Question 1

How is DNA denaturation (conversion to single stranded form)usually accomplished in PCR?

Accepted Answer

A) Alkaline pH 
B) Formaldehyde 
C) Heat 
D) Any of the above, depending on the target DNA sequence 
A) Alkaline pH 
B) Formaldehyde 
C) Heat 
D) Any of the above, depending on the target DNA sequence C

Question 2

Review the PCR protocol herein and identify its name. A single- stranded probe with internal complementary sequences folds on itself into a "hairpin" shape bringing a fluorescent molecule at one end of the strand in proximity to the quencher molecule at the other end of the strand. After PCR product is formed, during the next denaturation step the probe becomes single- stranded, binds to PCR target DNA, and separates the fluorescent molecule from the quencher molecule. PCR product is detected as increased fluorescence.

Accepted Answer

A) Molecular beacon PCR 
B) 5' RACE PCR 
C) Reverse transcriptase PCR 
D) Branched chain PCR 
E) TaqMan PCR 
A) Molecular beacon PCR 
B) 5' RACE PCR 
C) Reverse transcriptase PCR 
D) Branched chain PCR 
E) TaqMan PCR A

Question 3

Discuss the factors that must be considered when designing primers for a PCR reaction.

Accepted Answer

Primers must be long enough (15-30 bases)to minimize nonspecific annealing to DNA sequences other than the target. Since guanine and cytosine bind with three hydrogen bonds and adenine and thymine bind with two hydrogen bonds, if the ratio of GC nucleotides to AT nucleotides in the two primers is significantly different, then one primer may bind better than the other, and the amplicon may form asymmetrically. The exact nucleotide sequence of the primers is also important to know so that appropriate annealing temperatures can be used as oligonucleotides with high GC content anneal at higher temperatures than those with low GC content. If the primers have complementary sequences to each other, then "primer dimers" will form, and if a primer has complementary sequences within the primer itself, it can become folded in a "hairpin loop." Both primer dimers and looped primers function poorly, if at all.

Question 4

If the optimal pH for Taq polymerase is about 7.2, why are the reaction buffers manufactured to have a pH of about 8.5?

Accepted Answer

A) Unincorporated nucleotides are unstable at neutral to acidic pHs. 
B) Hydrogen bonds form poorly at neutral to acidic pHs. 
C) Optimal reaction conditions for Taq polymerase are generally not used because rapid incorporation of nucleotides into a growing DNA chains leads to more errors. 
D) pH is temperature dependent, and at the optimal temperature for Taq polymerase to function, the buffer pH will decrease. 
A) Unincorporated nucleotides are unstable at neutral to acidic pHs. 
B) Hydrogen bonds form poorly at neutral to acidic pHs. 
C) Optimal reaction conditions for Taq polymerase are generally not used because rapid incorporation of nucleotides into a growing DNA chains leads to more errors. 
D) pH is temperature dependent, and at the optimal temperature for Taq polymerase to function, the buffer pH will decrease.

Question 5

Real time PCR is not as fast as traditional PCR, but it is more sensitive.

Accepted Answer

A) True 
 B)False

Question 6

Which technique below is used to amplify messenger RNA (mRNA)?

Accepted Answer

A) Branched chain PCR 
B) Ligase chain reaction 
C) Reverse transcriptase PCR 
D) Molecular beacon PCR 
E) TaqMan PCR 
A) Branched chain PCR 
B) Ligase chain reaction 
C) Reverse transcriptase PCR 
D) Molecular beacon PCR 
E) TaqMan PCR

Question 7

Since multiple genes or gene products may be important in a particular disease, branched chain nucleic acid detection was developed to detect more than one target.

Accepted Answer

A) True 
 B)False

Question 8

Which amplification technique listed is best to use if one does not possess a thermal cycler?

