Deck 48: Nucleic Acid Techniques and Applications

Question 1

What is the key enzyme used in a polymerase chain reaction (PCR)?

A) Restriction enzyme
B) Lysozyme
C) Polymerase
D) Transcriptase

Answer 1

Polymerase

Question 2

An example of a signal amplification technique (as opposed to a target or probe amplification technique)would be:

A) polymerase chain reaction.
B) branched-chain amplification.
C) ligase chain reaction.
D) real-time PCR.

Answer 2

branched-chain amplification.

Question 3

When combined with real-time PCR,melting curve analysis is done to:

A) examine a single nucleotide variant genotype in a short amount of time.
B) quickly quantify the amplified target.
C) detect nucleic molecules at a specific wavelength.
D) examine the size of a fragment produced by RFLP.

Answer 3

examine a single nucleotide variant genotype in a short amount of time.

Question 4

If RNA is to be used in a PCR amplification procedure,what is the initial step that must be performed?

A) The RNA must be denatured to form single strands for annealing to primers.
B) RNA should never be used in a PCR reaction because thermostable enzymes cannot synthesize strands to anneal to it.
C) A reverse transcription procedure must be performed to form cDNA.
D) RNA must first be treated with RNases to remove interfering substances from the target.

Question 5

Which one of the following statements regarding DNA gel electrophoresis is true?

A) It is the charge of the pyrimidines in the DNA molecule that gives DNA its net negative charge and ability to migrate on a gel.
B) Agarose gel can resolve 1 bp differences in DNA fragments and is best to use for DNA sequencing.
C) Polyacrylamide gel can separate smaller fragments of DNA with high resolution and is best for single-stranded nucleic acid separation.
D) Because of the negative charge of DNA,it will migrate toward the negative electrode during electrophoresis.

Question 6

You have prepared a restriction enzyme digest of DNA from an individual who might have a genetic disorder.On the gel,you note that the digest from this individual produces one fragment,whereas the digest from a normal healthy individual produces two fragments.All controls worked correctly and you used the same reagents for all testing.What is your interpretation?

A) The enzymes were not working.
B) The diseased individual's DNA is missing a restriction site.
C) You must have skipped the amplification step.
D) The normal individual's DNA is missing a restriction site.

Question 7

You want to determine the accuracy of hybridization of a probe to a Southern blot to eliminate binding of the probe to incorrect target sequences.Which one of the following would be an appropriate positive control to assess assay sensitivity?

A) Sequences complementary to the probe
B) Sequences that are not complementary to the probe
C) Water
D) Sequences from a housekeeping gene such as beta actin

Question 8

In a pyrosequencing reaction,the incorporation of a nucleotide releases _____.Eventually,visible light is produced by an enzyme reaction.

A) pyrophosphate
B) ATP
C) luciferase
D) a primer

Question 9

The increase in the quantifiable signal observed early on in real-time PCR is dependent upon the:

A) amount of fluorescent dye added to the reaction.
B) initial amount of fluorescent primer added.
C) amount of fluorescent quenching.
D) initial amount of target DNA.

Question 10

How does a dideoxynucleotide (ddNTP)that is used in DNA sequencing methods differ from a typical deoxynucleotide (dNTP)present in normal DNA?

A) ddNTPs have a hydroxyl group at the 2' carbon
B) ddNTPs have a hydroxyl group at the 3' carbon
C) ddNTPs lack a hydroxyl group at the 3' carbon
D) ddNTPs lack a hydroxyl group at the 5' carbon

Question 11

Gene expression microarrays quantify:

A) a single copy of a nucleic acid target.
B) relative amounts of different messenger RNAs in samples.
C) RNA promoter regions that are adjacent to an inserted DNA sequence.
D) the number of specific base pairs in a DNA target.

Question 12

The annealing step in a PCR involves:

A) binding of the primers to the single-stranded DNA.
B) unwinding and separating the double-stranded DNA.
C) adding nucleotides to primed sites of the DNA strands.
D) making a cDNA from an mRNA strand.

Question 13

Which one of the following statements regarding single-stranded conformational polymorphism (SSCP)analysis is incorrect?

A) SSCP is used to assess a specimen for the presence of unknown variants in a nucleic acid sequence.
B) SSCP distinguishes altered gene sequences by detecting a change in the three-dimensional structure of a piece of single-stranded DNA.
C) SSCP is a polyacrylamide gel electrophoresis procedure.
D) In SSCP,separation of a PCR product is performed with a gel that includes a concentration gradient of denaturants.

Question 14

Which of the following procedures can be used to avoid contamination with PCR reaction product (amplicon)when performing a PCR procedure?

A) Use of positive displacement pipettes
B) Use of closed-tube methods
C) Physical separation of preamplification and postamplification rooms
D) All of the above

Question 15

The purpose of restriction fragment polymorphism analysis (RFLP)is to:

A) determine the purity of DNA isolation.
B) evaluate the integrity of isolated genomic DNA.
C) assess the exonuclease activity of DNA polymerase.
D) identify the presence of mutations or sequence changes.

Question 16

In real-time PCR:

A) an isolated mRNA and Thermus thermophilus is used.
B) one can observe amplified nucleic acid fragments as they are synthesized.
C) RNA:DNA hybrids are bound to a solid phase.
D) RNA targets are used in an isothermal reaction.

Question 17

False positive results in molecular testing are most likely caused by which one of the following?

A) Inhibitors present in the sample
B) Contamination with amplicon
C) Lengthy specimen prep time
D) Lengthy patient prep time

Question 18

What type of assay is hybrid capture?

A) Solid-phase hybridization
B) Signal amplification
C) Transcription-mediated amplification
D) Solution-phase hybridization

Question 19

When performing a PCR procedure,what is the best control to run to assess the presence of amplicon?

A) Positive control
B) Blank control
C) Oligoligated control
D) dTTP control

Question 20

In the dideoxy-termination sequencing method,what causes the termination of the newly synthesized DNA strand?

A) Addition of a dideoxynucleotide
B) Deletion of a deoxyribonucleotide
C) Addition of a deoxyribonucleotide
D) Addition of a ribonucleotide

Question 21

What is the purpose of the labeled oligonucleotide probe used in hybridization assays?

A) To stabilize the assay
B) To cut the DNA into smaller-size fragments
C) To reduce the background of the assay
D) To detect the presence of a specific nucleotide sequence

Question 22

Which one of the following is the name given to the probe types used in real-time PCR that change fluorescence through fluorescence resonance energy transfer (FRET)upon duplex formation?

A) Hybridization
B) Hydrolysis
C) Mixed mechanism
D) Primer

Question 23

Regarding detection methods,the most common and preferred sequence-specific label for probes used in nucleic acid analysis is a(n)_____ label.

A) enzyme
B) radioactive
C) fluorescent
D) colorimetric

Question 24

In a PCR,a control nucleic acid sequence that is different from the target sequence is added to each sample to:

A) control for the presence of amplicon contamination.
B) bind aerosols.
C) control for the presence of inhibitors in the sample that might inhibit polymerase activity.
D) compare with an internal standard for quantitative analysis.

Question 25

An enzyme that hydrolyzes one or more phosphodiester bonds in nucleic acid polymers is called a:

A) polymerase.
B) nuclease.
C) ligase.
D) reverse transcriptase.