Deoxyribonucleic acid (DNA)

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SRV 1
• DNA is biopolymer of high molecular weight with mononucleotide as its repeating unit linked by
phosphodiester bond
• Molecular repositories of genetic information; Molecules of heredity

SRV 2
 Components of DNA
or
Chemical structure of DNA

SRV 3
 Components of DNA

• Nitrogenous bases
• Deoxyribose sugar
• Phosphate

SRV 4
 Nitrogenous bases
• Heterocyclic; Nitrogenous (contain N atoms in ring)

• Aromatic

• Derivatives of purines and pyrimidines

• Purines (Pu): two fused rings: Adenine (A), Guanine (G)
• Pyrimidines (Py): single 6-membered ring: Cytosine (C), Thymine (T)

• Pu = R = A and G; Py = Y = C and T

• Free Py and Pu are weakly basic compounds and are thus called bases

• Hydrophobic and relatively insoluble in water at near neutral pH

• Atoms in ring(s) are numbered in unprimed numbers

• 1 to 9 in purines (e.g., N1, C2 etc.)
• 1 to 6 in pyrimidines (e.g., N1, C2 etc.)
• Exocyclic atoms are numbered in superscript, e.g., N6 in A
SRV 5
• It is the 'information' part of DNA
Imidazole moiety and
Pyrimidine moiety

A = 6-aminopurine
G and T = Keto form
G = 2-amino-6-oxypurine
C = 4-amino-2-oxypyrimidine
A and C = Amino form
T = 2,4-dioxy-5-methylpyrimidine (T is
SRV5-methyl uracil) 6
 Sugar

• Pentose sugar (5-C keto sugar)

• 2’-deoxyribose or deoxyribose sugar in β-configuration
• In DNA, deoxyribose sugar exists always in closed furanose ring form, as β-2’-deoxy-D-
ribofuranose
• Ribose without hydroxyl group at C2’

• Carbon atoms in ring are designated by prime

• To distinguish from positions of atoms in bases

• Part of DNA backbone alternating with phosphate

SRV 7
 Phosphate

• Contains three monovalent hydroxyl groups and a divalent oxygen atom, all linked to the
pentavalent phosphorus atom
• The phosphate groups are completely ionized and negatively charged at pH 7
• Anion at pH 7.0
• Hence DNA is polyanionic due to multiple phosphate groups
• Forms phosphodiester bond in DNA
• Between sugars
• Part of DNA backbone
• Backbone is hydrophilic due to phosphate and hydroxyl groups of sugar
• Alternate with sugar in DNA backbone
• Provides polarity to DNA
• Same orientation of all phosphate groups in a strand
• DNA strand has 5’ and 3’ ends – Phosphate is present at 5’ end of sugar
• 3’ → 5’ phosphodiester bond
SRV 8
SRV 9
 Nucleosides
And
Nucleotides or Nucleoside 5’-phosphate(s)

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SRV 11
 Deoxyribonucleosides

• Compounds in which nitrogenous bases (purines and pyrimidines) are conjugated to the pentose
sugars (deoxyribose) by a β-N-glycosidic linkage
• [Ribonucleoside - Compounds in which nitrogenous bases (purines and pyrimidines) are
conjugated to the pentose sugars (ribose) by a β-N-glycosidic linkage]

• Consist of a base joined to a pentose sugar at position C1’

• Trivial names of
• Purine deoxynucleosides end with the suffix –sine
• Pyrimidine deoxynucleosides end with suffix –dine

• The sugar C1’ carbon atom is joined to the N1 atom of pyrimidine and the N9 atom of purine
• This represents a β-N-glycosidic bond
• Purine deoxynucleosides are N-9 glycosides
• Pyrimidine deoxynucleosides are N-1 glycosides
SRV 12
R = Sugar
SRV 13
 Deoxyribonucleotides or Deoxyribonucleoside 5’-phosphate(s) or dNTPs

• Phosphate esters of deoxyribonucleosides

• Deoxyribonucleosides form deoxyribonucleotides by joining with phosphoric acid
• Phosphate is always esterified to the sugar moiety
• Phosphate residues are joined to the sugar ring by a phosphomonoester bond
• Several phosphate groups can be joined in series by phosphoanhydride bonds

• These occur either in the free form or as subunits in nucleic acids

• Roles
• Structural components of nucleic acids
• Energy carriers (e.g., ATP, GTP)
• Enzyme cofactors (e.g., NAD, NADP, FAD)
• Chemical messengers (e.g., cAMP, cGMP)

