pcr-primer-design/ for primer design
8-https://molbiol-tools.ca/PCR.htm more resources for primer design
See the following video for how to use the online tools
In the following Video
I am showing how to use program-based tools for designing primers to be used for conventional cloning. Program name is Vector NTI, Invitrogen.
For clonign design example: Select your gene of interest (ex. Insulin), download CDS from NCBI as .TXT, open in Vector NTI, and check restriction enzymes for cloning design, and followed by amplify required sequence. The program will emply specific parameters and will design the required primers, which can be used for ordering.