Forms of DNA

BANASTHALI VIDYAPITH A Detailed Report on “DNA structure and Function” By Sanjana Pandey MSc. Bioinformatics Department of Biotechnology and Biosciences Submitted to Dr. Himani Kuntal Prof. PhD. Bioinformatics Department of Biotechnology and Biosciences 1

Three conformations of the DNA double helix: A (left), B (center), and left-handed Z (right) as taken from the Protein Data Bank https://cdn.rcsb.org/pdb101/motm/images/ABZ.gif 2

Contents 1. Introduction and Brief History 2. Constituents i. Nitrogenous bases ii. Ribose sugar iii. Phosphate 3. Bond forming functional groups 4. Chargaff’s rule 5. Base pairing 6. Bonds and linkages 7. DNA structure assembly 8. DNA conformations 9. Tautomerism 10. B-form DNA 11. A-form DNA 12. Z-form DNA 13. C-form DNA 14. D-form DNA 15. Z-form DNA 16. Structural comparison between DNA and RNA 17. Functions of DNA 18. Summary 19. References 3

Introduction and Brief History It's all in our DNA! The basis for all life on this planet is a biomacromolecule called \"DNA\". The official name although is 2'-deoxy ribonucleic acid. The concept of nucleic acids was first introduced by Fredrick Miescher (1869) who as a result of his experiments on white blood cells discovered this ubiquitous molecule, initially named as \"nuclein”. After various experiments conducted by Avery-MacLeod-McCarty (1944) and Alfred Hershey -Martha Chase, it became scientifically verified that \"DNA\" is the only molecule carrying all the encoded information required to make a complete organism in the form of \"genes\". The revolutionizing work to further deepen the study was done by Rosalind Franklin and Maurice Wilkins who used X-ray diffraction to determine the structure of DNA molecules. They labelled the low-humidity form as A-DNA and the high-humidity one as B-DNA. One of their best X-ray pictures was instrumental to J. D. Watson and F. Crick in deducing the double-helix model of B- DNA in 1953. DNA is considered as a structurally uniform molecule but it isnt. The first crystal structure of DNA was established after a gap of 20 years (in 1979) since a long stretch of genomic DNA is quite difficult to crystallize. “Would the first crystalline structure be in the A or the B form?\" By surprise due to C-G-C-G-C-G-C hexamer adopted left-handed form called as Z-DNA. The standard double helical structure is the B-form DNA which we commonly study about but there are varied forms as well. 4

Such structural variations in conformation of DNA occurs as a result of environmental factors such as humidity, salt concentration, constituent bases etc. Since its discovery there has been immense work to study the structure of DNA since its functionality is ultimately the consequence of its components. Hence, in this report we aim to give a detailed analysis of the structure and function of various DNA conformations and its constituents too. Figure1. (On the left) The original diffraction pattern of B-DNA obtained by Rosalind Franklin. (On the right) The B-DNA double helical structure as proposed by Watson and Crick by using mathematical modelling on the diffraction pattern (particularly used a lattice approach via Bragg’s equation, 2dsinθ=nλ). 5

Constituents Figure2: Constituents of DNA 2’deoxyribonucleic acid is made up of the following chemical constituents: i. Nitrogenous base ii. Ribose sugar iii. Phosphate And many linkages and bonds via which depending on certain parameters individual components interact to make a double helical structure of left/right-handed DNA. i. Nitrogenous bases The four nitrogenous bases making up the building block of DNA are: adenine(A), guanine(G), cytosine(C) and thymine(T). Why nitrogenous? Simply because they have large amount of the element nitrogen relative to their overall mass. Bases? Since they are proton (hydrogen atom) acceptors and tend to carry a net positive electrical charge. 6

Hence, the name. Let us now look at the basic structure of two kinds of nitrogenous base-purines and pyrimidines. Purines- Adenine and Guanine Pyrimidine- Cytosine and Thymine (Uracil too, found in RNA) Purines 1. Heterocyclic aromatic compounds containing two fused rings in their structure. 2. These are the most common heterocyclic compounds having N. 3. Purine is both a very weak acid (pKa 2.39) and a weak base (pKa 8.93). 6-membered 5-membered pyrimidine ring imidazole ring Figure3: A fused ring structure of six(pyrimidine) and five(imidazole) membered rings: A Purine Biologically 8 types of purines are found (as listed below) of which adenine and guanine are of great importance. Adenine, Guanine, Hypoxanthine, Xanthine, Theobromine, Caffeine, Uric acid and Isoguanine 7

