1.
Structure and Properties of Nucleic Acid ,Types of
DNA Sequences and DNA Content Variation
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2.
Nucleic Acids
 Nucleic acids were first discovered in 1868 , by Friedrich Miescher
during working with pus cells he used term nuclein
 Later , nuclein was replaced with nucleic acid in 1889 by German
pathologist Richard Altmann
 Nucleic acids are biopolymers, or small biomolecules, essential to all
known forms of life
 Located in nuclei of cell
 They are composed of nucleotides, which are monomers made of three
components : 5- carbon sugar ,
Phosphate and
Nitrogenous base
Friedrich
Miescher
Richard
Altmann
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3.
Types of Nucleic Acids
 If the sugar is a compound of ribose, the polymer is RNA (Ribonucleic Acid) ; if
the sugar is derived from ribose as deoxyribose, the polymer is DNA
(Deoxyribonucleic Acid)
 So, There are two types of nucleic acids
1. Deoxyribonucleic Acid (DNA)
2. Ribonucleic Acid (RNA)
 DNA provides directions for its own replication
 DNA directs synthesis of messenger RNA (mRNA) and through mRNA,
controls protein synthesis and its occurs on ribosomes
 DNA is found in the nucleus with small amount in mitochondria and chloroplast
 RNA is found throughout the cell
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4.
Nucleic Acid Structure
 Nucleic Acids are polynucleotides
 Their building blocks are nucleotides
Nucleotides
 Energy rich compounds that drive metabolic process in cell
 Structural component of number of enzymes, cofactor and metabolic
intermediate
 Each nucleotide is formed by 3 units : Phosphate, Sugar and Nitrogenous
base
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5.
Nucleotide Structure
Phosphate
Sugar
Ribose or
Deoxyribose
Base
Purines Pyrimidines
Adenine (A) Cytosine(C)
Guanine (G) Thymine (T)
Uracil (U)
Nucleotide
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Phosphoric Acid
 Molecular formula : H3PO4
 Contain three monovalent hydroxyl(-OH) groups of which two are
involved in forming the sugar phosphate backbone of DNA and a
divalent oxygen atom
 A phosphate moiety joins the 5’C of one and 3’C of the other
neighbouring pentose molecule to produce the phosphodiester (5’C-
O-P-O-3’C) linkage
 All lined to pentavalent phosphorous atom
O
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Sugar
 5 carbon keto sugar or pentose
 One possess deoxyribose and other possess ribose
 Both sugar are present in furanose
 Pentose sugar form phosphodiester bond with phosphoric acid and
glycosidic bond with nitrogenous base
 The 5’ and 3’ carbons of the pentoses participate in phosphodiester linkage,
while 1’ carbon is always occupied by a nitrogenous base
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Nitrogenous Base
 Two types of nitrogenous base : Purine (double ring structure)
Pyrimidine (single ring structure)
 Purine are Adenine(A) and Guanine(G)
 Pyrimidine are Uracil(U), Thymine(T) and Cytosine(C)
 DNA contains Adenine, Guanine, Thymine and Cytosine
 RNA contains Adenine, Guanine, Uracil and Cytosine
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9.
Nucleosides
 When ribose or deoxyribose is linked with purine or pyrimidine base nucleoside is
formed
+ =
+ =
 In this linkage, the –H attached to the –N at position 1 of pyrimidine or 9 of purine ,
interacts with the –OH at 1’C of the pentoses and forms a C – N covalent bond
between pentoses and bases
 This reaction releases one molecule of H2O
Sugar Base Nucleoside
Phosphate
Nucleotide
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The Sugar – Phosphate Backbone
 The nucleotides are all oriented in the same direction
 The phosphate group joins the 3rd carbon of one sugar to the 5th
carbon of the next in line. Form the sugar – phosphate
backbone.
 The base are attached to the 1st carbon of sugar
 Their order is important to determines genetic information of
the molecule
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12.
The Sugar – Phosphate Backbone
Sugar – phosphate backbone Base
Nucleic acid
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13.
Types of bond found in DNA and RNA
 N-glycosidic linkage: N-9 of a purine or N-1 of a pyrimidine is attached to C-1 of the sugar The base lies
above the plane of sugar when the structure is written in the standard orientation; The configuration of the N-
glycosidic linkage is β .
 3’- to 5’ Phosphodiester linkage: The successive nucleotides of DNA covalently linked through phosphate-
group “bridges” . 5-phosphate group of one nucleotide unit is joined to the 3-hydroxyl group of the next
nucleotide .3’- to 5’ Phosphodiester linkage
 Covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, Nitrogenous bases
as side groups joined at regular intervals. Linkages can be cleaved hydrolytically by chemicals or
enzymatically by family of Nucleases.
 The covalent backbone of DNA and RNA is subject to slow, non-enzymatic hydrolysis of the phosphodiester
bonds. In the test tube, RNA is hydrolyzed rapidly under alkaline conditions but DNA is not.
 Hydrogen bonds : Involving the amino and carbonyl groups are the most important mode of interaction
between two complementary strands of nucleic acid. Required for specificity of base pairing.
