Question 1

Which end of the sequenced DNA is found at the bottom of a sequencing gel?

Accepted Answer

A

Question 2

Dideoxycytidine is added to one of four sequencing reactions. All of the DNA fragments produced in that reaction end with which of the following nucleotides?

Accepted Answer

Dideoxycytidine (ddC) is a chain-terminating nucleotide used in Sanger sequencing. When incorporated into a growing DNA strand, it prevents the addition of any further nucleotides, causing the strand to end. Thus, all DNA fragments in the reaction where ddC is added will end with ddC.

Question 3

Which of the following are included in sequencing reactions to deter secondary structure in the template and synthesized fragments?

Accepted Answer

Deaza-GTP is used in sequencing reactions to reduce secondary structure formation in the template and synthesized fragments, as it helps to destabilize G-C rich regions.

Question 4

In the Sanger sequencing method, which of the following when incorporated into the growing strand are used to determine the identity of the base at a particular position in a piece of DNA?

Accepted Answer

The Sanger sequencing method utilizes dideoxyribonucleotides (ddNTPs) in addition to the standard deoxyribonucleotides (dNTPs). These ddNTPs terminate the growing strand at specific positions, allowing for the identification of the identity of the base at that position. This is because the ddNTPs lack a 3' hydroxyl group, which is necessary for the formation of the phosphodiester bond that links nucleotides together. As a result, when a ddNTP is incorporated into the growing strand, it prevents the addition of any further nucleotides, effectively stopping DNA synthesis. The resulting fragments of different lengths can then be separated by gel electrophoresis and visualized to determine the DNA sequence.

Question 5

Which is the output from capillary electrophoresis of a fluorescent product?

Accepted Answer

Capillary electrophoresis produces an electropherogram as an output, which is a graph showing the separation of fluorescently labeled products.

Question 6

A pyrosequencer detects visible light, making it which type of instrument?

Accepted Answer

A pyrosequencer is a type of luminometer that detects visible light.

Question 7

A Sanger sequencing procedure has been performed on a 300-bp piece of DNA. When the fragments were resolved on the gel, there were bands distributed throughout the T, C and A lanes, but in the G lane, there was one thick band at the bottom of the gel. What is the likely cause of these results?

Accepted Answer

No dGTP was added to the G reaction mix.

Question 8

In Maxam-Gilbert sequencing, a band that is present in the lane from the tube treated with formic acid (G or A) but not the tube treated with dimethyl sulfate (G) is read as which of the following nucleotides?

Accepted Answer

The band present in the lane from the tube treated with formic acid (G or A) but not the tube treated with dimethyl sulfate (G) indicates that the nucleotide is either G or A. In Maxam-Gilbert sequencing, formic acid cleaves the DNA strands at G and A residues, while dimethyl sulfate cleaves at G residues only. Therefore, if a band is present in the lane from the formic acid-treated tube but not the dimethyl sulfate-treated tube, it means that the nucleotide is an A, which is not cleaved by dimethyl sulfate.

Question 9

An analysis that takes place in silico is happening in which of the following places?

Accepted Answer

Analysis that takes place in silico is happening on a computer, using computational methods and models to simulate and analyze biological data.

Question 10

In bioinformatics, when a sequence is entered and compared with all other sequences in a database, which of the following is being performed?

Accepted Answer

When a sequence is entered and compared with all other sequences in a database, it is considered a query, as the entered sequence is being searched within the database. An algorithm is a set of instructions for solving a problem or performing a specific task. A motif is a recurring sequence pattern in a protein or nucleic acid. Annotation is the process of adding information to a sequence to describe its features, such as genes or protein domains.

Question 11

Which of the following is a genetic sequence database that is sponsored by the National Institutes of Health?

Accepted Answer

GenBank is a genetic sequence database that is sponsored by the National Institutes of Health. PubMed is a database of medical literature, Swiss-Prot is a protein sequence database, and Interface is not a relevant database in this context.

Question 12

Which of the following is the most widely used method of DNA sequencing in clinical laboratories today?

