Major and minor grooves dna

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

1. ASSIGNMENT on MAJOR AND MINOR 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

2. 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.

3. The T wo 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

4. 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˚

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

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

7. 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

8. 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

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

10. 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

11. DISTINGUISHING BETWEEN G:C AND C:G:-

12. 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.

13. 2 types :- SPECIFIC - The region is particular, so bind to major grooves only. Ex-Transcription, R egulation, Replication and repair. NON-SPECIFIC(HISTONE) - Binding region not particular, so bind to any of Grooves. Ex- H istone, Ribosome, DNA Polymerase.

14. Helix-turn-helix: A DNA binding structure:- R ecognition and binding to DNA by done by the two α helices, O ne 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 H elix ". It binds to the major groove of DNA through a series of  Hydrogen B onds  and various  Van Der Waals interactions with exposed Bases . The other α helix stabilizes the interaction between protein and DNA.

15. 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