2: DNA and Genomics

Students analyze DNA isolation, FISH, SNP arrays, plasmids, gene libraries, PCR, Sanger and next-generation sequencing, RT-qPCR, CRISPR technology, RNA interference, GWAS, and synthetic biology.

Matching DNA Sequencing Techniques to Descriptions

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Match each of the following DNA sequencing techniques with their corresponding descriptions.
Note: Each choice will be used exactly once.

	Your Choice	Prompt
	Drop Your Choice Here	1. Ion Torrent semiconductor sequencing
	Drop Your Choice Here	2. Illumina sequencing by synthesis
	Drop Your Choice Here	3. ABI solid sequencing
	Drop Your Choice Here	4. Roche 454 pyrosequencing

Drag one of the choices below:

• A. detects the light from the luciferase enzyme as it consumes the diphosphate molecules released when nucleotides are added to the DNA template
• B. detects the light emitted from fluorescently tagged nucleotides as they are added to the DNA template
• C. detects sequences as they ligate to a di-base probe attached to a magnetic bead
• D. detects individual hydrogen ions released during DNA synthesis using microscopic pH meters

Check Answer Reset Game

 

Gene Expression Fold Change from RT-qPCR Data

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	Untreated Cells		Cells Treated with Experimental Drug
	House Keeping Gene	Gene of Interest	House Keeping Gene	Gene of Interest
Well 1	21.5	24.7	20.9	24.3
Well 2	21.6	26.1	21.2	24.4
Well 3	20.3	25.1	21.2	25.0
mean Ct	21.1	25.3	21.1	24.6
ΔCt
ΔΔCt

Given the data in the table above calculate the fold change (2^|ΔΔCt|) value for the effect of the drug on the cells.
Note: answers need to be within 4% of the correct number to be correct.

Check Answer

 

True/False Statements About xDNA and XNA

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Which one of the following statements is FALSE regarding the structure of xDNA and XNA?

• A. xDNA is wider than natural DNA
• B. xDNA stands for extra DNA because it has more letters
• C. XNA has more than four nucleobase letters
• D. xDNA is also known as benzo-homologated DNA
• E. xDNA can base pair with natural DNA

Check Answer

 

DNA Sequencing Techniques from Descriptions

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Which one of the following DNA sequencing techniques correspond to the description 'd'.

• A. Illumina sequencing by synthesis
• B. Ion Torrent semiconductor sequencing
• C. Oxford Nanopore sequencing
• D. Terminal-dye Sanger sequencing

Check Answer

 

Amplicon Copy Number After PCR Rounds

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Starting with genomic DNA, how many copies of the double-stranded amplicon of the exact length are there after 11 rounds of PCR?

• A. 2⁷ = 128 complete copies
• B. 2⁸ = 256 complete copies
• C. 2⁹ = 512 complete copies
• D. 2¹⁰ = 1,024 complete copies
• E. 2¹¹ = 2,048 complete copies

Check Answer

 

DNA Base Composition Using Chargaff's Rules (5 Choices)

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According to Chargaff's rules concerning the base pairing composition in double-stranded DNA, consider a sample where the percentage composition of 32% is thymine.
What are the percentages of the other three bases?

• A. adenine (A): 18% — cytosine (C): 18% — guanine (G): 32%
• B. adenine (A): 25% — cytosine (C): 18% — guanine (G): 25%
• C. adenine (A): 25% — cytosine (C): 25% — guanine (G): 18%
• D. adenine (A): 32% — cytosine (C): 18% — guanine (G): 18%
• E. adenine (A): 18% — cytosine (C): 32% — guanine (G): 18%

Check Answer

 

Complementary DNA Sequences Without Direction Labels

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DNA is organized as a double helix where two strands run in opposite, or anti-parallel, directions. The ends of these strands are referred to as 5′ (five prime) and 3′ (three prime) ends. The strands are held together by hydrogen bonds between complementary base pairs. Specifically, adenine (A) forms a pair with thymine (T), and guanine (G) pairs with cytosine (C). This base pairing is critical for the stability of the DNA molecule and is central to processes like DNA replication and transcription.

