Question 1

Which of the following statements best describes the difference between B-DNA and Z-DNA in terms of helical handedness and base pair repeat units?

Accepted Answer

B-DNA is right-handed with a 1 bp repeat unit, while Z-DNA is left-handed with a 2 bp repeat unit.

Question 2

A researcher observes that a DNA region with a long inverted repeat forms a structure with two hairpin arms and a four-way junction under negative supercoiling. Which structure is most likely being observed?

Accepted Answer

Cruciform DNA

Question 3

Which equation correctly relates the linking number ($$Lk$$), twist ($$Tw$$), and writhe ($$Wr) of a $$topologically closed DNA molecule?

Accepted Answer

$$Lk = Tw + Wr$$

Question 4

What is the biological significance of DNA unwinding elements (DUEs) in eukaryotic and prokaryotic genomes?

Accepted Answer

They serve as common features of replication origins by forming unpaired regions under superhelical tension.

Question 5

Which of the following conditions most strongly promotes the formation of Z-DNA in a DNA molecule containing alternating (CG)$$_n$$ sequences?

Accepted Answer

High salt concentration and negative supercoiling

Question 6

A mutation in a bacterial cell leads to the loss of topoisomerase II (gyrase) activity. What is the most likely consequence for DNA topology?

Accepted Answer

Accumulation of positive supercoils and reduced negative supercoiling

Question 7

Which DNA structure is most likely to form within a tract of direct repeats, such as (CTG)$$_n$$•(CAG)$$_n$$, and is associated with triplet repeat expansion diseases?

Accepted Answer

Slipped-strand DNA

Question 8

Which of the following best explains why A-DNA is less susceptible to UV-induced DNA damage compared to B-DNA?

Accepted Answer

Nucleobases in A-DNA are less exposed to UV due to their position in the helix.

Question 9

Which of the following equations correctly defines the superhelical density ($$\sigma) of a $$DNA molecule?

Accepted Answer

$$\sigma = \frac{Lk - Lk_0$}{Lk_0$}$$

Question 10

A DNA segment with a mirror repeat sequence forms a structure with a triple-stranded region and a single-stranded hinge under superhelical stress. What is this structure called?

Accepted Answer

H-DNA (intramolecular triplex)

Question 11

Which of the following is a plausible biological role for the formation of alternative DNA structures such as cruciforms, Z-DNA, and H-DNA?

Accepted Answer

They can modulate supercoiling, influence nucleosome positioning, and regulate transcription and replication.

Question 12

Which of the following best describes the effect of negative supercoiling on the formation of alternative DNA structures?

Accepted Answer

Negative supercoiling provides the free energy necessary to drive the formation of alternative DNA structures.

Question 13

A DNA region is found to be highly susceptible to single-strand specific chemicals and is located near a gene promoter. Which alternative DNA structure is most likely present?

Accepted Answer

Z-DNA

Question 14

Which of the following is a key structural feature of A-DNA compared to B-DNA?

Accepted Answer

A-DNA has a shorter rise per residue and base pairs are tilted relative to the helical axis.

Question 15

Which of the following best explains why certain DNA sequences are more likely to form alternative structures such as cruciforms or triplexes?

Accepted Answer

They contain defined symmetry elements such as inverted or mirror repeats.

Question 16

Which of the following is a likely consequence of slipped-strand DNA formation during DNA replication in regions with direct repeats?

Accepted Answer

Frameshift mutations leading to altered protein coding sequences

Question 17

Which of the following best describes the role of topoisomerase I in bacterial cells?

Accepted Answer

It relaxes supercoils by breaking one DNA strand at a time.

Question 18

Which of the following is a plausible reason why alternative DNA structures are often found near regulatory regions of genes?

Accepted Answer

They facilitate the binding of regulatory proteins and can modulate gene expression.

Alternative DNA Conformations and Their Biological Roles

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