confirmation of nucleic acid

1. Confirmation of nucleic
acid
lashika
CENTRE FOR BIOINFORMATICS
2116

2. INTRODUCTION
HISTORY- DNA was discovered in 1869 by
JOHANN FRIEDRICH MIESCHER , a swiss
researcher.
Nucleic acids includes DNA ( deoxyribonucleic
acid) and RNA( ribonucleic acid).
The demonstration that DNA contained genetic
information was first made in 1944 by AVERY,
MACLEOD and MACCRAY.

3. Functions of nucleic acids
1. DNA – chemical basis of heredity may be
regarded as the reserve bank of genetic
information.
2. DNA- maintain the identity of different
species of organisms over millions of years.
3. DNA- organised into genes.
4. GENE CONTROL- proteins synthesis through
the mediation of RNA.

4. Central dogma

5. Components of nucleic acid
 Nucleic acid are polymers of nucleotides
 NUCLEOTIDES-
1. Nitrogenous base + a pentose sugar+ a phosphate group.
2. They perform a wide variety of functions in the living cells.
3. They also include their role as structural components of
some co-enzymes of B-complex vitamins (Eg : NAD+,FAD+).
4. Involve- energy reactions of cells
5. In the control of metabolic reactions.

7. Structure of DNA
 DNA is polymer of deoxyribonucleotides or simply
deoxyribonucleotide
 DNA is composed of 4 deoxyribonucleotides
namely:
1. Deoxyadenylate [ dAMP]
2. Deoxyguanylate [ dGMP]
3. Deoxycytidylate [ dCMP]
4. Deoxythymidylate [ dTMP/TMP]

8. DNA double helix
 JAMES WATSON AND FRANCIS CRICK
in 1953 (Noble prize 1962 )
 The DNA is considered as the milestone
in the era of modern biology.
 Comparable to a twisted ladder.
 It contain two polynucleotide strands
wound around each other.
 The backbone of each consists of alternating
deoxyribose and phosphate group.
 The phosphate group bonded to the 5’ carbon
atom of one deoxyribose is covalently
bonded to the 3’ carbon of the next.

9. Silent features of DNA
1. Right handed double helix. Consists of
two polydeoxyribonucleotide chains ,
twisted around each other.
2. Two stands- antiparallel
3. The width diameter- 20A(2nm)
4. Each turn (pitch)-34A(3.4nm) , with 10 pairs
of nucleotides , each pair placed – 3.4(0.34nm)
5. Hydrophilic deoxyribose phosphate backbone
(3’-5’- phosphodiester bond)- outside

10. 6. Complementary to each other due to base pairing
7. Two strands- hydrogen bonds formed by complementary base pairs
8.The hydrogen bonds are formed between purines and pyrimidines.

12. A-form of DNA
 A-DNA is one of the possible double helical
structure which DNA can adopt along with
other two biologically active helix
structure (B-DNA, Z-DNA).
 Right handed double helix.
 Short and fat compared to B-DNA.
 Occur only in dehydrated sample of DNA ,
such as those used in crystallographic
experiments.

15. B-form of DNA versus Z-form of DNA
B- DNA Z- DNA
The typical form of double helix DNA in which the
chain twist up and to the right around the front
of the axis of the axis
The left handed uncommon form of double helix
DNA in which the chain twist up and to the left
around the front of axis of the helix and which
has 12 base pairs in each helical turn and one
groove on external surface
Form under normal physiological conditions Form under high salt concentrations
Right handed Left handed
Contains a wide and deep major groove and a
narrow and deep minor groove
Contains a narrow and deep major groove and
wide and shallow minor groove
The base occupy at the core and sugar-phosphate
backbone occur at the periphery of helix
The sugar phosphate backbone form a zig zag
pattern and therefore, bases occur at the core
as well as the periphery
The orientation of sugar residues: altering The orientation of sugar residues: not altering

16. B-DNA Z-DNA
The angle of twist per repeating unit – 36 degree The angle of twist per repeating unit – 60 degree
Rise per residue- 3.4Å Rise per residue- 3.75 Å
Helix pitch : 34Å Helix pitch : 45Å
Diameter : 20Å Diameter : 18Å
The tilt of base pair: 6 degree The tilt of base pair : 7 degree
Rotation of repeating unit : 36 degree Rotation of repeating unit : 60 degree
Glycosidic torsion angle : anti for deoxyguanosine
and deoxycytidine
Glycosidic torsion angle: syn for deoxyguanosine and
anti for deoxycytidine
Sugar pucker: C2 endo for deoxyguanosine and C3
endo for deoxycytidine
Sugar pucker :C3 endo for deoxyguanosine and C2
endo for deoxycytidine
The distance of P from axis : 9.0 Å for both dGpC
and dCpG
the distance of P from axis: 8.0 Å for dGpC and 6.9
Å for dCpG
Residues per unit : mononucleotide Repeating unit : Dinucleotide

19. Other types of DNA structure
 These structures are important for
molecular recognition of DNA by protein
and enzymes
1. BENT DNA
2. KINKED DNA
3. TRIPLE STRANDED DNA
4. FOUR STRANDED DNA

20. BENT DNA
 BENT conformation – when
adenosine tracts are replaced
by other bases.
 Bending of DNA structure due to
1. Photochemical damage or
mispairing of bases
1. Certain antitumour drugs
like { CISPLASTIN}

21. Triple stranded DNA
 Due to additional hydrogen bonds
 Thus ,thymine can selectively form
two “HOOGSTEEN-HYDROGEN BONDS” to
the ADENINE of A=T pair to form T-A-T
 C-G-C
 Also called as HOOGSTEEN-TRIPLE HELIX .
 Due to negatively charged backbone
strands in triple helix, an increased electrostatic
repulsion.

22. Four stranded DNA
 Polynucleotides with high contents of GUANINE
FORM TETRAMERIC STRUCTURE – “G-Quartets”
 These structures are planar and are connected
by HOOGSTEEN- Hydrogen bonds.
 Antiparallel four stranded DNA structure – “G-
tetraplexes” as the ends of eukaryotic
chromosome namely telomers- GUANINE