Understanding gel electrophoresis
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Understanding Gel Electrophoresis. Overview of topics covered. Basic Principles Demonstration of a gel Ladders as references Optimizing the separation. Gel electrophoresis separates a mixture of DNA fragments according to size

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Overview of topics covered l.jpg
Overview of topics covered

  • Basic Principles

  • Demonstration of a gel

  • Ladders as references

  • Optimizing the separation


Purpose of gel electrophoresis l.jpg

Gel electrophoresis separates a mixture of DNA fragments according to size

This is accomplished by drawing the DNA fragments through a gel

Purpose of Gel Electrophoresis


Slide4 l.jpg

Basic Principle of Electrophoresis according to size

A mixture of DNA molecules becomes organized by size


How does gel electrophoresis separate dna fragments l.jpg
How does gel electrophoresis separate DNA fragments? according to size

  • The gel acts as a sieve to filter the DNA fragments

  • The DNA fragments are naturally negatively charged due to the phosphate backbone

  • DNA fragments of differing sizes will move though the gel at differing rates

  • Smaller fragments move faster through the gel and larger fragments move slower


The need for an electric field l.jpg
The Need for an Electric Field according to size

  • The electrostatic charges set up in the gel act as the “force”

  • The anode has a relative lack of electrons and has a net positive charge

  • The cathode is rich in electrons and has a net negative charge

  • The DNA is loaded in wells near the cathode

  • The DNA is pulled towards the anode by electric attraction


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+ + + + + + + + + + + + + + + + + + + + + + + + ++ + + + + + + + + +

DNA is negatively charged and therefore repelled from the negative pole and attracted towards the positive pole

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Size selection in an agarose gel l.jpg
Size selection in an Agarose Gel + + + + + +

  • The agarose gel is full of tiny pores which the DNA can slide through. The smaller pieces can easily find a route to the positive terminal.

  • The larger fragments cannot slide through the pores as easily.

  • This results in the smaller fragments moving quickly to the positive end of the gel and the larger fragments move much slower and remain close to the negative end of the gel.


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+ + + + + + + + + + + + + + + + + + +

_ _ _ _ _ _ _ _ _ _ _ _


A typical electrophoresis gel setup l.jpg
A Typical Electrophoresis Gel Setup + + + + + +

Negative end- - - - - - - - - - - - -

Direction

of DNA

movement

Direction

of DNA

movement

Positive end+ + + + + + + + + +


A typical image of an agarose gel under uv light l.jpg
A Typical Image of an Agarose Gel Under UV Light + + + + + +

Largest DNA fragments

Decreasing

DNA

Size

  • The DNA fragments can be visualized using a special dye that specifically binds DNA and fluoresces under illumination with UV light

Smallest DNA fragments


The intensity of the band is proportional to the concentration of dna l.jpg
The Intensity of the Band is Proportional to the Concentration Of DNA

  • An important point to remember is that the intensity of the band is proportional to the amount of DNA found in the band

The upper band has far less

DNA when compared to the lower

band. The intensity of the bands

are proportional to the amount of DNA at that position in the gel


Sizing the fragments of dna l.jpg
Sizing The Fragments of DNA Concentration Of DNA

  • The sizes of the various fragments can be identified by including a “ladder” in the gel

    • A ladder is a mixture of DNA fragments of known size

    • A ladder is usually run beside the unknown sample so that the sizes of the various DNA fragments in the sample can be identified


Ladder l.jpg
Ladder Concentration Of DNA

  • A ladder is a mixture of DNA fragments of selected sizes

  • When run in a gel electrophoresis, these fragments will separate into distinct bands that can be used as references

  • The size of a fragment is always stated as [X] base pairs (bp)

  • Two common ladders are the 100bp and the 1kbp (1000 bp) ladders

  • Ladders are commercially available and purchased from suppliers


Typical ladders 100 bp 1 kbp 1000 bp l.jpg
Typical Ladders-100 bp & 1 kbp (1000 bp) Concentration Of DNA

  • The 100 bp ladder is composed of a mixture of small fragments (100 to 2000 bp)

  • The 1000 bp ladder is composed of a mixture of larger fragments (500 to 12000 bp)


Sizing a gel product l.jpg
Sizing a Gel Product Concentration Of DNA

Base

Pairs

(bp)

4000

3000

2000

1600

1000

500

2000 bp

1000 bp

1Kbp Sample

ladder


What is the size of this fragment l.jpg
What is the Size of this Fragment? Concentration Of DNA

4000

3000

2000

1600

1000

500

Sample 1Kbp

ladder


The size of this fragment is l.jpg
The size of this fragment is… Concentration Of DNA

