An investigator has a strand of chromosomal DNA whose sequence is shown. She wants to use polymerase chain reaction (PCR)to amplify and isolate the DNA fragment defined by the highlighted segment. Her first step is to design two PCR primers, each20 nucleotides long, that can be used to amplify this DNA segment. The final PCR product generated from the primers shouldinclude no sequences outside of the highlighted segment.5'---AATGCCTCAGCCGATCTGCCTCGAGTCAATCGATGCTGGTAACTTGGGGTATAAAGCTTACCCATGGTATCGTAGTTAGATTGATTGTTAGGTTCTTAGGTTTAGGTTCTGGTATTGGTTTAGGGTCTTTGATGCTATTAATTCTTTGGTTTTGATTTGGTCTTTATATGGTTTATGTTTTAAGCCGGGTTTTGTCTGG-GATGGTTCGTCTGATGTGCGCGTAGCGTGCGGCG---3'What are the sequences of the investigator's forward and reverse primer? Enter them 5' to 3'.forward primer:reverse primer:GGAGCTCAGTTAGCTACGACIncorrectCGCCGCACGCTA-Incorrect

PCR or polymerase chain reaction is a lab procedure that amplified fragments of DNA by using a…

Answered: 。. An investigator has a strand of…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Your graduate advisor asks you to amplify the following sequence of DNA by PCR: 5’-ATACGCATTCGGACCAGGTCCTAA-3’ 3’-TATGCGTAAGCCTGGTCCAGGATT-5’ a. To ensure that the entire sequence above is amplified, what 6-nucleotide DNA primers should you add to your PCR mix? You order the primers listed above, but instead receive the following set of primers: 5’-CGCATT-3’ 5’-GGACCT-3’ b. What portion of the double stranded DNA molecule will be amplified after 10 rounds of PCR? Your labmate attempts to rescue your PCR reaction by providing you with the following set of primers: 5’-ATACGC-3’ 5’-TCCTAA-3’ c. What is the result of running the PCR reaction with your labmate’s primers? How many double stranded molecules of DNA will result from 10 rounds of amplification?
A PCR reaction was performed to amplify the CHE2 gene. The PCR primers used were designed to amplify bp 936-4,635 of a 10,908 bp plasmid. Calculate the expected PCR product size (in bp).
PCR primers Below is a 300 base pair fragment of DNA. The top strand is written in the 5' to 3' direction. The bottom strand is written 3' to 5'. There are also two primer sequences; both primers are written 5' to 3'. Note that we are displaying a double-stranded DNA fragment, but primers will only bind to one of the two displayed strands. 5' ACCGȚAGCTATATGCTATCGTGACGTATCGGCGCATTAAȚCGGGATCGAT 3 50 3' TGGCÁTCGATATACOATAGCACTOCATAGCCGCGTAATTÀGCCCTAGCTÀ 5' 5' AGCTÇGCTAGCAGGAGAGAȚATCGÇTCATAGCTCCGATCGATGCCGCTAA 3 3' TCGAGCG ATCGTCCTCTCTÁTAGCGAGTATCGAGÓCTAGCTACGGCGATİ 5' 100 5' TATAGCTCTÇTGCGGATATÇGCATATACCẠ AGGCCCTACGTATGTAGCTA 3 150 3' ATATČGAGAGACOCCTATAGCGTATATGGTTCCGGGATGČATACATCGAŤ 5' 5 TGCGTATATÇGGAGAGTCCTGGATATGGAGCTTGACTGCAGAGAGCTCGA 3 200 3' ACGCÁTATAGCCTCICAGGÁCCTATACCTCGAACTGACGTCTCTCGAGCT 5' 5' TATGCGCTTAGGCCGTATATGCTTGGGGAAAGCTCTATGTATGCTATGTG 3 3. ATACGCGAATCCGGCATATACGAACCCCTÍTCGAGATACATACGATACAC 5' 250 5' TGCATGTGCTATGCAACGTTCOGATTGCGȚAGCAGTAATAGCGCCGATTG 3 300 3'…
Examine the DNA sequence shown below. You have been tasked with designing Primers for PCR amplification of the whole fragment shown. Your colleague said that she would design one primer and came up with this sequence – 5’ TGCTATC 3’. You, being a good scientist, need to confirm that her work is good. Where will this primer bind on the target DNA? 5’ CGATGCAATCGAGCTATGGCATATCATAAGCGATAGACAGATAGCA 3’ GCTACGTTAGCTCGATACCGTATAGTATTCGCTATCTGTCTATCGT a. This primer cannot be used in the PCR process. b. It will bind to the top strand on the left side of the fragment. c. It will bind to the bottom strand on the left side of the fragment. d. It will bind to the bottom strand on the right side of the fragment. e. It will bind to the top strand on the right side of the fragment.
PCR primers Below is a 300 base pair fragment of DNA. The top strand is written in the 5' to 3' direction. The bottom strand is written 3' to 5'. There are also two primer sequences; both primers are written 5' to 3'. Note that we are displaying a double-stranded DNA fragment, but primers will only bind to one of the two displayed strands. 5' ACCOȚAGCTATATOCTATCOTGACOTATCOGCOCATTAAȚCGGGATCGAT 3 3' TGGCATCGATATACGATAGCACTGCATAGCCGCGTAATTAGCCCTAGCTẢ 5 50 5' AGCTCGCTAGCAGGAGAGATATCGCTCATAGCTCCGATCGATGCCGCTAA 3 100 3' TCGAGCGATCGTCCICTCTATAGCGAGTAICGAGGCTAGCTACGGCGATİ 5' 5' TATAGCTCTCTGCGGATATÇGCATẠTACCAAGGCCCTACGTATGTAGCTA 3 150 3' ATATČGAGAGACGCCTATAGCGTATATGGÍTCCGGGATGČATACATCGAŤ 5 5' TGCGȚATATÇGGAGAGTCCTGGATAT GGAGCTTGACTGCAGAGAGCTCGA 3 200 3' ACGCATATAGCCTCICAGGACCTATACCTCGAACÍGACGICTCTCGAGCİ 5' 5' TATGCGCTTAGGCCGTATATGCTTGGGGAAAGCTCTATGTATGCTATGTG 3 250 3' ATACGCGAATCCGGCATATACGAACCCCTITCGAĞATACATACG ẢTACAČ 5' 5' TGCATOTGCTATOCAACGTTC GGATTGCGȚAGCAGTAATAGCGCCGATTO 3' 300 3'…
