This a very brief presentation on Nucleic acids. I hope you will learn some very basic points on Nucleic acids.

1. Nucleic Acids
Collected by Faysal Rahman (Dept. of
Pharmacy)

2. History of Nucleic Acids
• Discovered in 1868
• By physician Friedrich Miescher

3. • Nucleic acids are polymer of nucleotides held
by 3’ and 5’ phosphate bridges.
• Nucleotide = sugar + phosphoric acid + N-
bases ( i.e. purines and pyrimidines )
• Sugars in the NA are pentose sugars.

4. • Nitrogen bases are of two kinds.
• Purines ( Adenine, Guanine )
• Pyrimidines ( Thymine, Cytosine , Uracil )

5. Composition of Nucleotides
• They are the phosphate esters of nucleosides.
• The esterification occurs at 5th or 3rd hydroxyl
group of pentose sugar.
• Most of the nucleoside phosphates involved in
biological function are 5’ phosphates.

6. Functions of nucleotides
• Activated precursor of DNA and RNA.
• Components of coenzymes : NAD, FAD & CoA
etc.
• As metabolic regulators, e.g. cAMP , cGMP
• GTP is involved in protein biosynthesis as
source of energy.
• ATP is the universal currency of energy.

7. • Nucleotides can act as a source of high energy.

8. • Phosphodiester bond: In a DNA or RNA
nucleotides are joined into polymer by the
covalent bond / linkage of a PO4- group
between the 3’ carbon of one nucleotide and
the 5’ carbon of the adjacent nucleotide.
• This type of bond is known as the
phosphodiester bond.

9. Phosphodiester bond

10. DNA
• DNA, or deoxyribonucleic acid, is the
hereditary material in humans and almost all
other organisms.

11. • Most DNA is located in the cell nucleus.
• DNA has equal numbers of adenine & thymine
residues (A = T) and equal number of guanine
and cytosine residues ( G ≡ C ).
• This is called as Chargaff’s rule of molar
equivalence between purines and pyrimidines
in the DNA structure.
• RNA do not obey Chargaff’s rule.

12. DNA double helix
• Double helical structure was proposed by
Watson & Crick in 1953.
• DNA is a right handed double helix.
• It consists of two polydeoxyribonucleotide
chains twisted around each other on a
common axis of symmetry.
• The chains are paired in an antiparallel
manner, i.e.

13. DNA Cont…
• The 5’-end of one strand is paired with the 3’-
end of the other strand.
• The two strands are antiparallel, i.e. one
strand runs in the 5’ to 3’ direction while the
other runs in 3’ to 5’ direction.
• The width of double helix is 20 A0 (2.0 nm).
• Each turn of the helix is 34 A0 (3.4 nm) with 10
pairs of nucleotides.

14. DNA Cont…
• So, each pair placed at a distance of about 3.4
Ao
• In the DNA helix , the hydrophilic deoxyribose-
phosphate backbone of each chain is on the
outside of the molecule where as the
hydrophobic bases are stacked inside.

17. Some definitions
• Base stacking: The base pairs of DNA are flat
structures, stacked on top of each other . This
is called base stacking.

18. • DNA melting: If a mixture of DNA is heated to
a certain temparature(approx. 95oC) the two
strands of each piece of DNA will separate. Itr
is called DNA melting.
• DNA annealing: If the solution of melting DNA
is allowed to cold , the separate pieces
reassemble to their original pattern. This is
referred to as DNA annealing

19. • Circular DNA: When each of the two strands
of DNA formed a closed structure without free
strands , it is called circular DNA.
• All prokaryotic genomic
DNAs and many viral DNAs
are circular.
• It also occur in
mitochondria which are
present in all eukaryotic cells.

20. Different forms of DNA
• Usually there are 4 types of DNA.
• Natural or B-form DNA
• A-form DNA
• Z-form DNA
• Triple helical DNA

21. RNA
• Unbranched
• Protein synthesis
• Purines: Adenine, Guanine
• Pyrimidines: Cytosine,
Uracil
• -OH group at no.2 carbon;
easily hydrolised

22. Types of RNA
• Messenger RNA / mRNA
• Ribosomal RNA / rRNA
• Transfer RNA / tRNA
• Viral RNA
mRNA
• MW = 30,000 – 50,000 D
• Eukaryotes have more stable mRNA
• Carry info to synthesize protein structure.

23. rRNA
• Ribosome = rRNA + protein
• 85-90% of total cellular RNA.
• Catalyze assembly of AA into protein chain.
• Binds tRNA and accessory molecules.
tRNA
• Consists of about 75 nucleotides.
• MW = 25000 D
• Common CCA sequence at one end.

24. tRNA cont.
• Each tRNA has a specific alteration for one AA.
• Clover leaf structure
• Carry AA to ribosomes.

25. Viral RNA
• May occur in double strand , usually in single
stranded associated with protein.
• Carries genetic info.

26. Secondary structure of RNA
The simplest secondary structure in single
stranded RNA are formed by pairing a
complementary bases.
3 types of secondary structure of RNA
1. Hair pins (loops have 5-10 nucleotides)
2. Stem loops (loops have 50-100 nucleotides)
3. Pseudo knot

27. • Secondary structure of
RNA
• Tertiary structure of RNA

28. Denaturation of DNA
• DNA denaturation is the process of breaking
down the DNA molecule.
• There are two bonds i.e. hydrogen bonding
between base pairs and stacking interaction
between hydrophobic and Vander walls.
• There are a variety of ways to denature DNA.
• Methods of DNA denaturation are heat, NaOH
treatment, and salt.

29. Renaturation of DNA
• The denatured DNA can reformulate hydrogen
bonds between complementary single strand,
making it likely to reform double helix
structure again. It is called renaturation of
DNA.

30. DNA hybridization
• DNA Hybridization, is the process in which two
complementary single-stranded DNA
molecules bond together to form a double-
stranded molecule.
• The bonding is dependent on the appropriate
base-pairing across the two single-stranded
molecules.
• Hybridization is an important process in
various research and clinical laboratory
techniques.

31. DNA isolation
• DNA can be isolated from Animal cell, plant or
culture of bacteria.
• There are 3 steps to isolate DNA from a cells.
• Step-1:
Lysozyme or EDTA is used to rupture the cell
membrane and bring out cell contents
outside.
Partially digested cell membrane fragments
can be can be palliated by centrifugation.

32. DNA Isolation cont..
• Step-2:
In this step , RNA and protein are isolated in
various methods leaving only DNA in the cell
extract. Phenol or 1:1 phenol & CHCl3 mixture
to deproteinize(removal of protein).
Ribonuclease is used to break RNA to
ribonucleotide subunits.
• Step-3:
After purification step(step-2) , Ethanol is used
to precipitate the DNA molecules.

33. DNA Isolation cont..
Centrifugation pellet the DNA which may be
resuspended in a smaller volume than the
DNA extract in step-2.
Here is a brief diagram to show DNA
extraction.

34. References:
1. https://www.britannica.com/science/nucleic-acid
2. Richard I. GumportFrank H. Deis, Nancy Counts Gerber, Roger E. Koeppe, II - Biochemistry_
Student Companion-Freeman (2002), 51-82
3. https://www.slideshare.net/YESANNA/nucleic-acid-chemistry-40334502?qid=21972832-b5cc-
4998-9ba9-053663433831&v=&b=&from_search=1
4. C. Stan Tsai - An Introduction to Computational Biochemistry-J. Wiley (2002), 165-179