Accepted Answer

A) Branched chain DNA detection 
B) Ligase chain reaction 
C) In situ amplification 
D) 5' RACE 
E) Nucleic acid sequence based amplification (NASB
A)  
A) Branched chain DNA detection 
B) Ligase chain reaction 
C) In situ amplification 
D) 5' RACE 
E) Nucleic acid sequence based amplification (NASB
A)

Question 9

Which of the following typically produces a false positive in in situ nucleic acid amplification?

Accepted Answer

A) Incorporation of labeled nucleotides into DNA when DNA polymerase is repairing damaged DNA 
B) Poor thermal conductance into cells 
C) Low copy number of target sequence 
D) Poor cell permeability 
A) Incorporation of labeled nucleotides into DNA when DNA polymerase is repairing damaged DNA 
B) Poor thermal conductance into cells 
C) Low copy number of target sequence 
D) Poor cell permeability

Question 10

The composition of which PCR reagent below is most critical in insuring that amplification of only the target DNA occurs?

Accepted Answer

A) dNTPs 
B) Template DNA extraction buffer 
C) Oligonucleotide primers 
D) DNA polymerase 
E) PCR reaction buffer 
A) dNTPs 
B) Template DNA extraction buffer 
C) Oligonucleotide primers 
D) DNA polymerase 
E) PCR reaction buffer

Question 11

It is important for laboratory workers to wash their hands thoroughly prior to working with RNA extracts.

Accepted Answer

A) True 
 B)False

Question 12

Although ________ must be present in excess, if the concentration is too high, an increase in errors and/or nonspecific products will occur.

Accepted Answer

A) All four deoxynucleotides (dNTPs) 
B) Magnesium ions 
C) Primers 
D) All of the above 
A) All four deoxynucleotides (dNTPs) 
B) Magnesium ions 
C) Primers 
D) All of the above

Question 13

The instrument used to control the heating cycles in PCR is called a________ .

Accepted Answer

The answer of The instrument used to control the heating...

Question 14

List ways in which contamination of PCR reactions can be minimized.

Accepted Answer

1. Segregation of functions to different

Question 15

Which of the following is true regarding agarose gel electrophoresis of DNA?

Accepted Answer

A) The loading dye usually contains a marker dye and a heavy molecule such as glycerol. 
B) In general, good separation of DNA fragments in the 1000-20,000 base pair size range can be achieved. 
C) The usual buffer used is potassium phosphate at a pH of 7.2. 
D) The usual stain to visualize the DNA is propidium iodide. 
A) The loading dye usually contains a marker dye and a heavy molecule such as glycerol. 
B) In general, good separation of DNA fragments in the 1000-20,000 base pair size range can be achieved. 
C) The usual buffer used is potassium phosphate at a pH of 7.2. 
D) The usual stain to visualize the DNA is propidium iodide.

Question 16

The product of a PCR reaction is called an oligonucleotide.

Accepted Answer

A) True 
 B)False

Question 17

Which detection method below is frequently used in real time PCR to detect double- stranded DNA product?

Accepted Answer

A) Biotin 
B) SYBR Green II dye 
C) Propidium iodide 
D) SYBR Green I dye 
A) Biotin 
B) SYBR Green II dye 
C) Propidium iodide 
D) SYBR Green I dye

Question 18

A standard PCR assay uses ________(how many?)primer(s).

Accepted Answer

The answer of A standard PCR assay uses ________(how many?)primer(s)....

Question 19

Exposing work areas and equipment to ________ is a useful decontamination method as it will cross- link and/or nick nucleic acids, and they will not be able to be amplified in PCR reactions.

Accepted Answer

The answer of Exposing work areas and equipment to ________...

Question 20

Using SYBR green as a detection dye in real time PCR is more specific than traditional PCR, but it is not as sensitive.

Accepted Answer

A) True 
 B)False

How is DNA denaturation (conversion to single stranded form)usually accomplished in PCR?

Discuss the factors that must be considered when designing primers for a PCR reaction.

If the optimal pH for Taq polymerase is about 7.2, why are the reaction buffers manufactured to have a pH of about 8.5?