Adenine and Guanine Figure4: Structure of purine nucleobases- Adenine(C5H5N5) and Guanine(C5H5N50). IUPAC name: 1. Adenine- 6-aminopurine 2. Guanine- 2-amino 6-hydroxypurine Similar properties: 1. Same precursor i.e. Inosine Monophosphate 2. Similar purine structure 3. Similar molar mass 120 g/mol (approx.) 4. Similar melting point of 360°C Both the purines share the same precursor i.e. IMP and are synthesized by de-novo or salvage pathway in the liver. Though Adenine and Guanine share many similar properties but they differ in the functional groups attached to their fused ring structure. While adenine has an amine group at the 6th position(C-6) in the pyrimidine ring, Guanine has an amine group at the 2nd position(C-2) of the pyrimidine ring. Also, Guanine has an additional carbonyl group at the 6th position(C-6) of the same ring. 8

Pyrimidines • Pyrimidines are heterocyclic, six-membered, nitrogen-containing carbon ring structures, • organic compound similar to benzene and pyridine • contains two nitrogen atoms at positions 1 and 3 of the six-member ring Figure5: Representative pyrimidine IUPAC names: 1. Cytosine: 2. Thymine: 3. Uracil: Similarity: 1. C4H4N2. 2. Single ring with alternating carbon and nitrogen atoms 3. Molar mass ~80.088 g/mol 4. Melting point is at 20-22 °C. Figure6: Cytosine(C), Thymine(T) and Uracil(U) nucleobases 9

Cytosine • can be distinguished from the other pyrimidines by having a keto group at position 2 • an amine group at position 4 in its heterocyclic aromatic ring. • Chemical formula C4H5N3O. • In DNA and RNA, cytosine matches with guanine forming three hydrogen bonds Thymine • has a chemical formula of C5H6N2O2. • It has two keto groups at positions 2 and 4, and a methyl group at position 5 in its heterocyclic aromatic ring. • Thymine complementary base pairs with adenine by two hydrogen bonds. However, unlike cytosine that is present in both DNA and RNA, thymine is present only in the DNA molecule because it is replaced by uracil in RNA Uracil • is similar to thymine in terms of structure except for the methyl group at position 5 in the heterocyclic aromatic ring present in thymine. • It has a chemical formula of C4H4N2O2. • In complementary base pairing, uracil pairs with adenine. To sum up, Figure7: Summary for depiction of all the nitrogenous bases. 10

ii.Ribose sugar • The sugars found in nucleic acids are pentose sugars; a pentose sugar has 5-C atoms • A combination of a base and a sugar is called a nucleoside. • Ribose, found in RNA, is a \"normal\" sugar, with one oxygen atom attached to each C atom. Ribose, found in DNA, is a modified sugar, lacking one oxygen atom at C2’ position (hence the name \"deoxy\"). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms. • In order to distinguish numbering of the sugar carbon atoms from that of the bases, the sugar carbons are numbered with a prime (’), starting with the atom which is connected to the base, and continuing around the sugar ring, away from the oxygen atom Figure8: Ribose and deoxy ribose sugars in nucleotides. iii.Phosphate Nucleotides can have one, two, or three phosphate groups. When phosphate is added to a nucleoside, the molecule is called a nucleotide. Multiple phosphate groups have a strong tendency to repel each other, because of the high concentration of negative charge in the very polar and usually ionized oxygen atoms. When suitable enzymes are present, this repulsive force drives the transfer of phosphate groups to other molecules, with some energy being liberated as heat. Figure9: Formation of nucleotides from nucleosides. 11

