If you design a primer that is 23 base pairs long and you have a genome...
If you design a primer that is 23 base pairs long and you have a genome of 3.2 x 109 bp. How many theoretical recognition sites are there for that primer assuming even G, C, A, T, ratios and no repetitive regions of DNA? Should this yield a single, unique PCR product?
Homework Answers
As the primer is 23 base pair long, attachment sites for this primer expected to occur for every 423 bp or once for every 70,368,744,177,664 bp. This is much larger than genome size of 3.2 x 109 bp. Thus, theoretically primer would have a single binding site in the entire genome & we will yield a unique PCR product.
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If you design a primer that is 23 base pairs long and
you have a genome...
The Psilotum nudum genome is 2.5 x 1011 bp. You wish to design a primer to...
The Psilotum nudum genome is 2.5 x 1011 bp. You wish to design a primer to amplify a specific gene in the genome. - Part A In general, what length of oligonucleotide would be sufficient to amplify a single unique sequence? To simplify your calculation, assume that all bases occur with an equal frequency. Hint: The frequency of occurrence of a PCR primer in genomic DNA is given by this equation: genomic DNA length x sequence frequency The sequency frequency...
You found a bacterium that has a genome of 2 millions base pairs. How long is...
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You found a bacterium that has a genome of 2 millions base pairs. How long is...
You found a bacterium that has a genome of 2 millions base pairs. How long is the stretch of 16S rDNA that you want to sequence to make sure that you can know what specific species it is? You will first assume that there is no history in biology and then you will say in which direction the length of the DNA stretch (bigger or smaller) if you suppose that all bacterial species have evolved from a common ancestor.
You PCR amplify a 500 bp (base pairs) piece of DNA that has diagnostic value in...
You PCR amplify a 500 bp (base pairs) piece of DNA that has
diagnostic value in determining whether a patient has a mutation
within a specific DNA region. You know that this DNA segment of the
“normal” gene does not include an EcoRI restriction site; but the
mutated DNA segment of the same gene contains an EcoRI restriction
site due to a point mutation at the 100th bp from the 5’ DNA end.
After PCR amplification, you subject your DNA...
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Question 2: a) You determine that xpd is expressed preferentially in muscle. Your colleague wants to...
Question 2:
a)
You determine that
xpd
is expressed preferentially in muscle. Your colleague wants to
know
if any of the mutations affect the stability of the RNA
transcript, thereby leading to higher
turnover and lower overall mRNA levels. What techniques could
you use to test her
hypothesis? List the pros and cons of each method. (hint: try to
think of at least three methods
you could use)
b) You find that your collegue is correct, and that the xpda...
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restriction enzymes. Using agarose gel electrophoresis, the DNA
fragments can be separated on a gel, based on their lengths. In
order to see the fragments, a stain is typically added to the gel.
The size of each fragment can be determined by comparing each one
to a DNA molecular weight marker of known size.
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number of the...
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The Psilotum nudum genome is 2.5 x 1011 bp. You wish to design a primer to amplify a specific gene in the genome. - Part A In general, what length of oligonucleotide would be sufficient to amplify a single unique sequence? To simplify your calculation, assume that all bases occur with an equal frequency. Hint: The frequency of occurrence of a PCR primer in genomic DNA is given by this equation: genomic DNA length x sequence frequency The sequency frequency...
You PCR amplify a 500 bp (base pairs) piece of DNA that has
diagnostic value in determining whether a patient has a mutation
within a specific DNA region. You know that this DNA segment of the
“normal” gene does not include an EcoRI restriction site; but the
mutated DNA segment of the same gene contains an EcoRI restriction
site due to a point mutation at the 100th bp from the 5’ DNA end.
After PCR amplification, you subject your DNA...
1) Imagine that you are interested in studying the enzyme dihydrofolate reductase (DHFR) from Mycobacterium tuberculosis (this enzyme is a potential drug target). The amino acid sequence of the protein is: MTMVGCIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNWL SRQADFMASGAEWGSLEEALTSPETWVIGGGQVYALALPYATRCEVTEVDIGLPREAGDALAPVLD ETWRGETGEWRFSRSGLRYRLYSYHRS The DNA sequence within the M. tuberculosis genome that codes for the protein is: ATGACGATGGTGGGGCTGATCTGGGCTCAAGCGACATCGGGTGTCATCGGCCGCGGCGGCGACATCCCCT GGCGCTTGCCCGAGGACCAGGCGCATTTCCGGGAGATCACCATGGGGCACACGATCGTGATGGGCCGGCG CACATGGGATTCGCTGCCGGCTAAAGTCCGGCCGCTGCCCGGCCGGCGAAATGTCGTACTGAGCCGCCAA GCTGACTTTATGGCCAGCGGGGCTGAGGTTGTCGGTTCACTCGAGGAGGCGCTGACCAGCCCGGAGACGT GGGTGATCGGAGGCGGACAAGTCTATGCGCTGGCGCTGCCGTACGCGACCAGATGTGAGGTTACCGAGGT CGACATCGGCCTGCCGCGCGAAGCCGGTGACGCGCTGGCCCCCGTGCTGGACGAGACATGGCGGGGCGAG ACGGGGGAGTGGCGCTTCAGCCGGTCCGGGTTGCGGTACCGGTTGTACAGCTACCACCGCTCATGA Assume that you have been given a sample of the bacterial genomic DNA, restriction enzymes Ndel and BamHi, and a plasmid from Novagen called PET-28b....
Carolina Savirana Craz 3/12/20 GECC-Polymerase Chain Reaction 1. What is the purpose of the polymerase chain reaction? a. To repair damaged DNA b. To make copies of entire chromosomes c. To make copies of specific regions of DNA d. To prepare cells for cell division 2. The polymerase chain reaction is most comparable to what cellular process? a. Mitosis b. Replication c. Transcription d. Translation 3. When enzymes are elongating (building) a newly synthesized DNA strand in PCR, new nucleotides...
Question 2:
a)
You determine that
xpd
is expressed preferentially in muscle. Your colleague wants to
know
if any of the mutations affect the stability of the RNA
transcript, thereby leading to higher
turnover and lower overall mRNA levels. What techniques could
you use to test her
hypothesis? List the pros and cons of each method. (hint: try to
think of at least three methods
you could use)
b) You find that your collegue is correct, and that the xpda...
Chromosomal and plasmid DNA can be cut into manageable pieces by
restriction enzymes. Using agarose gel electrophoresis, the DNA
fragments can be separated on a gel, based on their lengths. In
order to see the fragments, a stain is typically added to the gel.
The size of each fragment can be determined by comparing each one
to a DNA molecular weight marker of known size.
Below is a map of pBR22 plasmid. The position and base pair
number of the...
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