 

A

C

A

,

T

G

A

,

T

A

C

Which one of the following DNA sequences is complementary to the direction-less DNA sequence shown above?

• A.  

  T

  G

  T

  ,

  A

  G

  T

  ,

  A

  T

  C

• B.  

  T

  G

  T

  ,

  A

  C

  T

  ,

  A

  T

  G

• C.  

  A

  T

  G

  ,

  T

  C

  T

  ,

  A

  T

  G

• D.  

  A

  C

  A

  ,

  T

  C

  A

  ,

  T

  A

  G

• E.  

  C

  A

  T

  ,

  A

  G

  T

  ,

  A

  C

  A

Check Answer

 

Degenerate Primer Codes from Sequence Alignments

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C	T	C	,	A	G	C	,	T	A	A
G	A	C	,	A	A	G	,	T	T	C
G	T	A	,	A	T	A	,	T	C	A
G	A	T	,	A	T	C	,	C	T	C
C	A	A	,	A	A	C	,	C	A	C
C	T	C	,	A	G	G	,	C	T	C
G	T	T	,	A	A	C	,	T	A	C
C	T	C	,	A	A	C	,	T	T	A
C	T	A	,	A	G	G	,	T	C	A
C	A	T	,	A	G	C	,	T	C	C

What is the arbritrary sequence code for degenerate primer design in the table above?
You may include a comma every 3 letters, but do NOT include any extra commas or spaces in your answer.

Check Answer

 

Consensus Sequences from Simple Alignments (Fill in the Blank)

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A	G	T	,	G	T	C	,	G	A	G
T	G	A	,	C	T	G	,	A	A	G
C	T	A	,	C	T	G	,	A	A	G
A	A	A	,	T	T	G	,	A	A	G
A	G	C	,	C	G	G	,	A	A	G
A	C	A	,	C	T	G	,	T	C	A
A	G	G	,	A	C	T	,	A	G	G
A	G	A	,	C	T	A	,	A	T	C
G	G	A	,	C	A	G	,	C	A	T

What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.

Check Answer

 

Consensus Sequences from Tables (Fill in the Blank)

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C

T

A

,

A

A

A

,

A

T

G

,

A

A

T

T

A

C

,

T

A

G

,

G

C

A

,

C

A

A

G

G

A

,

C

A

C

,

C

T

C

,

T

T

T

T

A

A

,

G

C

A

,

C

A

A

,

G

C

G

A

T

G

,

G

G

T

,

C

A

C

,

T

G

G

T

C

A

,

C

C

A

,

T

T

A

,

A

T

C

C

T

A

,

C

T

A

,

A

C

C

,

A

A

G

A

G

T

,

G

G

C

,

T

T

T

,

G

C

C

T

T

T

,

G

A

A

,

C

C

C

,

C

G

G

What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.

Check Answer

 

Consensus Sequences from Alignments (Multiple Choice)

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What would be the consensus sequence for the following aligned sequences?

C	G	G	,	T	C	G	,	G	C	C
C	A	G	,	G	G	C	,	G	G	C
C	G	C	,	G	G	T	,	G	A	A
C	C	A	,	C	T	G	,	C	C	G

• A.

  C

  C

  A

  ,

  C

  T

  G

  ,

  G

  C

  C

• B.

  C

  G

  G

  ,

  T

  C

  G

  ,

  G

  C

  C

• C.

  C

  A

  G

  ,

  T

  C

  G

  ,

  G

  C

  C

• D.

  C

  G

  G

  ,

  G

  G

  G

  ,

  G

  C

  C

• E.

  C

  G

  G

  ,

  C

  T

  G

  ,

  G

  G

  C

Check Answer

 

DNA Fragment Migration in Agarose Gel Electrophoresis (Closest/Farthest)

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Which one of the following fragments of DNA would travel furthest from the wells during agarose gel electrophoresis?