4000

3000

2000

1600

1000

500

Sample 1Kbp

ladder

The fragment is between the 2000 bp and 3000 bp band (in red)

It is approximately 2500 bp in size


Reference bands in ladders l.jpg
Reference Bands in Ladders Concentration Of DNA

  • Ladder scales are not written on a gel but one is given certain characteristic bands to use as landmarks and are easily identifiable

    For Example:

    • In the 100 bp ladder, the 500 bp and the 1000 bp bands are made to stand out

    • In the 1 kbp (1000 bp) ladder, the 1600 bp band stands out


The 100 bp ladder l.jpg
The 100 bp Ladder Concentration Of DNA

  • In the 100 bp ladder the reference bands are the 500 and 1000 bp

    (0.5 and 1.0 kbp)

  • Every band above and below increase by 100 bp


The 1 kbp ladder 1000 bp l.jpg
The 1 kbp ladder (1000 bp) Concentration Of DNA

  • The reference (bright) band is 1.6 kbp

  • The band directly above is 2.0 kbp and increases by 1.0 kbp as you go up

  • Below the reference band lies the 1.0 kbp and the 0.5 kbp bands

1.6 kbp reference band


Using a ladder l.jpg
Using A Ladder Concentration Of DNA

  • To use a ladder for size estimation, one must locate the reference band(s). This is usually one band that is particularly bright.

  • Once you have found this band and know the distribution of fragment sizes of the ladder, one can start estimating the sizes of the samples.


What is the size of this fragment23 l.jpg
What is the Size of this Fragment? Concentration Of DNA

The 100 bp ladder was used

Reference Ladder


The size of the fragment is l.jpg
The size of the fragment is… Concentration Of DNA

Size In Base Pair (bp)

1500

1200

1000

600

500

400

300

200

≈175 bp

100


What is the size of these fragments l.jpg
What is the Size of these Fragments? Concentration Of DNA

The 1 kbp ladder was used

4000

3000

2000

1600

1000

500


The size of the fragments are l.jpg
The size of the fragments are… Concentration Of DNA

Sizes in Base Pairs (bp)

5000

4000

3000

≈1800 bp

2000

1600

≈1100 bp

1000

500


What is the size of these fragments27 l.jpg
What is the Size of these Fragments? Concentration Of DNA

The 1 kbp ladder was used

4000

3000

2000

1600

1000

500


The size of the fragments are28 l.jpg
The Size of the fragments are… Concentration Of DNA

6000 bp

5000

4000

3000

≈1800 bp

2000

1600

≈1100 bp

1000

≈800 bp

500


Optimizing your gel electrophoresis l.jpg
Optimizing Your Gel Electrophoresis Concentration Of DNA

One parameter that can be altered to optimize a gel electrophoresis is the agarose concentration in the gel


Background about agarose l.jpg
Background About Agarose Concentration Of DNA

  • Agarose is a mixture of long chains of saccharides (sugar)

  • It is extracted from a seaweed and is used in oriental cuisine as a gelling agent for deserts, much like gelatin is used in European cuisine

  • The greater the agarose concentration, the smaller the pores within the gel

  • This changes the ease with which the DNA can travel through the gel


Effects of changing gel concentration l.jpg
Effects of Changing Gel Concentration Concentration Of DNA

  • By increasing the agarose concentration the smaller DNA fragments will give a clearer separation

  • By lowering the agarose concentration the larger fragments of DNA will give a clearer separation

  • By optimizing the % agarose one can clearly separate a mixture of similar DNA fragments


Effect of percent agarose on fragment separation l.jpg
Effect of Percent Agarose on Fragment Separation Concentration Of DNA

As stated, the % agarose in the gel affects the size of the pores in a gel, which affects the speed to which DNA can travel through the gel.

Higher percent agarose gels resolving smaller base pair fragments better than low percent agarose gels

High base pair fragments resolve better in low percent agarose gels


Effect of percent agarose on fragment separation an example l.jpg
Effect of Percent Agarose on Fragment Separation Concentration Of DNAAn example

The 1kbp ladder and the 100bp ladder were run with 0.8 and 1.6 % agarose gels under the same conditions

1600

1000

1600 bp

500

400bp

1000 bp

300 bp

500 bp

200 bp

0.8% Agarose

80V – 2 hours

1.6% Agarose

80V – 2 hours

Note how the bands have moved further in the low % agarose gel and the higher bp fragment are better defined. The low bp fragments are better defined in the high % agarose gel and are unresolved in the low % agarose gel


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