DNA andForces Stabilizes DNA Structure

Prepared by-Dr. Sanjeev Kumar (M.V.SC at DGCN, COVAS, CSKHPKV, Palampur India)Dr. Kritika Dhial (M.V.SC at DGCN,COVAS, CSKHPKV, Palampur India)

Historical facts about DNA

DNA ?• DNA Stands for “DeoxyriboNcleic Acid”.

• Term DNA was given by Zaccharis

• DNA is biopolymer consist of nucleotide as monomeric unit.

• DNA is double helical strcture in eukaryote and prokaryote, but in virus it may

be double stranded or single stranded and presented as monopartite or

multipartite.

• In eukaryotes, DNA is presented in nucleus surrounded by nuclear membrane

• In prokaryotes, DNA is presented in nucleoid region of Cytoplasm without

nuclear membrane

• In virus, DNA is presented in the core of virus surrounded by Protein layer

(called as capsid).

DNA ?

• Cell perform various functions in specific way as per directed by DNA

contained by it.

• DNA contains all biological information of a cell/individual like

functioning, development, growth, life span etc. .

• The biological information transferred from one generation to the next

generation in the chemical form as DNA, so it is called as hereditary

material.

• DNA can be measured by the unit picogram

• DNA can be synthesized in vitro (in the laboratory).

Composition of DNA ?• DNA is a biopolymer consist of repeated units called as nucleotides.

• Nucleotide= Nitrogen base + Sugar+ Phosphate group.

• Nitrogen bases are two types- 1. Purines, 2. Pyrimidine.

• Sugar present in DNA is 2-Deoxyribose.• Purines are heterocyclic double ring molecules and contain nitogen

atoms at 1,3,7, and 9 positions.• Purines are two types Adenine and Guanine.• Pyrimidines are hterocyclic single ring molecule contain nitrogen

atoms at 1, and 3 positions.• Pyrimidine are thee type thymine, cytosine, and uracil ( present in

RNA).

Composition of DNA ?

Watson and Crick model of DNAIn 1953, J.D. Watson (an American biologist) and F.H.C. Crick (a British Physicist) proposed the three-dimensional model of physiological DNA (i. e B-DNA) on the basis of X-ray diffraction data of DNA obtained by Franklin and Wilkins.The important features of Watson – Crick Model or double helix model of DNA are as follows:1. The DNA molecule consists of two polynucleotide chains or strands that spirally twisted around each other and coiled around a common axis to form a right-handed double-helix.2. The two strands are antiparallel i.e. they ran in opposite directions so that the 3 end of one ′chain facing the 5 end of the other.′3. The sugar-phosphate backbones remain on the outside, while the core of the helix contains the purine and pyrimidine bases.

Watson and Crick model of DNA4.The two strands are held together by hydrogen bonds between the

purine and pyrimidine bases of the opposite strands.

5. Adenine (A) always pairs with thymine (T) by two hydrogen bonds

and guanine (G) always pairs with cytosine (C) by three hydrogen

bonds. This complimentarily is known as the base pairing rule.

Thus, the two stands are complementary to one another.

6. The base sequence along a polynucleotide chain is variable and a

specific sequence of bases carries the genetic information.

7. The base compositions of DNA obey Chargaff s rules (E.E. Chargaff,

1950) according to which A=T and G=C; as a corollary ∑ purines

(A+G) = 2 pyrimidines (C+T); also (A+C) = (G+T). It also states that

ratio of (A+T) and (G+C) is constant for a species (range 0.4 to

1.9)

Watson and Crick model of DNA

8. The diameter of DNA is 2nm or 20 A.

Adjacent bases are separated 0.34

nm or by 3.4 A along the axis. The

length of a complete turn of helix is

3.4 nm or 34 A i.e. there are 10bp

per turn. (B- DNA-Watson rick DNA)

9. The DNA helix has a shallow groove

called minor groove (-1.2nm) and a

deep groove called major groove (-

2.2nm) across.

The conformation of a nucleotide unit is determined by the seven indicated torsion angles.

Forms of DNADNA is remarkably flexible molecule. Considerable

rotation is possible a number of bonds in the sugar-

phosphate backbone, and thermal fluctuation can

produce bending, stretching, and unpairing of strands.

Many significant deviations from the Watson-Crick.