 Other bonds: The stacking also involves a combination of van der Waals and dipole-dipole interactions
between the bases. Base stacking helps to minimize contact of the bases with water, and Base -stacking
interactions are very important in stabilizing the three dimensional structure of nucleic acids. Base stacking in
DNA is also favored by the conformations of the relatively rigid five-membered rings of the backbone sugars.
The sugar rigidity affects both the single-stranded and the double-helical forms.
 DNA stability is determined by hydrogen bonding, but base stalking also plays an important role.
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Deoxyribo Nucleic Acid
 Living organism contain DNA
 Material of inheritance
 Discovered in 1953 by Franklin, Watson and Crick, through series of
experiment concluded that DNA is the genetic material present in nucleus of
cell
 Genes are stretch of DNA that carries codes of protein production
 DNA are very long molecules with specific sequence of the for principal
bases : Adenine, Guanine, Thymine and Cytosine
 In 1953 Watson and Crick deduced structure of DNA as double helix
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15.
 Chargaff’s Rules :
1.the number of pyrimidine base (C + T) is equal to that of purine bases (A +
G). (A+G = C+T)
2.The quantity of A in DNA was always equal to that of T, while the quantity of
G was comparable to that of C. (A=T, C=G)
 The two strands of a DNA molecules are coiled together in a right handed helix
forming the DNA double helix
 The diameter of this helix is 2 nm ,while pitch is 3.4 nm. In each DNA strand,
the bases occur at a regular interval of 0.34 nm so that 10 base pairs are present
in one pitch of a DNA double helix
 A=T , G= T. Adenine and Thymine are bind with two hydrogen bond and
Cytosine and Guanine are bind with three hydrogen bond
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Types of DNA
 Most of the DNA is in the classic Watson-Crick model simply called as B- DNA
 There are different forms of DNAs are found based on their structural diversity :
A-DNA, B-DNA, C-DNA, Z-DNA, D-DNA, E-DNA
B-DNA:
 Described by James D. Watson & Francis crick.
 Consist of 2 helical polynucleotide chains coiled around common axis.
 2 helices are wound in such a way so as to produce 2 interchain spacing or
groove, 1.Major groove(width 1.2 nm, depth 0.85 nm)
2. Minor groove (width 0.6 nm, depth0.75 nm)
 This grooves provide surface with which proteins, chemicals, drugs can interact.
 Right handed twisting
 Uniform diameter (2 nm), base pair per turn is 10.4, rise per base pair is 0.34nm
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18.
A-DNA:
 Right handed double helix.
 Short and fat compared to B-DNA.
 Occur only in dehydrated sample of DNA, such those used in
crystallographic experiments.
 The grooves are not as deep in B-DNA.
 The bases are more tilted (2nm)
 The base pairs per turn is 11.
 Rise per base pair is 0.23 nm
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Z-DNA:
 Discovered by Rich, Nordheim & Wang in 1984.
 Left handed double helix structures winds to left in zig-zag manner, so they
are termed as Z-DNA.
 It has antiparallel strands as B-DNA.
 Long and thin as compared to B-DNA.
 Remarkable characteristic: adjacent sugar have altering orientation
 In Z-DNA, 1. Purines: syn confirmation(bases & sugar are near and on
same side)
2. Pyrimidines : anti (bases & sugar are distant and on opposite
side)
 Only one deep helical grooves.
 There are 12 base pairs per turn with axial rise 0.38nmand angle twist 600
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20.
C-DNA:
 Right handed with axial rise 0.332nm per base pair
 9.33 base pair per turn
 Helical pitch 0.332nm x 9.33=3.097nm
 Base pair rotation at 38.580
 Diameter of 1.9nm, smaller than that of A and B-DNA
 Tilt of base is 7.80
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21.
Characteristics A-DNA B-DNA C-DNA Z-DNA
Shape Broadest Intermediate Narrow Narrowest
Helix sense Right Right Right Left
Helix diameter 2.55nm 2.07nm 1.90nm 1.84nm
Rise per basepair(H) 0.23nm 0.34nm 0.332nm 0.38nm
Base pair per turn(N) 11 10.4 9.33 12
Helix pitch(HxN) 2.55nm 3.536nm 3.097nm 4.56nm
Rotation per basepair +32.720 +34.610 +38.580 -600
Base pair tilt 190 10 7.80 90
Glycosidic bond Anti Anti - Anti for C and T, syn
for A and G
Maor groove Narrow and very deep Wide and quite deep - No
Minor groove Very broad and shallow Narrow and quite deep - Very narrow and deep
Difference between A , B, C and Z-DNA
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22.
Ribo Nucleic Acid
 RNA, like DNA, is a polynucleotide
 It is produced by phosphodiester linkages between ribonucleotides in same
manner as in case of DNA
 RNA have ribose sugar
 Thymine is absent in RNA, and Uracil is found in place
 Usually RNA is single stranded, but double stranded RNA is also found(
 In most organisms RNA performs non genetic functions, but in some viruses
it serves as genetic material
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 There are seven types of RNA: mRNA, tRNA, and rRNA, miRNA, snRNA,
lncRNA, snoRNA
mRNA (messenger RNA):
 mRNA is the intermediary between the nucleus, where the DNA lives, and the
cytoplasm, where proteins are made.
