Identification and amplification of homology arms for heparan sulfate gene

Dengue fever is a disease caused by a family of Flaviviridae that are transmitted by mosquitoes. This disease caused by the dengue virus, a flavivirus which is caused by Aedes sp. until now, there is no approved drug for the treatment of dengue disease or an effective vaccine agent for the virus. Heparan Sulfate is one of the receptors that are believed to be crucial for Dengue Virus entry process, but the details on the mechanisms are still unclear. SDCJ (Syndecan 1) is a Protein Coding gene. The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan. This research purposes are to identify the suitable region of SDCJ gene for generating homology arms and also amplify the homology arms for SDCJ gene by using the polymerase chain reaction. PrimerBlast online software was used as the tool to design the target-specific primers of SDCJ gene which are forward and reverse primer for both left and right homology arms. The length of the primers design for this gene around 20 base pair. The primers that have been designed can generate the PCR product by using Polymerase Chain Reaction amplification together with 0.25µL GoTaq® DNA Polymerase. In this project, the expected PCR product is 1000 base pair. All the PCR products were purified and analyzed with 1.5 % agarose gel electrophoresis methods by running alongside with 1kb DNA Ladder Marker and resulting in successful generation of the homology arms of the SDCJ gene. The both left and right homology arms SDCJ Heparan Sulfate gene have been successfully identified and amplified. This homology arms can be used in further investigation in order to produce the knock out on the SDCJ Heparan Sulfate gene.