Restriction Mapping &

Southern Blotting Made SimpleClass instructions

In this lesson• Importance of complementary base pairing• Importance of 5’ and 3’ ends of DNA• Electrophoresis separates by size• Blotting keeps the DNA in the same position• The bands visible on the blot are the labeled ones but other

DNA bands are still present• Southern blotting can be used to find exact matches or

similar matches• Dye labels are used instead of radioisotopes due to safety

considerations• How to interpret restriction maps and Southern blots• How restriction enzymes produce sticky ends

The devil is in the detail!

• The 5’ prime and 3’ prime ends of the bases must be round the right way!

IMPORTANT: Do not take

bases apart!!!

Correct base pairing is critical!

• Green (Guanine) pairs with yellow (Cytosine)

• Blue (Adenine) pairs with orange (Thymine)

DNA

Black sugars = sense strand

Red sugars = antisense strand

Probe

• Single strand of DNA• Labeled with radioactivity• Used to visualise DNA• Sticks ONLY to sense strand (black

sugars)

The activity

• Divide class into three groups - each group gets a double stranded section of DNA

• Group 1 digest DNA with Taq1• Group 2 digest DNA with Sma1• Group 3 digest DNA with Taq1 and

Sma1

The activity overview• Cut the template with enzyme and separate the DNA at these sites leaving sticky ends.  

• How many fragments do you get and how big are they (measure the black sense strand only)? 

• Separate the fragments using DNA gel electrophoresis. Put fragments in size order (measure the black strand) from largest to smallest as in a DNA gel.

• Blot the DNA bands onto a membrane. Denature the DNA so it is single stranded by removing the red antisense strands from the bands leaving the black sense strands.

• DNA is blotted onto a nitrocellulose or nylon membrane so you have a replica of the positions of the DNA in the gel preserved on the membrane.

• Hybridise the DNA probe. In our example, the probe binds to one region. The probe has white sugars. Remember to keep the 5’ to 3’ prime orientation the correct way round.

• Visualise the band. Probe is labeled so it can be visualised after hybridisation. Which band does the probe bind to?

Restriction Digest Sites

Taq1

5’ - T C G A - 3'3’ - A G C T - 5’

Sma1

5’ - C C C G G G - 3'3’ - G G G C C C - 5’

Starting DNA

Black sugars = sense strand

Red sugars = antisense strand

Taq1 digest

probe is visible

BlotResult after

electrophoresis and denaturation

Sma1 digest

probe is visible

Result after electrophoresis and

denaturationBlot

Taq1& Sma1 double digest

probe is visible

Result after electrophoresis and

denaturation

Gel results

Uncut TaqI SmaITaqI

& SmaILadder Uncut TaqI SmaITaqI

& SmaILadder

DNA gel electrophoresis Southern Blotting

Restriction mapping

• Find restriction enzyme sites in DNA • Combine single & double digest

results• Use to localize where the region of

interest is on a piece of DNA (such as a genome) Hint – start with SmaI, then double digest and use TaqI result to put them in the correct order

Gel results

Uncut TaqI SmaITaqI

& SmaILadder Uncut TaqI SmaITaqI

& SmaILadder

DNA gel electrophoresis Southern Blotting

Restriction Mapping

Uncut

TaqI digest

SmaI digest

TaqI and SmaI digest

Restriction Map

SmaI

Ta

qITaqI

Ta

qI Taq

I

SmaI

uncut

SmaI & TaqI

TaqI

SmaI

17

62 54

102 5

8 9