Real time PCR is not as fast as traditional PCR, but it is more sensitive.

Which technique below is used to amplify messenger RNA (mRNA)?

Since multiple genes or gene products may be important in a particular disease, branched chain nucleic acid detection was developed to detect more than one target.

Which amplification technique listed is best to use if one does not possess a thermal cycler?

Which of the following typically produces a false positive in in situ nucleic acid amplification?

The composition of which PCR reagent below is most critical in insuring that amplification of only the target DNA occurs?

It is important for laboratory workers to wash their hands thoroughly prior to working with RNA extracts.

Although ________ must be present in excess, if the concentration is too high, an increase in errors and/or nonspecific products will occur.

The instrument used to control the heating cycles in PCR is called a________ .

List ways in which contamination of PCR reactions can be minimized.

Which of the following is true regarding agarose gel electrophoresis of DNA?

The product of a PCR reaction is called an oligonucleotide.

Which detection method below is frequently used in real time PCR to detect double- stranded DNA product?

A standard PCR assay uses ________(how many?)primer(s).

Exposing work areas and equipment to ________ is a useful decontamination method as it will cross- link and/or nick nucleic acids, and they will not be able to be amplified in PCR reactions.

Using SYBR green as a detection dye in real time PCR is more specific than traditional PCR, but it is not as sensitive.

What Is Immunology

Overview of the Immune System

Immunoglobulins

Infection and Immunity: Hostparasite Relationships

The Complement System

Hypersensitivity

Immunologic Detection of Infectious Diseases

Autoimmune Diseases and Immunodeficiency Disorders

Transplant Immunology

Tumor Immunology

Clinical Applications of Flow Cytometry

Hybridization Techniques

Molecular Applications in Cytogenetics

Histocompatibility Laboratory Techniques and Applications

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Exam 13: Amplification Techniques

How is DNA denaturation (conversion to single stranded form)usually accomplished in PCR?

Discuss the factors that must be considered when designing primers for a PCR reaction.

If the optimal pH for Taq polymerase is about 7.2, why are the reaction buffers manufactured to have a pH of about 8.5?

Real time PCR is not as fast as traditional PCR, but it is more sensitive.

Which technique below is used to amplify messenger RNA (mRNA)?

Since multiple genes or gene products may be important in a particular disease, branched chain nucleic acid detection was developed to detect more than one target.

Which amplification technique listed is best to use if one does not possess a thermal cycler?

Which of the following typically produces a false positive in in situ nucleic acid amplification?

The composition of which PCR reagent below is most critical in insuring that amplification of only the target DNA occurs?

It is important for laboratory workers to wash their hands thoroughly prior to working with RNA extracts.

Although ________ must be present in excess, if the concentration is too high, an increase in errors and/or nonspecific products will occur.

The instrument used to control the heating cycles in PCR is called a________ .

List ways in which contamination of PCR reactions can be minimized.

Which of the following is true regarding agarose gel electrophoresis of DNA?

The product of a PCR reaction is called an oligonucleotide.

Which detection method below is frequently used in real time PCR to detect double- stranded DNA product?

A standard PCR assay uses ________(how many?)primer(s).

Exposing work areas and equipment to ________ is a useful decontamination method as it will cross- link and/or nick nucleic acids, and they will not be able to be amplified in PCR reactions.

Using SYBR green as a detection dye in real time PCR is more specific than traditional PCR, but it is not as sensitive.

What Is Immunology

Overview of the Immune System

Immunoglobulins

Infection and Immunity: Hostparasite Relationships

The Complement System

Hypersensitivity

Immunologic Detection of Infectious Diseases

Autoimmune Diseases and Immunodeficiency Disorders

Transplant Immunology

Tumor Immunology

Clinical Applications of Flow Cytometry

Hybridization Techniques

Molecular Applications in Cytogenetics

Histocompatibility Laboratory Techniques and Applications

Filters