2. DNA structure

Question 1

How many turns in B helix?

Answer 1

10

Question 2

How many turns in A helix?

Answer 2

11

Question 3

How is DNA B helix defined?

Answer 3

Average structure of DNA in solution

Question 4

How does A helix differ from B helix?

Answer 4

More compressed, shorter, wider

Question 5

When is Z helix formed?

Answer 5

Transiently during transcription, also for specific sequences

Question 6

Which DNA structure does dsRNA commonly adopt?

Answer 6

A helix

Question 7

Which non-covalent interactions form between bases?

Answer 7

Hydrogen bonds and Van der Waals interactions

Question 8

What drives helix formation?

Answer 8

The hydrophobic effect

Question 9

Which parts of the DNA are hydrophobic and hydrophillic?

Answer 9

Bases are hydrophobic, the backbone is hydrophillic

Question 10

What is the distance between two sugars in the DNA backbone?

Answer 10

6 Angstrom

Question 11

What is the typical with of a nucleotide base?

Answer 11

3.3 Angstrom

Question 12

Why do bases stack on top of each other?

Answer 12

Because otherwise there would be a water-filled hole between bases, which is energetically discouraged

Question 13

Why do bases twist with respect to each other?

Answer 13

To maximise exposure of hydrophillic parts to water and to maximise H-H bonds between bases

Question 14

Which bases are purines?

Answer 14

A and G

Question 15

Which bases are pyrimidines?

Answer 15

C and T

Question 16

Why were AT and GC pairings favoured?

Answer 16

Because their width is nearly the same, therefore can form a helix without disrupting its structure

Question 17

What are the two Hoogsten base pairs?

Answer 17

Flipped A + T (disrupts regular structure of the helix)

Flipped G + C (only in acidic pH)

Question 18

What bases, other than cytosine, make good H-bonds with guanine?

Answer 18

Thymine and uracil

Question 19

What technique is most widely used for DNA structural studies?

Answer 19

High resolution X-ray crystallography

Question 20

What are the 4 terms used to describe changes in DNA structure?

Answer 20

Twist, Roll, Slide and Propeller twist

Question 21

What is the difference between major and minor groove?

Answer 21

Minor groove is where sugars are closest together

Question 22

What is the definition of angle of twist?

Answer 22

Rotation of one base pair with respect to the next

Question 23

What is the typical range and mean for the twist angle in B helices?

Answer 23

Range 24-40 degrees, typically 32 degrees

Question 24

What is the difference between twist and propeller twist?

Answer 24

Twist occurs between base pairs, propeller twist occurs within a base pair

Question 25

What is a typical propeller twist angle at which H-bonds are still maintained?

Answer 25

10-15 degrees

Question 26

What is the function of propeller twist?

Answer 26

Allows neighbouring base pairs to interact with a larger surface area

Question 27

Why are twist, slide and roll properties dependent on each other?

Answer 27

Change in one property must be accommodated by a change in the other properties

Question 28

Which base pair can form an additional H-bond upon propeller twisting?

Answer 28

AT

Question 29

Upon propeller twist, a clash between two countering purine bases can occur. What are the two ways in which it can be resolved and what are the consequences?

Answer 29

1) Negative slide | 2) Positive slide and roll, allows for additional purine-purine interactions

Question 30

Which two properties of the DNA helix remain constant despite twist, slide and roll transformations?

Answer 30

Direction and vertical axis

Question 31

What is the function of helix untwisting/underwinding?

Answer 31

To destabilise and separate the strands, making them more accessible

Question 32

Rank GC-rich, AT-rich, poly-A/T and mixed regions in terms of decreasing stability

Answer 32

GC-rich, mixed, poly-A/T, AT-rich

Question 33

Give an example of an AT-rich region

Answer 33

TATA box

Question 34

What does gradual change in roll angle result in?

Answer 34

Curvature of DNA

Question 35

Why is gradual change in roll angle more common that stepwise?

Answer 35

It is easier to accommodate by the backbone

Question 36

In protein-binding regions of DNA, what is the importance of the regions flanking the recognition sequence?

Answer 36

They must accommodate a bend in DNA for the recognition sequence to bind to a protein

Question 37

What technique was used to prove intrinsic DNA sequence susceptibility to bending?

Answer 37

Electron microscopy