describes about the molecular structure of DNA, structure of its grooves, the A:T G:C pairing , proteins

1. ASSIGNMENT
on
MAJOR ANDMINOR GROOVES OF DNA
Submitted To: Submitted By:
Dr. D.K. Garg Smrutishree Sahoo
Professor M.Sc.(Ag.) PBG Previous
Department of PLANT BREEDING AND GENETICS
College of Agriculture
Swami Keshwanand Rajasthan Agricultural University, Bikaner

3. James D. Watson & Francis H. Crick
 In 1953 presented the double Helix model of DNA
 Two primary sources of information:
1. Chargaff Rule: #A#T and #G#C.
2. X-ray diffraction studies of Rosalind Franklin & Maurice
H. F. Wilkins.

5. The Two Grooves of DNA
A DNA has two grooves i.e. Major
and Minor groove.
Grooves are not equal size and
opposite to each other.
Simple consequences of Different
geometry of the base pair results
grooves.
Larger is Major groove
Smaller is Minor groove
Major groove occupied by many
water molecule than the minor
grooves

6.  Each base pair rotated in 36 ˚around the axis
 10 base pairs rotated in 360˚ makes a complete turn.
 Twisting of the two strands around one another forms a
double helix with a minor groove with 12A˚ across and a
major groove with 22A˚ across .
 Angle at which the sugar protrude out from the base
pair(i.e. angle between Glycosidic bond) is 120˚ or 240˚.
 Major Groove - 240˚
 Minor Groove - 120˚

8. Comparison of the grooves present in B , A and Z form of DNA:-

9. A-DNA has a shallow minor groove and a deep major groove:-
B-DNA A-DNA

10. FEATURES OF GROOVES
The characteristic patterns of H-bond and of overall shape
that are exposed in major groove distinguishes an A:T from
G:C, A:T from T:A and G:C from C:G.
from the chemical information of the contents of major
groove we can distinguish the base pairs.
Ex- ADAM in A:T and MADA in T:A
 AADH in G:C and HDAA in C:G

11. A:T PAIR
 Large angle of MAJOR GROOVES
contain following structures-
 A hydrogen bond acceptor (N7 of
Adenine)
 A H-bond donor(Amino group on
C6 of Adenine)
 A H-bond acceptor (Carbonyl
group on Thymine)
 A hydrophobic surface(Methyl
group on C5 Thymine)
 MINOR GROOVE has
 Two H-bond Acceptor
 One H-atom

12. DISTINGUISHING BETWEEN A:T AND T:A:-

13. G:C pair
 MAJOR GROOVES-
 A H-bond acceptor(N7 of
guanine)
 A H-bond acceptor(carbonyl
group on C6 guanine)
 A H-bond donor (amino group
on C4 of Cytosine)
 A small nonpolar hydrogen( C5
of cytosine)
MINOR GROOVES-
 2 H-bond acceptor
 1 H-bond donor

14. DISTINGUISHING BETWEEN G:C ANDC:G:-

15. DNA BINDING PROTEINS:-
 Expression of the biological phenomenon in a genome
mediated by a DNA binding protein.
 These proteins attach to the double helix in a specific site
and regulate the gene activity.
 Major groove is rich in chemical information that's why
most of the DNA binding proteins bind with major groove.
 The DNA sequence can be read without the helix being
opened up by breaking the base pairs.

16.  2 types:-
 SPECIFIC - The region is particular, so bind to major
grooves only.
 Ex-Transcription, Regulation, Replication and repair.
 NON-SPECIFIC(HISTONE)- Binding region not particular, so
bind to any of Grooves.
 Ex- Histone, Ribosome, DNA Polymerase.

17. Helix-turn-helix: A DNA binding structure:-
 Recognition and binding to DNA by done by the two α
helices,
 One occupying the N-Terminal end of the motif, the other
at the C-Terminus.
 In most cases, such as in the Cro repressor, the second
helix contributes most to DNA recognition, and hence it is
often called the “Recognition Helix".
 It binds to the major groove of DNA through a series
of Hydrogen Bonds and various Van Der Waals
interactions with exposed Bases.
 The other α helix stabilizes the interaction between
protein and DNA.

19. Major vs minor grooves:-
N.B-
We need to develop drugs which attack any part or DNA
rather than the specific part of DNA because it will take
more time to cure.
So the drugs must bind to non specific site of DNA so it
binds to the minor grooves.
particulars Major groove Minor groove
Specific binding protein binds Doesn’t bind
Non-specific binding protein binds binds
groove binding drugs --- Binds