Accepted Answer

Sanger sequencing is the most widely used method of DNA sequencing in clinical laboratories today. This is because it is highly accurate, reliable, and affordable for routine diagnostic testing. Pyrosequencing and array sequencing are used in research settings, while Maxam-Gilbert sequencing is an older method that is no longer commonly used due to its complexity and high cost.

Question 13

Incomplete cleaning of the fluorescently labeled sequencing ladder will result in what effect?

Accepted Answer

Incomplete cleaning of the fluorescently labeled sequencing ladder can result in dye blobs, which are large, diffuse areas of fluorescence that can obscure or interfere with the reading of the sequencing data.

Question 14

A portion of a sequencing gel is described as follows: the first band at the bottom of the gel was in the ddATP lane; the next band going up the gel was in the ddTTP lane, then the ddCTP lane, the ddGTP lane, the ddATP lane, the ddTTP lane, the ddCTP lane, the ddCTP lane, the ddATP lane, and the ddGTP lane. Which of the following is the correct sequence as determined on this gel?

Accepted Answer

The sequencing gel indicates that the first band at the bottom of the gel was in the ddATP lane. This suggests that the first nucleotide in the sequence is an A.

Going up the gel, the bands are in the order ddTTP, ddCTP, ddGTP, ddATP, ddTTP, ddCTP, ddCTP, ddATP, and ddGTP. This suggests that the sequence is: 
ATCGATCCA

The sequencing gel also indicates that the first band at the top of the gel was in the ddGTP lane. This suggests that the last nucleotide in the sequence is a G.

Putting it all together, the correct sequence as determined on this gel is:
5' ATCGATCCAG 3'

Therefore, choice C is the correct answer.

Question 15

The ddNTP:dNTP ratio is too high (too much ddNTP). How will this affect sequencing results?

Accepted Answer

The high concentration of ddNTPs will cause premature termination of the sequencing reaction, resulting in shorter fragments and therefore a ladder of only short fragments.

Question 16

Cycle sequencing was made possible through the development of what reagents?

Accepted Answer

Cycle sequencing requires the use of a heat-stable polymerase, such as Taq polymerase, to withstand the repeated heating and cooling cycles during the sequencing reaction. Fluorescent dyes and labeled primers may also be used in cycle sequencing, but they are not essential reagents for the technique. dITP (deoxyinosine triphosphate) is not specifically required for cycle sequencing.

Question 17

Sequencing ladders resolved by gel electrophoresis are read in which of the following directions?

Accepted Answer

Gel electrophoresis separates DNA fragments based on size, with larger fragments staying closer to the top of the gel and smaller fragments moving towards the bottom. Since sequencing ladders are run as a ladder of known- sized fragments, they are read bottom to top to determine the sequence of the DNA being sequenced.

Question 18

When two sequences are found to be exactly the same, they have which of the following?

Accepted Answer

Two sequences that are exactly the same have identity, meaning that every nucleotide or amino acid in the sequences is identical. Heterology refers to differences between sequences, alignment refers to the process of comparing and positioning sequences, and motif refers to a pattern or recurring sequence motif found in a larger sequence.

Question 19

In Maxam-Gilbert sequencing, co-migrating bands that are present in lanes from the tube treated with hydrazine (T or C) and the tube treated with hydrazine plus salt (T) are read as which of the following nucleotides?

Accepted Answer

Co-migrating bands in Maxam-Gilbert sequencing are read as the nucleotide that is complementary to the one that was removed by the chemical treatment. Hydrazine treatment removes guanine (G) and xanthine, while hydrazine plus salt removes adenine (A), cytosine (C), and thymine (T). Therefore, co-migrating bands in lanes from the tube treated with hydrazine (T or C) and the tube treated with hydrazine plus salt (T) would indicate the presence of thymine (T) nucleotides.

Question 20

Dye terminator sequencing has been performed using capillary electrophoresis to separate the fragments. ddATP has been labeled with a "green" fluor, ddTTP with "red," ddCTP with "blue," and ddGTP with "black." The colors are detected in the following order: red, green, black, red, green, blue, red, black, black, green, blue. What is the sequence of this fragment?

Accepted Answer

The answer of Dye terminator sequencing has been performed using...

Quiz 10: DNA Sequencing