Bond-forming groups 1. Exocyclic NH2 group at C6 position in the pyrimidine ring of adenine 2. N1 of imidazole ring of adenine 3. Exocyclic NH2 at C2 position in the pyrimidine ring of guanine 4. N1 of imidazole of guanine 5. Carbonyl O at C6 of imidazole of guanine Chargaff’s Rule Proposed by Erwin Chargaff Rule1: The number of guanine units equals the number of cytosine units and the number of adenine units equals the number of thymine units Rule2: The relative amounts of guanine, cytosine, adenine and thymine bases vary from one species to another A=T G=C Figure10: Representation of Chargaff’s rule. Base pairing 1. The Watson–Crick form of base pairs have the same width for A.T, T.A, G.C and C.G base pairs, and they all readily fit within the phosphate backbone of the DNA double helix 2. Another form of base pairing is known as Hoogsteen base pairs, but in this conformation the G.C base pair is stable only under slightly acidic conditions (pH 4–5), due to the necessary protonation of cytosine. 12

(a) (b) (c) Figure11: (a) Watson Crick base pairing between A and T.(b) Watson Crick base pairing between G and C.(c)Hoogsteen base pairing between A and T. 13

Tautomerism Watson-Crick base pairing requires that the bases are in their preferred tautomeric, states. “Keto and enol forms” “Tautomerism is a phenomenon where a single chemical compound tends to exist in two or more interconvertible structures that are different in terms of the relative position of one atomic nucleus which is generally the hydrogen” The four bases of DNA can exist in at least two tautomeric forms as shown below. Figure11: Tautomeric forms of each base • Adenine and cytosine (which are cyclic amidines) can exist in either amino or imino forms, • Guanine, thymine, and uracil (which are cyclic amides) can exist in either lactam (keto) or lactim (enol) forms. • The tautomeric forms of each base exist in equilibrium but the amino and lactam tautomers are more stable and therefore predominate under the conditions found inside most cells. • The rings remain unsaturated and planar in each tautomer. 14

DNA Structure Assembly Figure12: Chemical structure of DNA. (a) The chemical structure of the nucleotide adenosine triphosphate (ATP). (b) The phosphodiester backbone for the sequence d(ACGT). Modified from Sinden et al. (1998). 15

1. The polar sugar-phosphate backbones of each strand form the helical scaffold, with the nitrogenous bases in the interior of the molecule, their planes nearly perpendicular to the helical axis. 2. The backbone continues on in a simple repetitive pattern: with the DNA bases sticking out at the side. The phosphate groups have a negative charge, giving the outside of the DNA an overall negative charge. This charge is neutralized in solution by Na+, 3. Each base form hydrogen bonds (indicated by dashed lines) with a base from the opposite strand. 4. The polarity of the backbones is antiparallel, with one strand running 3' ---> 5' and the other 5' --->3'. This can readily be seen by observing the reversed orientations of the ribose sugars on opposite strands. 5. In order to have a direction, one has to look at the ends. The top end in Figure 2b has a 5’ phosphate on it, and this is called the 5’ end, while the other end has a 3’ hydroxyl (OH) on it, and is called the 3’ end. Why is DNA a helix? 1. The tendency towards a helix comes from the stacking of the individual bases on top of one another. Both the sugar and phosphate which constitute the backbone are quite soluble in water. 2. However, the DNA bases which are in the middle of the helix are relatively hydrophobic and insoluble. 3. Since the bases are flat, they stack on top of each other in order to form a more hydrophobic ‘mini-environment’. 4. The bases twist slightly in order to maximize their hydrophobic interactions with each other, and it is this twisting of the stacked bases that gives rise to a helix Figure13: Double helical model of B-DNA 16

Bonding and linkage Phosphodiester bond 1. A phospodiester bond is a covalent bond in which a phosphate group joins adjacent carbons through ester linkages. 2. The bond is the result of a condensation reaction between a hydroxyl group of two sugar groups and a phosphate group. 3. The diester bond between phosphoric acid and two sugar molecules in the DNA and RNA backbone links two nucelotides together to form oligonucleotide polymers. Figure14: Formation of phosphoester bond by condensation reaction between two bases. A water molecule is removed during each bond formation. 4. The phosphate backbone consists of deoxyribose sugar molecules linked together by phosphate groups, as shown in the oligonucleotide. 5. The backbone continues on in a simple repetitive pattern: with the DNA bases sticking out at the side. The phosphate groups have a negative charge, giving the outside of the DNA an overall negative charge. 6. This charge is neutralized in solution by Na+, although in the cell (where much less Na+ exists), the polyamines spermine and spermidine bind along the phosphate backbone and help neutralize some of the charge. 7. (The charge is also neutralized by divalent cations, such as Mg, and many DNA-binding proteins often contain the positively charged amino acids lysine and arginine, which are attracted to the negatively charged phosphate backbone.) 17

