Final answer:
To estimate the size of a DNA fragment, a DNA ladder is used as a reference on an agarose gel during electrophoresis. By measuring the distance DNA samples travel relative to the ladder, the fragment sizes can be inferred. DNA's compact nature in cells involves supercoiling and protein interactions enabling large genomes to fit into tiny cellular spaces.
Step-by-step explanation:
To determine the size of a DNA fragment, one typically uses a DNA ladder on an agarose gel alongside DNA samples. The DNA ladder consists of DNA fragments of known lengths, which serve as a reference for estimating the sizes of other DNA fragments within the gel. After running an agarose gel electrophoresis, the DNA is visualized commonly by ethidium bromide staining, and the distance each fragment travels from the well is measured. The distance is inversely proportional to the DNA fragment's size due to the gel's sieving effect.
A standard practice is to construct a plot of the log of the known DNA ladder fragment sizes (in kilobases, kb) versus the distance they traveled through the gel. From this plot, a standard curve can be generated, and the DNA fragment sizes in question can be estimated by comparing their migration distances to the standard curve.
DNA can be densely packed within cells through supercoiling and protein interactions, despite being relatively long molecules. For example, the E.coli genome, which is 4.6 million base pairs long (approximately 1.1 mm when stretched out), is packed into a small bacterial cell by supercoiling, where it is either under-wound or over-wound from its normal relaxed state.
This principle of electrophoresis is also applicable to other nucleic acid or protein size determinations. For example, a PCR product observed on a gel can be compared against a 600 bp DNA marker to estimate its size. DNA's remarkable ability to be compacted is also seen in human cells, where approximately two meters of DNA is packed into the nucleus that is only about 10 um in diameter.