Working on this lab help me these questions Thank you DNA, I pvorten Part ll Lab

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Working on this lab
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DNA, I pvorten Part ll Lab 2: Structure of DNA Lab 2: Structure of DNA Introduction DNA he previous lab, you setup 37 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 procedure will attempt to visualize the digested DNA products by running them.on an ágarose gel and staining, with ethidium Figure 3, Ethidium Bromide Ethidium Bromide The structure of Ethidium Bromide (EtBr) is shown on the left. Like other intercalating Gel electrophoresis takes advantage agents, EtBr can bind to DNA by stacking of the charged nature of DNA. The regular between the bases) 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 harder to move"), they centain more charge to counteract the increased mass Because of this, DNA moves through a gel because of its chargé but the charge alone does not cause different DNA fragments to run differently. This is accomplished by the average pore sizs of the agarose matrix. Tiny DNA fragments pass easily through the matrix and thus travel further through the gel. Larger -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 ONA mutagen (and thus tarcinogen) that causes meshift mutations in a replication-dependent manner. For the purposes of this lab fra tBr is a "stain" that emits fluorescent light when subjected to UV radiation tBr is within double-stranded ONA (4. 5) Obiectives 1. Visualize the digested genomic products from the previous lab 2. Determine the approximate size of nucleosome-associated DNA 3. Become familiar with EndNote reference managing software. oroscevce

Explanation / Answer

3. cell free DNA are found in cerculationg blood plasma. nucleosomes are inffered with this cfDNA. cfDNA are small fregments of DNA that are freely ciculating in blood plasma. hence the two band appeared in high resolutation gel of nucleomonomers are, one is low molecular weight cfDNA band and other is nucleosome DNA band. or the linker DNA binds two nucleosome so the other band may be of linker DNA.

4. in the nick DNA some of the nucleotides are mission their pair with other nucleotide, hence the phosphodiester bond between some of nucleotides are broken due to stress or repeated thawing, the nick is generated. this nick release some tansion of supercoiled DNA. it is appeared as light stright band because EtBr can not intercalated with some of the nucleotide pairs.

conformation of DNA molecules also affects the motility of DNA. supercoiled DNA are coiled upon itself and become more and more compact and tightly packed. so supercoiled DNA can pass easily from the gel and migrates faster. now kicked DNA are somewhat is in released state and more open than supercoiled DNA so it will face difficulty migrating in gel and remain behind the supercoiled DNA.

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