Hydrogen Bond 1. The hydrogen-bonding patterns of bases have important consequences for the three- dimensional structure of nucleic acids. 2. Complementarity in terms of hydrogen bonds exists between the nucleotides of DNA. They follow the Chargaff’s rule (credited to Erwin Chargaff) according to which A double bondedly pairs with T and G triple-bondedly pairs with C. The groups and their hydrogen bonding pattern involved is explained below: A-T Adenine and thymine are said to be complementary bases since two hydrogen bonds can form between them. One between the exocyclic amino group at C6 on adenine and the carbonyl at C4 in thymine; and another between N1 of adenine and N3 of thymine. Figure15: A-T double bond formation and calculation of hydrogen bond length (3.2Å and 2.9Å) Pymol v1.3 was used to construct the following image. 18

G-C Similarly, guanine and a cytosine, so that there is both hydrogen bonding and shape complementarity in this base pair as well. A G:C base pair has three hydrogen bonds, because the exocyclic NH, at C2 on guanine lies opposite to, and can hydrogen bond with, a carbonyl at C2 on cytosine. Likewise, a hydrogen bond can form between N1 of guanine and N3 of cytosine and between the carbonyl at C6 of guanine and the exocyclic NR, at C4 of cytosine. Watson-Crick base pairing requires that the bases are in their preferred tautomeric, states. Figure16: G-C triple bond formation and calculation of hydrogen bond length(2.7 Å ,2.7 Å, 2.8Å). Pymol v1.3 was used to construct the following image. 19

DNA Conformations DNA can have several conformations. The most common one is called B-DNA. B-DNA is a right- handed double helix with a wide and narrow groove. The bases are perpendicular to the helix axis. DNA can also be found in the A form in which the major groove is very deep and the minor groove is quite shallow. A-DNA is also a right-handed double helix. A very unusual form of DNA is the left-handed Z-DNA. In this DNA, the basic building block consists of two nucleotides, each with different conformations. Why do such conformations exist? The answer is simple: It all depends on certain parameters affecting the conformation. Parameters: 1. Base composition 2. Humidity 3. Salt concentration 4. Certain interacting proteins 5. Angles of rotation Conformation A-DNA B-DNA Z-DNA Helix turn Right-handed Right-handed Left-handed Helical Diameter 26Å 20 Å 18 Å 34 Å 44 Å Helical pitch 28.6 Å 10 Å 12 Å Base pairs (per turn) 11.6 Å Flat Narrow, deep Wide, deep Major groove Wide, shallow Narrow, deep Narrow, deep Minor groove C3’ endo C2’endo, C3’endo C2’endo Sugar Anti Anti and Syn Anti Glyosidic bond Figure17: Comparative differences between three forms of DNA based on certain parameters. 20

B-DNA 20Å 10 bases(34Å) Hydrogen Bend bond 3.4Å Base stacking Water m Figure18: The classical B-DNA structure as proposed by Watson and Crick(1953).The specific measurements are depicted in (a) Notice the anti-parallel 5’-3’ double mhelical structure of B- DNA.(b) Water molecule interact with the major and minor grooves in the double helical structures(represeneted as cyan spheres).Base stacking interactions can be clearly seen between the bases. Watson and Crick model highlights: 1. It consists of two polynucleotide strands that wind about a common axis with a right handed twist to form a 20 A0 in diameter double helix. 21

2. The two strands are antiparallel (run in opposite direction) and wrap around each other such that they cannot be separated without unwinding the helix (a phenomenon known as plectonemic coiling). 3. The base occupies the core of the helix while its sugar – phosphate chains are coiled about its periphery thereby minimizing the repulsions between charged phosphate groups. 4. The planes of the bases are nearly perpendicular to the helix axis. 5. Each base is hydrogen bonded to a base on the opposite strand to form a planar base pair. It is the hydrogen bonding interactions, a phenomenon known as complementary base pairing that result in the specific association of the two chains of the double helix. 6. The ideal B-DNA helix has 10.4 base pairs per turn. 7. The vertical rise per base pair is 3.40 Angstrom. 8. The helix pitch i.e. the helix in B-DNA moves a total distance 3.4x10.4 or 35.36 Å. 9. The value of rotation per base pair is 360/10.4 or 34.610. 10. One consequence of intertwining is that the two strands cannot be separated without the DNA rotating, one turn of the DNA for every \"untwisting\" of the two strands. 11. Many bases are strongly propeller twisted--they are not in one perfect plane. This improves the way that the bases stack on top of one another along each strand, stabilizing the whole double helix. 12. The bonds that make up the sugar-phosphate backbone of a polynucleotide have a lot of conformations in the 3-dimensional space. They have free rotations around many bonds. Although, certain angles are prohibited, some are allowed and that is what gives rise to all the conformations. Figure19: Duplex DNA has the two strands wrapped around each other in a plectonemic coil (left), not a paranemic duplex (right). 22

