2: three forms of double helix

B form DNA

< The complementary chains are parallel and run in opposite directions.

< Together the twist into a righthanded double helix.

< The helix forms two grooves called major and minor groove.

< The major groove is accessible for regulatory proteins or other molecules.

< The base is in the anti-conformation with respect to the sugar.

< Bases lay straight on to the axis which is in the center of the stacked bases.

< Adopt the C2’endo sugar pucker.

A-form

< Double helical structure present in RNA.

< The sugar pucker is C3’endo.

< DNA can also adopt the A-form, this only occurs when limited water is available to hydrate the DNA.

< The two strands are antiparallel, form a right-handed spiral with the phosphate groups on the outside and the bases on the inside.

< The base pairs in A-form helices are displaced from the helix axis, which leads to a deepening of the major groove.

< It is more difficult for proteins to read out the sequencespecific information.

Z-form

< Is a left-handed helix adopted by segments of DNA that have alternating C and G nucleotides.

< The sugars alternate between C2’endo and C3’endo puckers.

< G residues are in syn conformation and C residues are in anti-conformation.

< The function is not quite understood  triggers the opening of DNA base pairs resulting in melted base pairs.

Can DNA transform between different forms?

Yes, DNA is able to transform from one form to another, demonstrating its deformability.

What is an intercalator DNA complex?

An intercalator DNA complex forms when a molecule inserts itself between DNA base pairs, often altering the structure.

What is Distamycin, and how does it interact with DNA?

Distamycin is a molecule that binds to DNA sequences rich in A-T base pairs. These sequences can accommodate one or two ligands in the minor groove, but the groove must widen significantly for a second ligand to bind.

What is the persistence length of DNA, and how does it affect DNA structure?

• The persistence length is the maximum length of a DNA segment that behaves like a rigid rod. DNA segments shorter than the persistence length are relatively rigid, while longer segments can bend. For B-form DNA, the persistence length is approximately 500 Å (~140-150 bases).

How does the persistence length affect DNA's behavior as a rod?

DNA segments shorter than the persistence length (~500 Å) act as rigid rods, while longer segments can bend more easily.

What happens to DNA stored in plasmids?

DNA stored in plasmids can undergo supercoiling, which involves over or under winding of the DNA, making it more compact.

What is the difference between over winding and under winding of DNA?

• Over winding adds a right-handed twist to DNA, while under winding adds a left-handed twist, affecting the compactness of the DNA.

How is the amount of twists in DNA defined, and what does it indicate?

• The amount of twists is defined by writhe (W). Positive writhe indicates over winding, and negative writhe indicates under winding.

What enzymes are responsible for introducing and removing supercoiling in DNA?

Gyrases introduce supercoiling, while topoisomerases remove supercoiling in DNA.