6 - Electrophoresis

Question 1

electrophoresis

Answer 1

phosphodiester linkages have a net negative charge, therefore they will migrate in an electron field

Question 2

electrophoresis gel

Answer 2

agarose or acrylamide

Question 3

speed of migration

Answer 3

• proportional to the voltage
• proportional to the charge
• inversely proportional to molecular weight
• inversely proportional to friction/length

Question 4

DNA on gel

Answer 4

shorter nucleic acids will run faster

Question 5

intercalating fluorescent dyes

Answer 5

complex organic aromatic rings have electron delocalization, therefore electrons can be excitable and fluoresce when going back to resting state

Question 6

intercalating

Answer 6

in between the bases, driven by hydrophobic effect

Question 7

intercalating longer molecules

Answer 7

will be brighter as more dyes can be intercalated

Question 8

intercalating CCCDNA/plasmids

Answer 8

unable to unwind, therefore intercalating dyes will be restricted

Question 9

intercalating open-ended DNA

Answer 9

more dyes will push strands apart, therefore intercalation must be limited

Question 10

DNA ladder

Answer 10

data with known lengths and is used in electrophoresis as a control/estimate the size of a fragment

Question 11

unresolved zone

Answer 11

fragments have not ran long enough and are too clustered

Question 12

resolution zone

Answer 12

distinguishable fragments where the distance migrated is proportional to the length of the base pair

Question 13

over-resolved zone

Answer 13

fragments are too small or indistinguishable from gel

Question 14

mistakes at curves in electrophoresis

Answer 14

a line of best fit will not work if it does not cross the original data point and will give an incorrect answer