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Report On “From DNA to Bioinformatics: A Journey through the Lab” Workshop

Report On “From DNA to Bioinformatics: A Journey through the Lab” Workshop

Date: 6 August 2009

Time: 9.00am-5.00pm

Venue: SMJK Yu Hua, Kajang

Topic: Extraction of DNA

Presented by: Malaysian Genomics Resource Centre Sdn Bhd (MGRC)

Participants: Students of 6BS3, led by Puan Sang Fay Lee

Flow Of Workshop

All students were divided into four groups, which were led by Dr Micheal Ricos, Amy Chin, Ali Reza, Yong Shiuh Rong, Patrick Chia and Mazlina Mat Ali.

Activities

An opening speech was delivered by Pn Sang to welcome the six prominent instructors from Malaysian Genomics Resource Centre Sdn Bhd (MGRC).

Subsequently, Dr Micheal Ricos gave a short briefing regarding the experiment program that was to follow by.

The apparatus was set up by the students in tandem with the instructors.

The students were given revision on DNA.

A case scenario was given to the students as to let them carry out their investigations concerning the case through analytical experiment technique.

The meeting was adjourned for a short breakfast break from 10.10am to 10.30am.

The respective experiment was carried out:

6.1 DNA Extraction

a) The food sample given was crushed by using the pestle and mortar

provided.

b) 3 ml of the DNA extraction solution was added to the food sample.

c) 2 ml of the DNA extraction buffer was added and stirred till it was well

mixed with the food sample.

d) The mixed DNA solution was transferred via a filter funnel lined with

cheese cloth into a test tube.

e) The filtrate dripped slowly into the test tube.

6.2 DNA Visualization

a) The DNA solution was carefully overlaid with 2 ml of ice cold isopropanol.

The isopropanol was let slowly streaming down the inside wall of the tube.

The upper layer will be formed as isopropanol is less dense than water.

b) The end of a glass rod was slowly submerged just below interface of the

isopropanol and the aqueous DNA solution.

c) The rod was gently twirled several times in a circular motion. The white

strands and clumps form at the interface. This is the DNA we extracted.

d) 2 drops of methylene blue dye was added by using a pasteur pipette

into the tube containing the DNA solution. The dye bind with the DNA in the

solution.

6.3 Melting Process of the Agarose

a) The cap of the agar bottle was made-loosen.

b) The agar was melted on “High” setting for 2 minutes by using a

microwave oven. It was continued to be heated on “Medium” for an

interval of 5 minute until the agar has melted completely.

c) A dry towel was wrapped round the bottle. The bottle was gently shook to

homogenize the agar.

d) The gel tray was prepared by taping it to prevent leakage.

e) The comb was placed in the gel tray. When the agarose has cooled down

sufficiently, it was poured gently into the gel tray. Extra caution was given

to prevent the formation of air bubbles. The agarose gel was let to

solidify before the samples are loaded (approx. 45 minutes to 1 hour).

f) In the midst of the waiting process, a briefing about the nature of MGRC

as a researching company was presented by Dr Micheal Ricos.

g) After the agarose gel has solidified, it was placed into the gel chamber.

The gel running buffer was poured till it covered the top of the gel.

h) The gel set was assembled and connected to a power source.

6.4 Loading DNA samples

a) Each group was given one DNA sample.

b) 20µl of DNA sample was loaded into the appropriate wells of the gel by

using a micropipette.

c) The gel set was covered and the power was switched on. (85V; 85mA

constant)

d) The gel set was let running for about 30-45minutes. The status of the DNA

samples was checked periodically.

The experiment was halted in progress to permit a lunch break of one hour from 2.00-3.00pm.

The experiment was resumed after the break:

8.1 Loading DNA Samples (continued)

a) The Methylene Blue quick stain dye was poured into the tray to cover the gel completely. It was stained for 2-3 minutes, but not for more than 3 minutes. Using a funnel, the quick stain was poured into a storage bottle and saved for future use.

b) Excess dye was removed from the gel by submerging them in clean warm tap water(40-55 Celsius).The gel was gently shaked for 10 seconds to rinse.

c) The gel was transferred into a container of clean warm tap water. The gel was gently shaked once every 5 minutes and the water was changed.

d) The step above is repeated until the DNA bands can be seen. This took about 20 minutes.

Ali Reza, a lecturer, has given a briefing about the differences between sequence-matching done manually by human and the experiment protocol of the “SynaSearch” at website:www.mgrc.com.my.

The picture of the visualized DNA was pasted onto a diagram.

The lanes were labeled in the diagram accordingly.

The results obtained were utilized in resolving the case scenario stated previously.

Each group was to present their result and come to a conclusion to solve the food poisoning case.

We close our coloqium session at about 5.00pm with each group printed out the DNA finger printing results.

The ending of the ceremony

The workshop ended at about 5.00pm with Pn Sang presenting souvenirs to instructors.

Students felt enlightened because it was an eye opener and lead them to the door of biotech. We would like to extend our sincere appreciation to the instructors from MGRC and Pn. Sang for their enormous effort in making this workshop a reality. They fully sponsored this workshop including the instruments, materials, apparatus and even our food. They do not mind taking trouble to load and unload the expensive and heavy machine including the laptops just to perform the workshop for us. Even though we have to share the experiment sets as they are limited, we could not deny that Pn. Sang managed to instill the fire of interest in biotech in each and every one of us. At least we understand DNA more and electropherosis which is in our syllabus.

Event Photos

Electropherosis & Ultracentrifugation apparatus Microwave oven and boiler