Major and Minor grooves Major groove Minor groove Figure20: Surface model of B-DNA depicting the major and minor grooves in the double helical structure. Why do grooves form? 1. The attachment of bases to the backbone sugars through glyosidic bonds is asymmetrical. This results in the formation of two different grooves on opposite sides of the base pairs, the major and minor grooves. 2. The major groove is considerably wider than the minor groove the distance between the sugar-phosphate backbones is greater in the major groove than in the minor groove. 3. The major and minor grooves lie 180o opposite each other in the double helix, spiralling along the axis of the molecule. 23

4. Although the dimensions of the major and minor grooves are different for the three different helix families, from the point of view of the bases, the major groove is always on the same side for a given base pair. 5. The sugars are closer to one side of the base pair than the other. There is less space on the side between the sugars. The convention is that the side closest to the sugars is called the minor groove side. Importance of Grooves? 1. For B-DNA helices, proteins binding in the major groove usually bind to specific sequences, often through the insertion of a helix into the major groove. 2. Proteins that bind DNA non-specifically (such as chromatin proteins) will often bind DNA in the minor groove, through interactions with a protein b strand. In addition, water molecules and small ions can bind to, and stabilize, the minor grooves. 3. There are characteristic patterns of hydrogen bonding and of overall shape that are exposed in the major groove that distinguish an A:T base pair from a G:C base pair, and, for that matter, A:T from T:A, and G:C from C:G. We can think of these features as a code in which A represents a hydrogen bond acceptor, D a hydrogen bond donor, M a methyl group, and H a nonpolar hydrogen. 4. In such a code, A D A M in the major groove signifies an A:T base pair, and A A D H stands for a G:C base pair. Likewise, M A D A stands for a T:A base pair and H D A A is characteristic of a C:G base pair. 5. In all cases, this code of chemical groups in the major groove specifies the identity of the base pair. 6. These patterns are important because they allow proteins to unambiguously recognize DNA sequences without having to open and thereby disrupt the double helix Figure21: The bases forming major and minor grooves of DNA. 24

Sugar pucker • Puckering means “tightening or folding in a specific arrangement” • The sugar puckers in DNA/RNA structures are predominately in either C3′-endo (A- DNA or RNA) or C2′-endo corresponding to the A- or B-form conformation in a duplex. Figure22: Sugar puckering in deoxyribose • In these two sugar conformations, the distance between neighbouring phosphorus (P) atoms and the orientation of P relative to the sugar/bases are also dramatically different. Syn and Anti 1. In the anti- conformation the base is rotated so that it is as far from the sugar as possible. This is the most stable conformation and it's found in most DNAs. 2. In the Syn conformation the base is rotated so that it's over the sugar leading to a much more compact structure. Figure23: The conformations of bases: syn and anti-conformations. These are favored by allowed rotations along certain bond angles. 25

Hydrogen bonding 1. The heterocyclic bases of single-stranded DNA have polar amido, amidino, guanidino and carbonyl groups that form a complex network of hydrogen bonds with the surrounding water molecules. 2. There are two hydrogen bonds for an A.T base pair, and three hydrogen bonds for a G.C base pair. 3. Hydrogen bonds (H-bonds) are weak, and in DNA, the hydrogen bonds have only about 2 kcal/mol energy. Base stacking interactions and Stacking energies • Base-stacking interactions are hydrophobic and electrostatic in nature, and depend on the aromaticity of the bases and their dipole moments. • Base-stacking interactions in nucleic acid duplexes are partly inter-strand and partly intra- strand in nature. Figure24: Base stacking interaction between G and C (red-color) G-C stacking energy is ~23.82 kcal/mol 26

