Sequence of DNA

Question

While giving an amateur reading to DNA. I was stuck within the first few lines:
Refined resolution of the structure of DNA, based on X-ray crystallography of short synthetic pieces of DNA, has shown that there is a considerable variance of the helical structure of DNA, based on the sequence. For example, a 200-bp piece of DNA can run as if it were more than 1000 bp on an acrylamide gel if it has the right sequence. The double helix is not the same uniform structure.
What does this highlighted portion mean?

Maximilian Press · Accepted Answer

DNA sequence is what we call a string of nucleotides in the DNA polymer, such as GATTACA, representing a chemical structure wherein each letter ("G", "A", "T", "T", "A", "C", "A") represents a nucleotide that has a chemical bond to the next nucleotide. Possible nucleotides in DNA are adenine, guanine, thymine, and cytosine, e.g. A, G, T, C (you may also see such terms as thymidine, thymosine etc. depending on what piece of the DNA molecule you're talking about). What such a sequence implies for double-stranded DNA is that those nucleotides are then hydrogen-bonded to another "reverse complement" sequence, which for every nucleotide in the first sequence has a "C" for every G, a "A" for every T, a "G" for every C, and a "T" for every A. One way of representing this would be as follows:
GATTACA
|||||||
CTAATGT

Where | represents a hydrogen bond between the two strands of DNA at each nucleotide. A single-stranded DNA however would not have the H-bonds or the (lower) complement sequence.
Altogether, this is what is implied by DNA "sequence", though normally we only write GATTACA for simplicity.
What your quote means is that GATTACA can have a different behavior in a polyacrylamide gel than GGGGGGG or ATATATA or CCGGCCG, or any number of other 7-nucleotide DNA polymers. This has to do with the shape of the different nucleotides, each of which has a distinct chemical structure:

Some of the nucleotides force the DNA polymer molecule to take on different shapes, or to be stiffer or more flexible, because of their underlying chemical shape.
A polyacrylamide gel is basically a big tangle of polyacrylamide molecules and bonds. So think of DNA moving through it like trying to drag a rope through a forest. A very long rope will tangle more than a short one and will take more effort/time to pull through the trees. However, a rope of the same length that has a different structure (maybe it has lots of knots tied in it, or it is stiff rather than flexible) may also be harder to pull through the forest, even though it's not any longer.

swbarnes2 · Answer

It means what it says.
DNA runs through a gel at a speed which is due to its shape, which is mostly determined by its size.  What it's saying is that certain sequences alter the shape of the DNA so much that its passage through a gel resembles that of a much longer piece with a more standard helical shape.

Sequence of DNA

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