class 15 dna structure

why is diameter of the double helix pretty constant

because base pairing rules define a purine (two rings) always go with a pyrimidine (one ring)

what drives DNA duplex formation

mainly hydrophobic effect and van der waals. complementary base pairs make it better but are not necessary for duplex to form

how are the nitrogenous bases oriented in the double helix

they rotate around the glycosidic bond to get optimal pi stacking favorable interactions (van der waals type interactions)

how many bp per turn of the double helix (B form)

10

B vs A vs Z form DNA

B form is the most common, it is hydrated DNA and found in vivo

A form is dehydrated conditions, or a one strand DNA one strand RNA hybrid. Turns tighter (squished) wider d

Z form observed in vitro, but likely found rarely in cells. left handed turning. sugar phosphate backbone is zig zagged. There are proteins that can bind Z-DNAs.

major and minor groove

every base pair has a major and minor groove side

major groove side, the two bases are farther away and this is where most of the h bond donating and accepting occurs.

minor groove side, the two bases are closer to each other and the two bases are simlar in structure on this side

you can tell which side is major or minor by looking relative to the glycosidic bond angles as they do not come together to face each other head on.

MAJOR is the longer path between the two glycosidic bonds

how many rings in purines, pyrimidines

purines have two

pyrimidines have 1

significance of RNA having the extra 2’ OH

makes it more reactive.

allows for splicing, the nucleophilic attack required for splicing and branch point functionality.

it can also attack itself and the molecule can spontaneously degrade

DNA, on the other hand, is very stable

intra molecular duplex formation

formation of hairprins. one strand BPs with itself.

same principles as behind inter molecular duplex formation, hydrogen bonds, vdw, hydrophobic effect

What kind of protein binding occurs in which groove and why

remember that the major groove is where most of the h bond donating and accepting occurs. therefore, the major groove shows more variance in response to the various bases that are in this given pair. on the other hand, the minor groove displays a more constant structure regardless of base pair identities.

thus,

Sequence specific binding proteins bind to the major groove of DNA

non seq spec. DNA binding occurs through interactions with the minor groove or the sugar P backbone.