• The ‘stacking energy’ is a measure of how much energy is required to destack or melt a region of double-stranded DNA. • As a general trend, alternating pyrimidine–purine steps have less energy, and in particular T.A steps have the lowest • G.C steps have the largest value and require the most energy to melt since they are triple bonded base pairs • The stacking energy, ΔE(X–Y)/(X′–Y′) π–π is calculated as the energy difference between the stacked base pairs and the individual base pairs (X–Y and X′–Y′) Figure25: Table of stacking energies with the corresponding nucleobase pairs. 27

Intra base pair interactions Buckle, Open-angle, Propeller, Stagger, Shear and Stretch Figure26: All the allowed intra base pair interaction between bases. Propeller twist 1. The propeller twist is a measure of the angle between the planes of the two bases. 2. Each base is planar, but when two bases pair, they do not always line up perfectly flat with each other; this angle is called propeller twist because the bases are twisted away from each other like an aeroplane propeller 3. This is likely to be due in part to propeller twisting of the bases, which results in strain in the H-bonds Propeller twist between the bases Figure27: Propeller twist as seen in B-DNA model. 28

A-DNA 2.86Å Helical pitch 26Å Figure28: A-form of DNA with distinct parameters. Basic highlights: 1. The major difference between A-form and B-form nucleic acid is in the confirmation of the deoxyribose sugar ring. 2. It is in the C2′ endoconformation for B-form, whereas it is in the C3′ endoconformation in A-form. 29

3. A second major difference between A-form and B-form nucleic acid is the placement of base-pairs within the duplex. 4. In B-form, the base-pairs are almost centered over the helical axis but in A-form, they are displaced away from the central axis and closer to the major groove. The result is a ribbon-like helix with a more open cylindrical core in A-form. 5. Right-handed helix 6. 11 bp per turn; 0.26 nm axial rise; 28o helix pitch; 20o base-pair tilt 7. 33o twist angle; 2.3nm helix diameter 8. In A-DNA, the minor groove is almost the same size as the major groove. Water Minor Major groove groove Base stacking Figure29: (On the left) A form DNA with major and minor grooves and base stacking interactions. (On the right) Cartoon model of A-form DNA with salmon spheres of water indicating its interaction and stabilizing role in the 3-dimensional structure. 30

Z-DNA Figure30: Z-form of DNA with its distinguishing parameters. Notice the zig-zag conformation to which it owes its name. Basic highlights: 1. Z-DNA is a radically different duplex structure, with the two strands coiling in left-handed helices and a pronounced zig-zag (hence the name) pattern in the phosphodiester backbone. 2. Z-DNA can form when the DNA is in an alternating purine-pyrimidine sequence such as GCGCGC, and indeed the G and C nucleotides are in different conformations, leading to the zig-zag pattern. 31

3. The big difference is at the G nucleotide. 4. It has the sugar in the C3′ endoconformation (like A-form nucleic acid, and in contrast to B- form DNA) and the guanine base is in the synconformation. Water Minor Major groove groove Figure31: (On the left) B form DNA with major and minor grooves and base stacking interactions. (On the right) Cartoon model of B-form DNA with salmon spheres of water indicating its interaction and stabilizing role in the 3-dimensional structure 5. This places the guanine back over the sugar ring, in contrast to the usual anticonformation seen in A- and B-form nucleic acid. Note that having the base in the anticonformation places it in the position where it can readily form H-bonds with the complementary base on the opposite strand. 6. The duplex in Z-DNA has to accommodate the distortion of this G nucleotide in the synconformation. The cytosine in the adjacent nucleotide of Z-DNA is in the “normal” C2′ endo, anticonformation. 7. The minor groove is deep and narrow, and the major groove is almost non-existent. 8. It has antiparallel strands as B-DNA. 9. It is long and thin as compared to B-DNA. 10. 12 bp per turn; 0.45 nm axial rise; 45o helix pitch; 7o base-pair tilt 11. -30o twist angle; 1.8 nm h 32