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SRV 15
SRV 16
Nomenclature

SRV 17
Chargaff’s Rule

SRV 18
Formulated by Erwin Chargaff in 1950

1. Complementary base pairing rule

• DNA base pairs are always adenine with thymine (A-T) and cytosine with guanine (C-G)
• A purine always pairs with a pyrimidine and vice versa
• A does not pair with C, despite that being a purine and a pyrimidine
2. DNA molecules have distinctive base composition
• Base composition of DNA varies from one species to another
• It is more or less constant among related species
• It ranges from ~25 to 75% G+C in different species of bacteria
• In mammals, G+C ranges from ~39 to 46%
3. DNA specimens isolated from different tissues of the same species have the same base
composition
4. The base composition of DNA in a given species does not change with age, nutritional state or
changes in environment
5. The deoxyribose sugar and phosphate components occur in equal proportions

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6. Rule of Molar Equivalence of Few Bases: In all cellular DNAs, regardless of species, amount of A
is always equal to T and the amount of G is always equal to C, i.e.,
• A = T and G = C
7. Purines and pyrimidines are always in equal amounts
• A+G=T+C
3. Base ratio A + T / G + C may vary from one species to other, but is constant for a given
species
• This ratio is used to identify the source of DNA and can help in classification

SRV 20
DNA structure

SRV 21
• Double stranded
• Two strands are antiparallel
• Handedness / chirality: Normal form of DNA is right handed helix
• If we hold DNA pointing away from us, it twists clockwise moving away from us
• [Handedness is left, if it is clockwise moving towards observer]
• Direction of the spiral (or helix) when seen upward twists to the right

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Sugar-phosphate (S-P) backbone

• Alternating sugar and phosphate residues, from which bases project inwards

• S-P chains are coiled about its periphery, thereby minimizing the repulsions between charged
phosphate groups

• Hydrophilic due to hydroxyl groups of sugar residues and phosphates

• Not rigid; S-P backbone is flexible

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Single strand SRV 24
Base pairs (bp)

• Bases project inwards from sugar phosphate backbone (hydrophobic interior)

• Bases from two S-P backbones form base pair by H-bonding

• A in one strand base pairs with T in other strand through 2 H-bonds
• G in one strand base pairs with C in other strand through 3 H-bonds
• A-T, T-A, G-C, C-G are Watson-Crick base pairs

• Base pairs are accessible through major and minor grooves

• The length / size of DNA is described in base pair (bp)

SRV 25
 Watson-Crick base pairing
• Purine base pairs with pyrimidine
• A base pairs with T with 2 H bonds; G base pairs with C with 3 H bonds
• A-T, T-A, G-C, C-G are Watson-Crick base pairs

Positions involved in H-bonding

A =T
(N6, N1) = (O4, N3)

G≡C
(O6, N1, N2) ≡ (N4, N3, O2) SRV 26
SRV 27
Antiparallel
• Two strands of DNA are antiparallel
• It is a stereochemical consequence of the way that A and T and G and C pair with each other

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Bonds

Phosphodiester bonds

Hydrogen bonds

Glycosidic bonds

Base stacking interactions

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Phosphodiester bond

• Deoxyribonucleotides are joined to each other in DNA through 3’ OH of deoxyribose of one nucleotide
and the phosphate attached to 5’ OH of another nucleotide; This is phosphodiester linkage
• 3’-5’ phosphodiester bond
• Orientation is same in one strand and antiparallel in other strand of dsDNA
• Provides inherent polarity to DNA strands

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Glycosidic bond

• Bond linking the nitrogenous base to the sugar C1’ atom

• It extends from the same side of the sugar ring as does the C4’-C5’ bond (the so called β-
configuration)
• β-N-glycosidic bonds
• Purines form glycosidic bonds to deoxyribose sugar via their N9 atoms
• Purines are N9 glycosides
• Pyrimidines form glycosidic bonds to deoxyribose sugar via their N1 atoms
• Pyrimidines are N1 glycosides

H H

SRV 31
Deoxycytidine Deoxyadenosine
H-bonding

• H-bonds involve amino and carbonyl group between bases in nucleic acids

• Leads to complementary base pairing

• H-bonds between bases permit a complementary association of two (and occasionally 3 or 4)
strands of nucleic acid

• There is specificity in association between bases in a base pair

• A base pairs with T with 2 H-bonds
• G base pairs with C with 3 H-bonds
• It is this specific pairing of bases that permits the duplication of genetic information

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• Forms Watson-Crick base pair

• Slight contribution to the stability of DNA helix

• GC base pair is more stable than AT base pair (due to 3 H-bonds in GC base pair)