Your amplicon from PCR was subjected to AGE for analysis. You are shown the image of the gel loaded with the following lanes: (A) negative control, (B) size ladder (1, 2, 3, 4, 6, and 10 kb), (C) gDNA extract, (D) PCR amplicon. However, due to mishaps while loading the gel with the samples, you are not sure which lane is which. You are shown a diagram of the obtained gel below. a. Label each lane of the gel. Write only the corresponding letters in the wells above. b. Above each band in the size ladder, write its size (in kb). c. Approximate the size (in kb) of the polystyrenase gene. Write your answer above the band corresponding to the gene. Bonus: If you wish to identify the bacterial species in this scenario, what gene is most commonly and routinely sequenced? Answer: __________________________________
Polymerase chain reaction (PCR) is a technique that enables multiplication of specific DNA sample at minute amount to millions or billions of copies at a short time span. (i) (ii) Figure 1 indicates the chemicals added into the PCR reaction tube prior to the addition of thermostable DNA polymerase. Do you agree with the list? Justify your answer. DNA template Buffer (containing Tris-HCI, KCI, Mg2+) ddNTP Forward primer Reverse primer Figure 1 If TA cloning is planned to be carried out after amplification of the gene, which thermostable DNA polymerase will you select and the reason for your selection?
The final amount of each primer required in a PCR reaction is 25 picomol. If the total volume of the PCR reaction is equal to 100 µl and the stock concentration of each primer is equal to 0.0025 mM. Calculate the volume of stock primer that needs to be added in order to ensure a primer amount of 25 picomol.
For the STR site diagramed below, each repeat unit, represented by a rectangle, is known to be 5 bp long. The total length of the amplified PCR product for the chromosome shown below is 420 bp long. PCR product - 420 bo Primer Left STR STR STR STR Primer Right What size would the PCR product be for a different chromosome where there were only two tandem repeat units, instead of four? SHOW YOUR WORK.
a) (iii) (iv) Polymerase chain reaction (PCR) is a technique that enables multiplication of specific DNA sample at minute amount to millions or billions of copies at a short time span. (i) Figure 1 indicates the chemicals added into the PCR reaction tube prior to the addition of thermostable DNA polymerase. Do you agree with the list? Justify your answer. DNA template Buffer (containing Tris-HCI, KCI, Mg2+) ddNTP Forward primer Reverse primer Figure 1 If TA cloning is planned to be carried out after amplification of the gene, which thermostable DNA polymerase will you select and the reason for your selection? Why is the optimal annealing temperature vital in this technique? Explain how this temperature (too high or too low) will affect the efficiency of this reaction. If the primers you purchased possessed the following information: Number of Guanine: 4 Number of Adenine: 3 Number of Thymine: 4 Number of Cytosine: 5 Calculate the melting temperature of this primer and estimate the…
Examine the DNA sequence shown below. You have been tasked with designing Primers for PCR amplification of the whole fragment shown. Your colleague said that she would design one primer and came up with this sequence – 5’ TTGCATCG 3’. You, being a good scientist, need to confirm that her work is good. Where will this primer bind on the target DNA, and will this primer work as part of a pair to successfully amplify this fragment of DNA? 5’ CGATGCAATCGAGCTATGGCATATCATAAGCGATAGACAGATAGCA 3’ GCTACGTTAGCTCGATACCGTATAGTATTCGCTATCTGTCTATCGT a. It will bind to the bottom strand on the left side of the fragment, and is suitable to amplify the fragment by PCR. b. It will bind to the top strand on the left side of the fragment, but it is unsuitable to amplify the fragment by PCR. c. It will bind to the top strand on the right side of the fragment, but it is unsuitable to amplify the fragment by PCR. d. It will bind to the bottom strand on the right side of the…
Three pieces of cut DNA were isolated using gel electrophoresis.The DNA that is the longest will be closest to the positive or negative electrode?

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