this presentation contain physical and chemical properties of dna.

2. Physical properties
Ultraviolet absorption
Denaturation
Renaturation
Chemical properties
Nucleophiles
Hydrazine
Hydozlyamine

3. Alkylating agents
Nitrous acid
Bifunctional alkylating agents
Electophiles

4.  DNA absorbs uv in range of
(240nm-280nm).
 MAX absorption at 260nm.
 This absorption is monitored by
spectrophotometer
 Calculations are done by using
BEER LAMBERT LAW
A=ECl

5.  E FOR DNA IS 6600L/MOL cm.
 Absorbance(A)=1 at 260nm is equivalent to
50ug/ml DNA.
 A260/A280 is a measure of DNA purity.
 Single stranded DNA has absorbance 40%
more then double stranded.
 Absorbance at 260nm
free bases 1.60 units
single strand 1.37 units
double strand 1.00 units

8.  When two strands of the DNA
separate as single strands.
 Effect of various factors on DNA
TEMPERATURE
ACIDS
ALKALI

10. TM linear relationship between
Base stacking energy G+C CONTENT
Temp. at which 50% of the DNA melts
Melting temperature(Tm)
TEMPERATURE
Increase in temp. disrupts H-bond & shell
of hydration.

11. ACIDS
PH<2 ionizes
the bases of
two strands
Thus disrupts
H bonding &
base stacking.
Phosphodiester
bond & glycosidic
bond are susceptible
to lowPh.
ALKALI
Above ph 12
base tend to
change polarity
Disrupts H
bonding

13. Renaturation
Denatured DNA may reform when Hbond forms
btw complementary base pairs.
Slow cooling or addition of ions may lead to
renaturation.
The rate limiting step in this reaction is collision of
complementary DNA molecules.
Once the nucleation has initiated, rest double
helix coils very fastly.

14. NUCLEOPHILE
Electron rich reagent that can attack on +ve ly
charged carbon next to nitrogen in nitrogen bases.

15.  H2N-NH2
 It is widely used to modify DNA.

16.  Stronnucleophile and powerfull
mutagen.
 It can disrupt h bonding physically by
formation of hydroxlamino group thus
prevent A-T & C-G pairing.

17.  Seek an unbranched electron pair.
 Good site for e attack are ring nitrogen and
oxygen on nitrogen bases.
ALKYLATING AGENTS
 Ethylmethylsulphonate
 Ethylnitrosourea
 N –methyl-N’-nitro-N-nitosoguanidino

18.  Depending upon site of alkylation they
may alter keto enol equillibrium.
 Bulky alkyl adduct on the base will affect
H bonding.
Bifunctional alkylating agents
Have two reactive group
Nitogen and sulphur mustard gas
They form intra or inter crosslinking
btw two strands of DNA

19.  HNO2 REACTS WITH AMINO GROUP OF C,G
OR A in an oxidative deamination rx
 The deamination leads to carbonyl group
cytosine
uracil
Reverse h
bond polarity
adenine
hypoxa
nthine
Reverse H
bond polarity
guanine
xanthine
No mismatch
pairing

20.  Richard r sinden
 Voet and voet
 Cell and molecular biology
genarld karp