DNA structure and basics Flashcards
(38 cards)
scientific name of ADENINE
6 amino purine
scientific name of thymine
2,4-dioxo-5-methyl pyrimidine
scientific name of cytosine
4-amino-2 oxo pyrimidine
scientific name of uracil
2,4-dioxopyrimidine
what is chargaffs rule and what does it indicate if it is not being followed
py = pu
if chargaffs rule is not being followed then most probably it is a single stranded DNA.
write down the characteristics of the PDB backbone
the pdb bond is ionisable and lends to the acidic nature of the DNA and therefore gives rise to the negative backbone
what is the most important interaction of the DNA structure
base stacking
it helps in keeping the h bond linear
How do you disrupt the base stacking structure?
urea,
formaldehyde,
acridine orange,
EtBr
glycosidic bond can be disrupted by
glycosylase and extreme NaOH
how do you break the phosphodiester bond?
endonuclease, . . . exonuclease specific RE non specific dnase1
what are the types of topoisomerase and what are there functions
type 1 and type 2
type 1 breaks 1 strand only and
type 2 breaks 2 strands
what are the conditions for denaturation of the DNA
High temperature
low salt concentration
high ph value
disruption of the base stacking
what are the conditions for the renaturation of the DNA
- tempr must be about 25-30 degrees lower than the denaturation temp.
- salt concentration
- size of the fragments
- Conc. of renealling fragments
what type of reaction is denaturation and the renaturation of DNA
denaturation: 1st order reaction
renaturation: 2nd order reaction
sequence of reactions for 5’ labelling
- treat with phosphatase which will lead to the removal of alpha phosphate
- phosphorylation with the help of Gamma 32 labelled phosphate ATP with the help of KINASE.
sequence of reactions for the 3’ labelling
use of alpha p32 labelled along with TDT
what happens if glycosidic bond is broken down
AP condition will be formed
Apurinic
Apyrimidinic
what if dna is treated with strong acid?
acidic treatment leads to AP CONDITION
what if DNA is treated with strong base?
ALkali treatment
hydrolysis
deprotonation
tautomerisation
ketoenol formation
denaturation
eg. of crosslinking agents
Psorlan
Mitomycin C
nitrogen and sulphur mustard
cis platin
what happens with the use of crosslinking reagents
cells will die
as the opposite strands will get attached and it would lead to halt in DNA replication fork
where is positive supercoiling seen and what do they have in exception
T even bacteriphages
they have 5 HMC in place of Cytosine
what is the condition corresponding to the hypochromic or hyperchromic shift?
when there is a change in the amount of molecule
what are conditions corresponding to the bathochromic shift or hyprochromic shift?
- change in proprety of molecules
2. surrounding of molecule
