The document discusses the major and minor grooves of DNA, highlighting their significance in genetic processes and the binding of proteins. Major grooves contain more chemical information and are preferred by specific DNA-binding proteins, while minor grooves are involved in non-specific binding. Additionally, the structural characteristics and differences between the grooves in various DNA forms (A, B, and Z) are examined.

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