• A. 200 base pairs
• B. 450 base pairs
• C. 3,000 base pairs
• D. 6,000 base pairs

Check Answer

 

DNA Fragment Size from Agarose Gel Migration (Numeric)

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Gel Migration Problem

DNA Marker	# of Base Pairs (bp)	Migration Distance (cm)
500 base pairs	500	2.68
1,000 base pairs	1000	2.26
2,000 base pairs	2000	1.84
3,000 base pairs	3000	1.59
5,000 base pairs	5000	1.28
10,000 base pairs	10000	0.86
Unknown	? ?	1.40

The standard DNA ladder and unknown DNA strand listed in the table were separated using an agarose gel
Estimate the number of base pairs of the unknown DNA strand.
Note: answers need to be within 13% of the correct number to be correct.

Check Answer

 

DNA Melting Temperature Extremes from Sequence (12 Bases)

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Which one of the following DNA sequences below will have the HIGHEST melting point (T_m).

Hint: I tried to make this question pretty easy and it does not require a calculator.

• A.

  5′–

  A

  G

  G

  ,

  G

  T

  G

  ,

  G

  G

  G

  ,

  A

  C

  G

  –3′

  3′–

  T

  C

  C

  ,

  C

  A

  C

  ,

  C

  C

  C

  ,

  T

  G

  C

  –5′

• B.

  5′–

  G

  A

  A

  ,

  T

  T

  G

  ,

  G

  C

  A

  ,

  T

  A

  T

  –3′

  3′–

  C

  T

  T

  ,

  A

  A

  C

  ,

  C

  G

  T

  ,

  A

  T

  A

  –5′

• C.

  5′–

  G

  C

  T

  ,

  A

  A

  T

  ,

  T

  A

  A

  ,

  T

  A

  T

  –3′

  3′–

  C

  G

  A

  ,

  T

  T

  A

  ,

  A

  T

  T

  ,

  A

  T

  A

  –5′

• D.

  5′–

  G

  C

  C

  ,

  T

  T

  A

  ,

  A

  T

  A

  ,

  A

  T

  T

  –3′

  3′–

  C

  G

  G

  ,

  A

  A

  T

  ,

  T

  A

  T

  ,

  T

  A

  A

  –5′

Check Answer

 

Inverse PCR Primer Selection (15 nt)

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EcoR1 overhang	left unknown sequence	central known sequence	right unknown sequence	EcoR1 overhang
5′–      A   A   ,   T   T   C  – 3′–              ,           G  –	–  N   N   N   ,   N   N   N   ,   N   N   N  – –  N   N   N   ,   N   N   N   ,   N   N   N  –	–  C   T   C   ,   A   G   T   ,   C   C   T   ,   G   A   G   ,   C   A   T  – –  G   A   G   ,   T   C   A   ,   G   G   A   ,   C   T   C   ,   G   T   A  –	–  N   N   N   ,   N   N   N   ,   N   N   N  – –  N   N   N   ,   N   N   N   ,   N   N   N  –	–  G           ,              –3′ –  C   T   T   ,   A   A      –5′

Choose the correct pair of RNA primers that will amplify the both the known and unknown region of DNA shown above using inverse PCR.
The RNA primers are 6 bases in length.
Pay close attention to the 5′ and 3′ ends of the primers.

• A.  

  5′–

  A

  U

  G

  ,

  C

  U

  C

  –3′

  AND  

  5′–

  A

  C

  U

  ,

  G

  A

  G

  –3′

• B.  

  5′–

  G

  A

  G

  ,

  U

  C

  A

  –3′

  AND  

  5′–

  U

  A

  C

  ,

  G

  A

  G

  –3′

• C.  

  5′–

  G

  A

  G

  ,

  C

  A

  U

  –3′

  AND  

  5′–

  G

  A

  G

  ,

  U

  C

  A

  –3′

• D.  

  5′–

  U

  G

  A

  ,

  C

  U

  C

  –3′

  AND  

  5′–

  U

  A

  C

  ,

  G

  A

  G

  –3′

• E.  