C-DNA 1. Formed at 66% relative humidity and in presence of Li+ and Mg2+ ions. 2. Right-handed with the axial rise of 3.32A° per base pair 3. 33 base pairs per turn 4. Helical pitch 3.32A°×9.33°A=30.97A°. 5. Base pair rotation=38.58°. 6. Has a diameter of 19 A°, smaller than that of A-&B- DNA. 7. The tilt of base is 7.8° D-DNA 1. Rare variant with 8 base pairs per helical turn 2. These forms of DNA found in some DNA molecules devoid of guanine. 3. The axial rise of 3.03A°per base pairs 4. The tilt of 16.7° from the axis of the helix. E- DNA 1. Extended or eccentric DNA. 2. E-DNA has a long helical axis rise and base perpendicular to the helical axis. 3. Deep major groove and the shallow minor groove. 4. E-DNA allowed to crystallize for a period time longer, the methylated sequence forms standard A-DNA. 5. E-DNA is the intermediate in the crystallographic pathway from B-DNA to A-DNA. 33

Functions of DNA 1. Genetic information: DNA encodes all the information required to make a complete organism in the form of genes. Phenotype:2. This information is then responsible for various phenotypes and genotypes of the organism which affect the behaviour and characteristics by the route of 3. Genetic diversity: DNA undergoes recombination and mutational events which .results in the genetic diversity and variation among different species and organism 4. Cellular metabolism: It controls the metabolic reactions of the cells through the help of specific RNA synthesis, enzymes and hormones. 34

Structural Comparison: DNA & RNA Figure32: Three-dimensional structural organisation of DNA and RNA (as taken from Nucleic acid database NDB) 35

Points of differences between DNA and RNA DNA (Deoxyribonucleic acid) RNA (Ribonucleic acid) It has a deoxyribose and phosphate backbone It has a ribose and phosphate backbone with having four distinct bases: thymine, adenine, four varying bases: uracil, cytosine, adenine, cytosine, and guanine. and guanine. It is located in the nucleus of a cell and in the It is found in the cytoplasm, nucleus, and in mitochondria. the ribosome. It has 2’-deoxyribose sugar It has Ribose sugar Due to absence of 2’OH it can’t form bond It has 2’OH and forms bond with water, a with H20 and so is stable water molecule is released DNA is functional is the transmission of RNA is functional is the transmission of the genetic information. It forms as a media for genetic code that is necessary for the protein long-term storage. creation from the nucleus to the ribosome. The DNA is a double-stranded molecule that The RNA is a single-stranded molecule which has a long chain of nucleotides. has a shorter chain of nucleotides. DNA replicates on its own, it is self- RNA does not replicate on its own. It is replicating. synthesized from DNA when required. The base pairing is as follows: GC (Guanine The base pairing is as follows: GC (Guanine pairs with Cytosine) A-T(Adenine pairs with pairs with Cytosine) A-U(Adenine pairs with Thymine). Uracil). 36

(c) Figure33: (a)2’deoxyribose and ribose sugar.(b)Thymine and Uracil nucleobases in DNA nad RNA respectively.(c)Nucleotide organisation of DNA and RNA 37

References 1. Structure of a b-dna dodecamer. conformation and dynamics https://doi.org/10.1119/1.5020051 2. http://www.ncbi.nlm.nih.gov/pubmed/6941276 3. Why Adenine Does Not Pair with Cytosine https://www.alpfmedical.info/base-pairs/h- tvg.html#:~:text=Adenine%20and%20thymine%20match%20up%20so%20that%20a,betw een%20Nl%20of%20adenine%20and%20N3%20of%20thymine. 4. DNA duplex stabilityhttps://www.atdbio.com/content/53/DNA-duplex- stability#:~:text=DNA%20duplex%20stability%20is%20determined%20primarily%20by%2 0hydrogen,but%20base%20stacking%20also%20plays%20an%20important%20role. 5. http://people.bu.edu/mfk/restricted566/dnastructure.pdf DNA Structure: A-, B- and Z-DNA Helix Families 6. http://earth.callutheran.edu/Academic_Programs/Departments/BioDev/omm/bdna_white1/ bdna.htm 7. B-DNA structure and stability: the role of hydrogen bonding, π–π stacking interactions, twist- angle, and solvation† https://pubs.rsc.org/en/Content/ArticleLanding/OB/2014/C4OB00427B#!divAbstract 8. Intra base pair interactions http://www.saha.ac.in/biop/www/db/local/BP/intrabp.html 38