• Positions involved in H-bonding

• A =T [(N6, N1) = (O4, N3)]
• G≡C [(O6, N1, N2) ≡ (N4, N3, O2)]

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Base stacking

• Base stacking involves hydrophobic, van der Waal and dipole-dipole interactions
• Minimizes contact of the bases with water
• Imparts helical conformation
• Most important in stabilizing the 3D structure

• DNA is shaped as twisted ladder (double

helical) due to base pairing interactions
between base pairs

• The normal form of DNA is exclusively a right-

handed helix

• This is determined by the overall stability of

the stacking interactions, which favour right-
handed helices

SRV 34
Major and Minor Grooves

• Double helical nucleic acids contain two grooves – major and minor
• Grooves arise due to
• Base pair geometry
• Glycosidic bonds of a base pair are not diametrically opposite each other

SRV 35
 Minor groove
exposes that edge of a base pair
from which its C1’ atoms extend;
has O2 and N3 groups of Py and Pu,
respectively

In normal B-DNA, major groove is wider and deeper than minor groove

SRV 36
Axis

Helix axis / Central axis

• Average symmetry axis of all the base pairs
• Exists in the middle of the helix

Pseudodyad axis
• Each base pair also has pseudodyad axis
• Also called pseudo-two-fold symmetry axes or dyad axes
• Exists in the middle of H-bond in each base pair

• Helix axis is same as pseudodyad axis in B-DNA

Pseudodyad
axis
Long axis
• Perpendicular to helix axis or pseudodyad axis Long
• Passes through C6 of Py, C8 of Pu axis

SRV 37
Double helical structure of DNA
Watson-Crick Model

SRV 38
• Double helical structure determined in 1953
• Nobel Prize in Physiology and Medicine 1962 to James Watson, Francis Crick and Maurice
Wilkins

• Normal physiological form of DNA is called B-DNA

SRV 39
• DNA is double stranded (has two polynucleotide chains or strands)

• Two strands are

• Spirally twisted around each other around a common axis
• Form a right-handed double-helix
• Antiparallel, i.e., they run in opposite directions so that the 3′ end of one chain facing the 5′ end of
the other
• Held together by H-bonds between the Pu and Py bases of the opposite strands

• Bases occupy the core of the helix and the S-P chains are coiled about its periphery
• Planes of the bases are nearly perpendicular to the helix axis
• Bases are stacked with their hydrophobic and nearby planar ring structures close together
• Bases in base pair are coplanar (not coplanar – proved later)
• Each base is H-bonded to a base on opposite strand to form a planar base pair

SRV 40
• The most remarkable feature of Watson Crick structure is that it can accommodate only two types of
base pairs

• Two stands are complementary to one another (base pairing rule)

• A always pairs with T by two hydrogen bonds
• G always pairs with C by three hydrogen bonds
• AT, TA, CG and GC are Watson-Crick base pairs

• The base sequence along a polynucleotide chain is variable

• Specific sequence of bases carries the genetic information

SRV 41
• The geometrics of A.T and G.C base pairs are fixed

• The backbone-to-backbone distance of AT and GC bp is approximately same

• A:T bp - 1.11 nm
• G:C bp - 1.08 nm

• Duplex is held and stabilized by two forces

• H-bonding between complementary base pairs
• Base stacking interactions (hydrophobic, VDW, dipole-dipole interactions)

• The base compositions of DNA obey Chargaff s rules

• A=T and G=C
• Purines (A+G) = pyrimidines (C+T)
• (A+C) = (G+T)
• Ratio of (A+T) and (G+C) is constant for a species

SRV 42
• The offset pairing of two strands creates a major groove and minor groove on the surface of duplex
• Two grooves are of unequal sizes
• Shallow groove - minor groove
• Deep groove - major groove
• Minor groove exposes that edge of a bp from which its C1’ atoms extend
• Major groove exposes opposite edge of each base pair
• If the sugars pointed away from each other in a straight line, i.e., at an angle of 180°, then the two
grooves would be of equal dimensions and there would be no minor and major grooves

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• Diameter - 20 Å

• Each base pair is displaced (twisted) from the previous one by ~36° (helical twist)

• Distance between vertically stacked bases inside the double helix is 3.4 Å
• Adjacent bases are separated by 3.4 Å along the axis

• The length of a complete turn of helix is 34 Å

• It takes a stack of about 10 bp to go completely around the helix (360°)

• There are 10 bp per turn
• A consequence of the helical nature of DNA is its periodicity
• Helical periodicity is generally 10 bp per turn of the helix

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