100 50 104 1 10 104 Cot DNA renaturation curves occasionally show three distinct phases of renaturation. In this plot, DNA renaturation is plotted against “C,t" (initial concentration times time of renaturation, essentially a meas- ure of relative renaturation time). (a) Identify each part of this plot that corresponds to reannealing of (1) unique sequences, (2) moderately repetitive sequences, and (3) highly repetitive sequences. (b) Suppose that you cloned a single-copy gene, such as the gene for dihydrofolate reductase (DHFR), and subjected this to renaturation analysis. Sketch the curve you might expect. (c) Suppose that you cloned the DHFR CDNA instead of genomic DNA. Would you expect this to reanneal (1) more slowly, (2) more rapidly, or (3) at the same rate as genomic DNA? Briefly explain your answer. % Single stranded

100 50 104 1 10 104 Cot DNA renaturation curves occasionally show three distinct phases of renaturation. In this plot, DNA renaturation is plotted against “C,t" (initial concentration times time of renaturation, essentially a meas- ure of relative renaturation time). (a) Identify each part of this plot that corresponds to reannealing of (1) unique sequences, (2) moderately repetitive sequences, and (3) highly repetitive sequences. (b) Suppose that you cloned a single-copy gene, such as the gene for dihydrofolate reductase (DHFR), and subjected this to renaturation analysis. Sketch the curve you might expect. (c) Suppose that you cloned the DHFR CDNA instead of genomic DNA. Would you expect this to reanneal (1) more slowly, (2) more rapidly, or (3) at the same rate as genomic DNA? Briefly explain your answer. % Single stranded

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter28: Dna Metabolism: Replication, Recombination, And Repair

Section: Chapter Questions

Problem 10P: Homologous Recombination, Heteroduplex DNA, and Mismatch Repair Homologous recombination in E. coli...

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2b) If you denatured the random 1000 bp fragments of potoroo DNA by heating them to 95°C. and then cooled them down to 60°C and allowed them to reanneal, you would find that approximately 20% of the DNA fragments renatured very rapidly, another 30% of the DNAfragments renatured moderately rapidly, and the remaining DNA fragments renatured relatively slowly. From these results, whatfraction of the potoroo genome is composed of highly repetitiveDNA? helpful Information
DNA renaturation curves occasionally show three distinct phases of renaturation. In this graph, DNA renaturation is plotted against C0t (initialconcentration times time of renaturation—essentially a measure of relativerenaturation time). See Figure 21.3.(a) Identify each part of this plot that corresponds to reannealing of (1)unique sequences, (2) moderately repetitive sequences, and (3) highlyrepetitive sequences.(b) Suppose that you cloned a single-copy gene, such as the gene for dihydrofolate reductase (DHFR), into a plasmid vector and subjected it torenaturation analysis. Sketch the curve you might expect.(c) Suppose that you used reverse transcriptase to copy the ovalbumin mRNA and cloned this complementary DNA (cDNA) into a plasmid vector. Would you expect this cDNA to reanneal (1) more slowly, (2) more rapidly, or (3) at the same rate as genomic DNA? Briefly explain your answer.
consider the DNA segment with a sequence: 3'-TACGGTACGGGATTG-5'. if the given DNA sample was subjected to ion-torrent sequencing, sketch the expected profile of the sequencing output. assume that the sequential flooding of nucleotides follows the order G-C-A-T.
When Chargaffwas performing his experiments, the tetranucleotide hypothesis, which stated that DNA was composed of GACT nucleotide repeats, was the most widely accepted view of DNA’s composition. How did Chargaff disprove this hypothesis?
Homologous Recombination, Heteroduplex DNA, and Mismatch Repair Homologous recombination in E. coli leads to the formation of regions of heteroduplex DNA. By definition, such regions contain mismatched bases. Why doesnâ€™t the mismatch repair system of E. coli eliminate these mismatches?
(a) What two enthalpic factors stabilize DNA in double-helical form at lowtemperature?(b) What entropic factor destabilizes helical DNA at high temperature?(c) Why is the double-helical structure of DNA stabilized at moderate tohigh ionic strength?
Let’s say that a stretch of repeated AT issuccessfully sequenced. From what you know of the difficulties ofsequencing long repeated sequences, what other problems mightyou encounter in assembling these fragments?
What is the role of di-deoxy DNTPs in a Sanger sequencing reaction? Please select the answer that is most correct. The di-deoxy DNTPs are incorporated into the growing DNA molecule. The di-deoxy DNTPs terminate polymerisation of the growing DNA molecule, thereby creating fragments which all end in that specific di-deoxy base. Subsequent separation of the fragments by size facilitates the ascertainment of the sequence. The di-deoxy DNTPs facilitate polymerisation of the growing DNA molecule. this allows for multiple copies fo the template to be made for further analysis. The di-deoxy DNTPs terminate polymerisation of the growing DNA molecule. Ending the replication ensures that the molecules are not too long to be sequenced.
The specificity of Watson-Crick nucleobase pairing enables the biological information to be encoded and passed down through generations of cells and organisms. This specificity arises from the chemical structure of the base pairs, namely the pattern of hydrogen bond donors and acceptors that stabilize only two pairing interactions] relative to the others. How many possible pairwise interactions could potentially exist at a single position within a sequence, including the correct pairs, and all possible other combinations of DNA bases?
Why is the double-helical structure of DNA stabilized at moderate to high ionic strength?
A duplex DNA molecule contains a random sequence of the four nucleotides with equal proportions of each. What is the average spacing between consecutive occurrences of the sequence 5'-ATGC-3'? Between consecutive occurrences of the sequence 5'-TACGGC-3'?
2c) If the whole potoroo genome is 4.2 x 10' bp, and the highlyrepetitive DNA in the potoroo genome is composed entirely ofcopies of the sequence 5'AAGACT' and its complement, howmany copies of this sequence are present in the potoroogenome?