Team:HK SKHLPSS/Description

Description

In iGEM 2017, a DNA three dimensional nano-structure was successfully designed to detect the presence and concentration of H3N2 influenza mRNA biomarker. However, the H3N2 influenza biomarker was synthesized in commercial lab. Designed DNA nano-structure is therefore detecting mRNA biomarker theoretically.

What inspired us this year?

The success in iGEM2017 allowed us to think a step further: Could we possible to use our nano-device to check for the presence of bacteria? One of the obstacles is that we could hardly use H3N2 virus in high school laboratories to conduct any experiment. However, our team members read an article about probiotic drinks. The articles suggested that consumers could hardly find whether probiotic drinks contain enough amount of specific probiotic bacteria such as Lactobacillus or Streptococcus themophillus. In this respect, we thought of using raw Lactobacillus sample as our target bacteria to prove that nano-device could be used to check for the presence and the concentration of real bacteria.

Before the kick off of this project, we were honored to have several meet up with Professor Kwan, Hoi Shan from The Chinese University of Hong Kong. Professor Kwan suggested that it could be feasible to design a nano-device to detect for the presence of the raw bacterial sample. He also instructed us to use various online platforms, such as BLAST, to find out the appropriate sequence of the bacteria as our target sequence of the nano-device. Suggestion form Professor Kwan is a vital source of our inspiration and thus the important fuel to complete our iGEM journey.

Probiotic, living microorganisms which when administered in adequate amounts confer a health benefit on the host (WHO, 2002), is important to our gut because of several potential action, such as blacking pathogen entry into epithelial cell, creating a mucus barrier by causing the release of mucus from goblet cells, preventing diarrhea (Gareau, M. G. et al. (2010), and even reducing the probability of getting cancer (Hanahan D and Weinberg RA, 2011). However, some probiotics do not have detailed information on the strain used. Some are even off label claims . Hence, there is an urgent need in detecting strains of probiotics in food supplement products to prove their claims on label.

Sequencing is one of the common methods used in detecting probiotic strains. However, it is quite expensive and long lead time may be need. Therefore, we would like to use single stranded DNAs to design a brand new nano-structure to detect Lactobacillus, one of the common strains found in probiotics.

SO what are we doing?

To prove the practicality of the DNA nano-structure, we need to use DNA nano-structure to detect the presence and the concentration of bacteria existing in real life. As mentioned above, we designed a DNA nano-structure to check for the presence and the concentration of the Lactobacillus extracted from a commercial product. Lactobacillus, a common strain found in most probiotic products, such as yogurt drinks, could best demonstrate as a target bacterium. Besides, it is not harmful when it is accidentally leaked to the environment or exposed to the team members or even general public.

What is a DNA nano-structure?

DNA nano-structure is a structure made by several single-stranded DNAs. These DNAs are bound with each other according to the complementary base pairing principle. This formed DNA nano-structure has the ability to bind with targeted DNA strand. In our assay, when target DNA is bound with the nano-structure, it could facilitate the formation of G-quadruplex in one end of the nano-structure, so that peroxidation could be taken place. Checking the peroxidation activity level could reflect how many DNA nano-structure is bound with target DNA and in turn the concentration of the target DNA.

Wet Lab involves...

Our project is divided into two parts. The first part is to check whether the Lactobacillus DNA fragment could be bound with designed DNA nano-structure. The second part of the project involves extraction of Lactobacillus from commercial products. Lactobacillus extracted are added into the DNA anno-structure to check whether the it could bind with designed DNA nano-structure.

References

• 1. B. Ruttkay-Nedecky, J. Kudr, L. Nejdl, D. Maskova, R. Kizek, V. Adam, G-quadruplexes as sensing probes Molecules, 2013, 18, 147604779
• 2. S. C.-C. Shiu, Y.-W. Cheung, R. M. Dirkzwager, S. Liang, A. B. Kinghorn, L. A. Fraser, M. S. L. Tang, and J. A. Tanner, Aptamer-Mediated Protein Molecular Recognition Driving a DNA Tweezer Nanomachine, Advanced Biosystems, pp. 1600006-n/a, 2016.
• 3. Gareau, M. G., Sherman, P. M., & Walker, W. A. (2010). Probiotics and the gut microbiota in intestinal health and disease. Nature reviews Gastroenterology & hepatology, 7(9), 503.
• 4. Hanahan, D., & Weinberg, R. A. (2011). Hallmarks of cancer: the next generation. cell, 144(5), 646-674.