I will work on this lab tomorrow I want to prepare for these questions so help m
ID: 190270 • Letter: I
Question
I will work on this lab tomorrow
I want to prepare for these questions
so help me answer this so that I can understand more
Lab 2: Structure of DNA Part II Introduction n the previous lab, you setup series of chromatin digests. After digestion with MNase, the nuclear proteins/were removed by phenol extraction and the genomic DNA fragments were precipitated using a cold ethanol solution Today's Ethidium Bromide procedure will attempt to visualize the digested DNA products by tunning them on an ágarose gel and staining with ethidium Figure 3, Ethidium Bromide. The structure of Ethidium Bromide (EtBr) is shown on the left. Like other intercalating Gel electrophoresis takes advantage of the charged nature of DNA. The reqular agents, EtBr can bind to DNA by stacking interval of phosphates along the DNA backbone provides a constant mass: charge ratio regardless of the DNA length. In simple terms, this means that although longer DNA fragments are heavier (and thus barder to move"), they centain more charge to counteract the increased mass Because of this, DNA moves through a gel because of its charge, but the charge alone does not cause different DNA fragments to run differently. This is accomplished by the etnts Eter can bind to DNA by stacking between the bases rage pore size of the agarose matrix. Tiny DNA fragments pass easily through the matrix and thus travel further through the gel. Largor DNA fragments navigate through the gel with more difficulty and thus do not travel as far. Sometimes large DNA can even become stuck"in the well of the gel; unable to even enter the gel matrix (1-3) EtBr is a DNA intercalating agent in that it inserts itself between adjacent bases (Figure 3). This is not to be confused with the separation of bases from opposing DNA strands. Because of this, EtBr is a DNA mutagen) (and thus carcinogen) that causes frameshift mutations in a replication-dependent manner. For the purposes of this lab EtBr i stain that emits fluorescent light when subjected to UV radiation. This fluorescence will only occur when the EtBr is within double-stranded DNA (4, 5) Objectives 1. Visualize the digested genomic products from the previous lab lvorsscence 2. Determine the approximate size of nucleosome-associated DNA 3. Become familiar with EndNote reference managing software SttoExplanation / Answer
If we ran single stranded DNA on agarose gel, we would be able to visualise it under uv light, provided it is stained. The gel concentration has to be different. For single stranded DNA of short stretches, the concentration of the gel has to be 2%. If the gel concentration is too less, the segments being small and single stranded will get diffused. The segments can be stained using EtBr. On a 1.5% gel, The bands will be diffused and cannot be visualised properly. The bands on a 3% gel will appear as bright bands. On a 3% gel, there would be sharp bands observed.