  5′–

  A

  C

  U

  ,

  G

  A

  G

  –3′

  AND  

  5′–

  U

  A

  C

  ,

  G

  A

  G

  –3′

• F.  

  5′–

  A

  C

  U

  ,

  G

  A

  G

  –3′

  AND  

  5′–

  G

  A

  G

  ,

  C

  A

  U

  –3′

Check Answer

 

Restriction Fragment Sizes (12 Length, 2 Sites)

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DNA Fragment Question: Shown below is a short DNA fragment that is only 12 kb in length. This fragment has been isolated for restriction enzyme analysis.

			PauI				GlaI										PauI
	0		1		2		3		4		5		6		7		8		9		10		11		12

Two (2) distinct types of restriction enzyme recognition sites, PauI and GlaI, are labeled at the top of this DNA segment.

Determine the sizes of the DNA bands that would appear on an agarose gel after digestion with PauI only.

• A. 1 kb
• B. 2 kb
• C. 3 kb
• D. 4 kb
• E. 5 kb
• F. 6 kb
• G. 7 kb
• H. 8 kb

Check Answer Clear Selection

 

Nested PCR Primer Pair Selection (24 nt)

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5′–  G   C   C   ,   A   T   T  – 3′–  C   G   G   ,   T   A   A  –

–  G   A   C   ,   T   T   C   ,   A   G   C   ,   A   T   T   ,   C   G   C   ,   T   A   C   ,   G   A   T   ,   C   T   T  – –  C   T   G   ,   A   A   G   ,   T   C   G   ,   T   A   A   ,   G   C   G   ,   A   T   G   ,   C   T   A   ,   G   A   A  –

–  A   T   G   ,   A   G   C  –3′ –  T   A   C   ,   T   C   G  –5′

The amplicon sequence of DNA shown above was replicated using 30 cycles of PCR, using the primers 5′-GCCATT-3′ and 5′-GCTCAT-3′.
But the first PCR run contained significant contamination due to mispriming. Probably from using too short of primers that were only 6 nucleotide in length.
Choose the correct pair of RNA primers that will amplify the remaining region of DNA inside the old primers using nested PCR. The nested RNA primers are 6 bases in length.
Pay close attention to the 5′ and 3′ ends of the primers.

• A.  

  5′–

  A

  A

  G

  ,

  A

  U

  C

  –3′

  AND  

  5′–

  C

  U

  G

  ,

  A

  A

  G

  –3′

• B.  

  5′–

  C

  U

  U

  ,

  C

  A

  G

  –3′

  AND  

  5′–

  C

  U

  A

  ,

  G

  A

  A

  –3′

• C.  

  5′–

  G

  A

  C

  ,

  U

  U

  C

  –3′

  AND  

  5′–

  C

  U

  G

  ,

  A

  A

  G

  –3′

• D.  

  5′–

  A

  A

  G

  ,

  A

  U

  C

  –3′

  AND  

  5′–

  C

  U

  U

  ,

  C

  A

  G

  –3′

• E.  

  5′–

  G

  A

  C

  ,

  U

  U

  C

  –3′

  AND  

  5′–

  A

  A

  G

  ,

  A

  U

  C

  –3′

• F.  

  5′–

  G

  A

  C

  ,

  U

  U

  C

  –3′

  AND  

  5′–

  C

  U

  A

  ,

  G

  A

  A

  –3′

Check Answer

 

Restriction Enzyme Overhang Sequences

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Restriction enzymes are proteins that cut DNA at specific sequences to produce fragments for further study. These enzymes are obtained from various types of bacteria and have the ability to recognize short nucleotide sequences within a larger DNA molecule.
The restriction enzyme we are focusing on is AscI, which is derived from the bacterium Arthrobacter species.
AscI cuts the DNA sequence as follows: 5'-GG|CGCGCC-3', where the '|' indicates the cleavage site.
Based on this information, which one of the following sequences below corresponds to the overhang region of the DNA after cleavage by the restriction enzyme AscI?

