You good with gel electrophoresis and DNA Fragments?

Question

The question is how how the principles of gel electrophoresis allow for separation of DNA fragments?

My belief is that When charged molecules are placed in an electric field, they migrate toward either the positive or negative pole according to their charge. All DNA fragments have a negative charge due to their sugar-phosphate backbone. When you run electricity through the gel, the DNA fragments will move from the negative pole to the positive pole. As they DNA fragments move through the gel, they will spilt and separate based on fragment weight, the length and size of each fragment and the intensity of the charge.

I just want to know if this is true, specifically the intensity of the charge part.

Answer 1

well your pretty much right: except that they don't travel towards "either" end, only towards the positive charge because of their negativity. Yes: they do migrate different speeds because of their size and thus their different ability to travel through the Agar gel, thus leaving a band if you stained it.

Answer 2

the DNA fragments do travel thru  the gel toward the  + charge, subject to  electric filed. The separation is based on the size of the fragments and not  their length, for many gels such as agarose. Types of gel is also the limiting factor, since the  size of pores in the gel can slow down the larger size fragments, so a DNA fragment could travel different  distances on different types of gel. ie, staking gel, agarose  and (SDA-PAGE) polyacrylamide.

The intensity of electric filed may only matters in     special experiments involving  linear  fragments, where the is a viscus drag   at constance voltage, but   normally it is not an issue.

Answer 3

Because the charge/length ratio is always the same the total charge is not critical. What determines the rate of movement is the size and the configuration. A given molecule can exist in three forms: linear, a 'relaxed' circle and a supercoiled circle. These will run at different speeds, even though they are the same size:

Nicked or open circle DNA runs the slowest (highest on gel)

Linear DNA runs in the middle and the size can be compared to any standard ladder.

Supercoiled DNA runs the fastest and should be the lowest on the gel. It often migrates farther than the corresponding size of the molecular weight ladder.

Answer 4

for standard electrophoresis the intensity of the charge is generally not a factor.  DNA charge to mass ratio is the same no matter the length.  Separation is primarily based on mass and shape

consider that a supercoiled plasmid will migrate faster than a linear DNA of the same length