1. DNA is hydrolyzed by acids below pH 7 via an SN1 reaction mechanism where the acid attacks nucleophilic nitrogens, especially N7 of guanine. This leads to depurination and complete hydrolysis at very low pH. 2. RNA is more resistant to acid hydrolysis than DNA but can still be hydrolyzed by stronger acids like 1N HCl at high temperatures. Acid treatment can depurinate DNA but not RNA. 3. DNA is not hydrolyzed by alkalis above pH 7 because it lacks the 2'-OH group required for base-catalyzed hydrolysis. RNA contains this group and can be easily hydrolyzed by alkaline pH through a mechanism

2. Effect of Acid: {pH<7}
DNA
 Hydrolysis occurs
 Depurination (hydrolysis of glycosidic bonds only)
at pH >3 and complete hydrolysis (also cleaving of
phosphodiester bond) into components at pH<2 +
heat.
 The hydrolysis and depurination proceeds by “acid-
catalysed SN1 reaction” mechanism.Nucleophilic
centres on Guanine and Adenine are N1,N3,N7 and
6th position in which the acid attacks electrophilicly
on N7 position.
 Extremely low pH digests the DNA completely and
this is why our stomach pH is low.

3. The electrophilic attack of acid on N7 gives rise to
depurination by hydrolysis

4.  Steps-(Figure on previous slide shows Guanine)
1. Electrophilic attack on Nitrogen at 7th position and
this increases leaving group ability of base.
2. This generates (a)free base and (b)oxocarbenium
ion which is positive.
3. The oxocarbenium ion undergoes subsequent
hydrolysis (nucleophilic attack of water) to
generate an abasic site(c).
4. This sites are mutagenic and are ring closed
acetal or exist as ring opened aldehyde (d).
5. Localisation of proton adjacent to aldehyde group
will result in elimination of phosphate residue on
3’ of abasic site.

5. RNA
 Acid effect on RNA is variable. RNA is more
resistant to acid hydrolysis compared to DNA.
 Duration of treatment with dilute acids will decide
the hydrolysis.
 Significant hydrolysis of RNA can be obtained by
treatment with 1N HCl (or more strong)at 100˚C
for about an hour.
 Treatment with 1N HCl at 60˚C for 10 minutes will
not hydrolyse RNA but can depurinate DNA. This is
used in Feulgen staining procedure and makes it
DNA specific staining.
 This indicates that RNA acid hydrolyses is more
resistant and requires certain extreme conditions.

6. Effect of Alkali {pH>7}
DNA
 DNA is not hydrolysed by alkali pH because it does
not contain the 2’-OH for base catalysed hydrolysis
mechanism.
 Although at high pH,there is more concentration of
negatively charged hydroxide ions(OH-
) which pulls
the hydrogen from DNA towards it and make it
deprotonated.
 The higher the pH(>10), there is extensive
deprotonation and this results in denaturation of
double stranded DNA.
 This alkali lysis method is used in isolation of
plasmid DNA from bacterial cell,where this
principle is applied.

7. RNA
 RNA can be easily hydrolysed at alkali pH as it
contains 2’-OH.
 Steps-(Figure in next slide)
1. The nucleophilic attack of OH-
on 2’-OH and
converts it to nucleophile which results in
intramolecular displacement be
2. This results in cleavage of phosphodiester bonds.
3. The product formed is 2’-3’ cyclic monophosphate
derivative and it is further hydrolysed to 2’ and 3’
monophosphate nucleotides.
 The DNA lacks 2’-OH and therefore is stable under
this condition.

8. The nucleophilic attack of base on 2’-
OH mediates the hydrolysis