• A. 5'-CCGCGC-3'
• B. 5'-CGCG-3'
• C. 5'-CGCGCC-3'
• D. 5'-GCGCGG-3'
• E. 5'-GGCGCG-3'

Check Answer

 

Restriction Enzyme Cut Types (5', 3', or Blunt)

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Restriction enzymes are proteins that cut DNA at specific sequences to produce fragments for further study. These enzymes are obtained from various types of bacteria and have the ability to recognize short nucleotide sequences within a larger DNA molecule.
The restriction enzyme we are focusing on is Mly113I and is obtained from the bacteria Micrococcus lylae 113.
Mly113I cuts the DNA sequence as follows: 5'-GG|CGCC-3' where the '|' indicates the cut location.
Based on this info, can you identify the type of cut this enzyme makes?

• A. 3′ overhang
• B. 5′ overhang
• C. blunt

Check Answer

 

Palindromic DNA Sequence Completion

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The following numbered sequences only contains half of a palindromic sequence.
Match the correct lettered sequence that would finish and replace the 'N's in the sequence to make them palindromes.
Letters will be used exactly once.

	Your Choice	Prompt
	Drop Your Choice Here	1.   5′–  N   N   N   A  –3′
	Drop Your Choice Here	2.   5′–  T   T   A   ,   N   N   N  –3′
	Drop Your Choice Here	3.   5′–  T   A   T   T   ,   N   N   N   A  –3′
	Drop Your Choice Here	4.   5′–  A   N   N   N  –3′

Drag one of the choices below:

• A.  

  A

  T

  T

• B.  

  T

  A

  A

• C.  

  T

  T

  A

• D.  

  A

  A

  T

Check Answer Reset Game

 

PCR Primer Selection (36 bp Template, 9-nt Primers)

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5′–

T

C

T

,

G

C

G

,

A

A

A

,

C

C

T

,

G

T

A

,

A

C

G

,

A

C

A

,

G

A

T

,

C

C

G

,

T

T

A

,

C

A

A

,

C

T

G

–3′

3′–

A

G

A

,

C

G

C

,

T

T

T

,

G

G

A

,

C

A

T

,

T

G

C

,

T

G

T

,

C

T

A

,

G

G

C

,

A

A

T

,

G

T

T

,

G

A

C

–5′

Choose the correct pair of RNA primers that will amplify the entire region of DNA shown above using PCR. The RNA primers are 9 bases in length.
Pay close attention to the 5′ and 3′ ends of the primers.

• A.  

  5′–

  A

  A

  A

  ,

  G

  C

  G

  ,

  U

  C

  U

  –3′

  AND  

  5′–

  A

  A

  U

  ,

  G

  U

  U

  ,

  G

  A

  C

  –3′

• B.  

  5′–

  C

  A

  G

  ,

  U

  U

  G

  ,

  U

  A

  A

  –3′

  AND  

  5′–

  U

  U

  A

  ,

  C

  A

  A

  ,

  C

  U

  G

  –3′

• C.  

  5′–

  U

  C

  U

  ,

  G

  C

  G

  ,

  A

  A

  A

  –3′

  AND  

  5′–

  A

  A

  U

  ,

  G

  U

  U

  ,

  G

  A

  C

  –3′

• D.  

  5′–

  C

  A

  G

  ,

  U

  U

  G

  ,

  U

  A

  A

  –3′

  AND  

  5′–

  A

  A

  A

  ,

  G

  C

  G

  ,

  U

  C

  U

  –3′

• E.  

  5′–

  U

  C

  U

  ,

  G

  C

  G

  ,

  A

  A

  A

  –3′

  AND  

  5′–

  A

  A

  A

  ,

  G

  C

  G

  ,

  U

  C

  U

  –3′

• F.  

  5′–

  U

  C

  U

  ,

  G

  C

  G

  ,

  A

  A

  A

  –3′

  AND  

  5′–

  C

  A

  G

  ,

  U

  U

  G

  ,

  U

  A

  A

  –3′

Check Answer