DNA structure are found in cellular DNA, some of

which may play important

• A- DNA

• B- DNA

• Z-DNA

• Cruciform DNA and Hairpin DNA

• H- DNA or triplex

• G4- DNA A- DNA B-DNA Z-DNA

Comparison Between different form of DNA

Cruciform and Hairpin DNA

H-DNA or Triplex DNA

G4- DNA

G4- DNA• FIG. 8.Hypothetical mechanism of formation

and/or stabilization of G4 DNA by Hop1 protein. In the model, bold and light DNA molecules represent homologs and closed circles denote guanine residues. Once a DSB is produced at a hot spot by Spo11 endonuclease, the free ends are resected by exonuclease and/or helicase activities to generate a 3 overhang. Subsequently, Hop1 ′protein, by binding to the guanine repeats in the 3 overhang and to the G-rich strand in the ′partially unwound homologous duplex DNA, promotes the formation of intermolecular G4 DNA. Alternatively (right side), interstitial interactions between chromatids could be mediated by the formation of intermolecular G-G pairing, regardless of whether the flanking nucleotide sequences are homologous. We suggest that such interactions might either join homologs (as diagrammed here) to facilitate interhomolog recombination or join sister chromatids in a manner that delimits sister chromatid exchange.

Quaternary structure of the DNA molecule

• DNA is associated with proteins: histones and non histone

proteins, to form the chromatin.

•DNA as a whole is acidic (negatively charged) and binds to basic

(positively charged) proteins called histones

•There is 3 x 10 9 nucleotide pairs in the human haploid genome

representing about 30 000 genes dispersed over 23

chromosomes for a haploid set.

DNA Packaging

DNA Stability…..?

DNA double stranded helical structure is stabilize by

• Hydrogen bonding

• Base stacking interaction

• Hydrophobic force

• Ionic interaction

DNA Stability…..?Hydrogen bonding- hydrogen bond b/w base pairs- G with C, and A

with T. It is important to note that three hydrogen bonds

can form between G and C, but only two bonds can be found in A and T pairs.

This is why it is more difficult to separate DNA strands that contain more G-C pairs than A-T pairs. On the other hand, A-T pairs seem to destabilize the double helical structures. This conclusion was made possible by a known fact that in each species the G content is equal to that of C content and the T content is equal to that of A content.

Although weak energy-wise, is able to stabilize the helix because of the large number present in DNA molecule

DNA Stability…..?Base stacking interaction-• also known as Van der Waals interactions between bases are weak, but the

large amounts of these interactions help to stabilize the overall structure of the helix.– Double helix is stabilized by hydrophobic effects by burying the bases in

the interior of the helix increases its stability; having the hydrophobic bases clustered in the interior of the helix keeps it away from the surrounding water, whereas the more polar surfaces, hence hydrophilic heads are exposed and interaction with the exterior water

– Stacked base pairs also attract to one another through Van der Waals forces the energy associated with a single van der Waals interaction has small significant to the overall DNA structure however, the net effect summed over the numerous atom pairs, results in substantial stability.

– Stacking also favors the conformations of rigid five-membered rings of the sugars of backbone.

– Evidence of Stacking interactions: Compounds that interfere with Hydrogen bonds (urea, formamide) don’t separate strands by themselves, still requires heat.

DNA Stability…..?

Ionic interaction-• Ion-ion repulsion of the negatively charged phosphate make DNA duplex

unstable.

• However the presence of Mg2+ and cationic proteins with abundant

Arginine and Lysine residues that stabilizes the double helix.

• Double-stranded helix structure thus, promoted by having phosphates on

outside, interact with H2O and counter ions (K+, Mg2+, etc.).

DNA Stability…..?

Hydrophobic force-• The hydrophobic interactions

between the planar base pairs stabilize the bases on the inside of the helix, so these provide stability to the structure but do not contribute to the specificity.

• Hydrophobic Interactions are important for the folding, stability and biological activity.

References• http://faculty.washington.edu/trawets/vc/theory/dna/DNA_big.jpg• nptel.ac.in/courses/104103018/module4/lec3/2.html• http://www.googleimage.com• http://chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/

Physical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_Interactions

• Text book of biology by True man• bioinfosu.okstate.edu/um/napsweb/Lec.htmlfolder/836NAPS.ppt• www.bio.brandeis.edu/classes/biochem104/DNA_lecture.pdf• http://atlasgeneticsoncology.org/Educ/DNAEngID30001ES.html• Principle of Biochemistry by Lehninger-forth edition

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