Introduction

In molecular biology, DNA, RNA and also protein extraction is one of the basic method that has
been conducted. The purpose of the DNA extraction is to isolate and obtain genetic material for
product development for analytical or preparative purposes. There are four steps that involve in
DNA extraction which is lysis, precipitation, purification and resuspension. In this experiment,
DNA extraction were conducted by using cheek cells and also bacteria cells which is [Link] .

While electrophoresis is a method to separate protein according to their size and also charge
properties which is positive (+) and negative (-). There are several factors that also can affects
the mobility of sample in the agarose gel such as shape, the type and condition of buffer used, gel
concentration and voltage amount. Then the prepared agarose gel well was loaded with bacterial
and cheek DNA that has been extracted . UV transillumintor is a machine that are used in order
to read the banding pattern in gel electrophoresis of DNA extraction. The picture through the UV
transillumintor can be used to determine the molecular mass of the mixture of proteins by
comparing the positions of the bands to those produced by proteins of already known size.

Activity 1 : Extraction of DNA

Objective

The main objectives of this experiment are :

1. To isolate the DNA from animal cells (cheek cells) and bacterial cells

2. To compare the effectiveness of method for extraction DNA

Materials

Sample :

- Cheek cells

- Fresh overnight bacteria solution

Apparatus :

- Appendorf tube

- Micropipette

- Micropipette tips
- Vortex

-Centrifuge

- Cotton swab

Chemicals :

- Sterile distilled water

- Sterile saline

- DNAZol Direct solution

- Cotton swab plastic or stirrer

Objective

1. To separate DNA fragments of different sizes in agareose gel

2. Observe DNA fragments by staining with gel star (stain solution )

3. To estimate the size of the DNA by comparison with a known DNA ladder

Materials

Sample :

- DNA sample (cheek and bacteria)

Apparatus :

- Micropipette

- Micropipette tips

- Electrophoresis set

- Conical flask

Chemicals :

- 1XTBE buffer

- Gel stain

- DNA ladder

- 6X loading dye
Result

Bacterial cells/ [Link] :

Sample 3
Sample 5

DNA ladder

Figure 1.1- View from

Discussion

This DNA extraction experiment has been conducted by using human cheek cells and
bacteria cell that comes from [Link]. From gel electrophoresis, the result was obtained from the
UV transillumintor only shows a DNA ladder band and two sample of bacteria cells band.
Supposedly, all of the band of bromophenol blue had migrated and can be seen clearly after
using UV transillumintor.

From the figure 1.1, the reading can be estimate by using the reference of 1kb DNA
ladder. The estimate reading for band that can be detect for bacteria cells (sample 5) could be
2.0kb (48ng) and also 1.0kb (42ng). From this sample also we can see that the well are broken
during sample loading. While for another bacteria cells ( sample 3) the band reading that I
estimate from the result obtained are also 1.0kb (42ng) . But this estimation can be wrong or
inaccurate because of the band that cannot be seen clearly.

For agarose gel electrophoresis, the smallest fragment will travel and migrate further than
the large one. So we can say that the bacterial cells extractions are in small molecule because the
smaller molecule or fragments are easier to push with electrical field. Also the band did travel
quite far. For this case, sometimes the DNA may get denatured while extraction procedure,
giving a smeared appearance like the result obtained. The smearing-like behind the DNA band
also can may due to high contamination of sample. The source of error also may be because of
the buffer is to old or the concentration of the buffer are already different and the pH of buffer
probably already changed.

From the result also, we can see that the cheek cell band are not visible at all. This may
due to some error while running the DNA extraction of cheek cells. Firstly, the cheek sample
may lost when conducting the pipette or accidentally being discard with the supernatant. The
source of error also might be from loading process of sample into the well that was not correctly
done. The sample for DNA extraction also could be load by more volume so that it can be visible
through the band. The error also may come from the preparation of the agarose gel or the
composition and the concentration of the buffer that was used are not right. When pipetting the
DNA sample also may be error in which it contains bubbles and there is still some that left
behind. So that can make the DNA sample might be trapped in the bubble.
Conclusion

In conclusion, we were able to extract the DNA of bacteria and also cheek cell by using
electrophoresis gel. But only because of several error during the experiment conducted, the result
are not clear to be observe. By using electrophoresis gel, any charge of ion or molecule migrates
when placed in electric field. The migration depend upon its size, shape, buffer and also gel
concentrations. Thus, the hypothesis is accepted.

Post lab questions

1. State the location of DNA in bacterial cells.

The DNA of bacterial cells can be found loose in the cytoplasm in which called chromosomal
DNA. It is not contained within a nucleus.

2. Identify the main function of Gel Star stain in electrophoresis.

The main function of gel star stains is, it will allows sensitive fluorescent detection of DNA and
RNA using a standard 300 nm UV transillumintor following gel electrophoresis

3. Show the direction of DNA migration when electrical current is applied to the gel. Why
DNA moves towards the pole.

DNA will migrate from negative charge to positive charge poles of gel electrophoresis. This is
because DNA is negatively charge, so DNA will migrate towards the opposite which is
positively charged electrode.

4. Name any latest technology to qualify the DNA concentration.

Nanodrop and QuBit

References

1. Tan, Chee, S., Yiap, & Chin, B. (2009, November 30). DNA, RNA, and Protein Extraction: The Past and
The Present. Retrieved from [Link]

2. The Basics of DNA Extraction. (n.d.). Retrieved from [Link]