 Produced during transcription. Carries the genetic instructions of a gene from the
nucleus to the ribosome in the cytoplasm.
 Translated into polypeptides.
 Encode for proteins that guard cell metabolism such as ensyme used in glycolysis
rRNA (ribosomal RNA):
 Together with proteins, composes the ribosome, the organelles that are the site of
protein synthesis.
 It makes up to 60% of the weight of the ribosomes since they play major role in the
function of the ribosomes such as binding of mRNA and recruitment of tRNA, and
catalyzation of peptide bond formation between amino acids.
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Transfer RNA (tRNA):
• (a) tRNAs are represented as cloverleaf structures in two
dimensions.
• (b) In three dimensions,
• tRNAs fold into an L-shape stabilized by intramolecular base-
pairing shown here by the tRNA Phe structure.
• In both diagrams, the tRNA structural elements are colored:
acceptor stem (green), dihydrouridine (D)-arm (purple),
anticodon stem (light blue), anticodon (bases 34, 35, 36 in dark
blue), variable arm (orange), T-arm (yellow) and the
discriminator base (red).
• Brings the correct amino acid to the ribosome during translation.
• tRNAs are coded by short molecules of 70-90 nucleotides (5nm).
• The set of the three nucleotides on the mRNA is known as a codon, while the corresponding
sequence on tRNA is known as an anticodon.
• The base pairing of the codon and the anticodon forms a translation mechanism
• At the end of the tRNA 3′ hydroxyl base, there is an anticodon amino acid sequence that is
attached, linking the ribosomes to form a peptide bond, thus elongating the polypeptide
chain. 25

26.
• Other parts of the tRNA structure are the D-arm and the T-arm, which are highly specific and are highly
effective.
• tRNAs have a sugar-phosphate backbone which gives it directionality.
• One end of the tRNA has a reactive phosphate group, which is attached to the fifth carbon atom of the
ribose (5′) and another end which has a free hydroxyl group on the third carbon (3′), giving rise to the 5′
to 3′ ends of RNA.
• The 3′ terminal end has three bases CCA (Cytosine, cytosine, adenine) which make part of the acceptor
arm of the molecule which is covalently attached to the hydroxyl group on the ribose sugar.
• The acceptor arm also contains parts of the 5’ end of the tRNA, made up of 7-9 nucleotides on the
opposite ends of the molecule base pairing with each other.
• The anticodon loop which is recognized by the aminoacyl tRNA synthetase (AATS) is paired to mRNA
and it determines the amino acid that attaches to the acceptor’s arm.
• The AATS reads and recognizes the D-arm from the 5′ end of tRNA.
• The D-arm plays a major role in stabilizing the structure of RNA; it affects and influences the kinetics
and accuracy of translation at the ribosomes.
• The T-arm also influences the tRNA effect on the translation by interaction with the ribosomes.
• The D-arm, T-arm, and the anticodon loop combined resembles a cloverleaf. When RNA folds into a
tertiary structure, it becomes L-shaped with an extended structure of the acceptor stem, T-arm, anticodon
loop, and D-arm.
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snRNA (small nuclear RNA):
snRNA are transcribed by RNA polymerase II or RNA polymerase III , of about 150
nucleotides.
• It has different genes in multiple copies, which play different roles in the synthesis of
other RNA classaes
• They also mediate the regulation of transcription factors and RNA polymerase II
• Also maintain telomeres.
• snRNA associate with specific proteins and small nuclear ribonucleoproteins.
miRNAs(micro RNAs):
• It is a small non-coding RNA that is single-stranded, containing 22 nucleotides.
• Its size is same as that of siRNAs.
• Found in plants, all animals and some viruses, with its primary role in RNA silencing
and post-transcriptional gene expression regulation.
• These miRNAs are encoded in the genome by stand alone genes or in portions of
introns of the genes where they regulate the mRNA.
• Their role in gene regulation by regulating the expression of mRNA by destroying the
mRNA sequences are evenly matched especially in plants and by repressing the
translation of mRNA when sequences are matched partially 27

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lncRNA(Long non-coding RNA):
 This is a heterogeneous group of non-coding transcript rna that are 200 Nucleotides in size.
 They are largest mammilian non-coding transcriptome
 An estimated 8000 lncRNA are encoded in human genome
 Its role in gene regulation and physiological machanism include: splicing, translation,
imprinting and transcription
 Bringing the enhancer and promoter regions of genes to close together by looping, which
helps in the regulation of gene transcription
snoRNA(Small Nucleolar RNA):
 Small RNAs of about 60-300 nucleotides found in the cell nucleolus
 They play a role in the synthesis of ribosomes, by cutting the large RNA precursor of the
28S, 18S and 5.8S
 Help in the splicing of pre-mRNA to different forms of mature mRNA
 It serves as a template for synthesis of telomeres
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Types of DNA Sequences
 The DNA of eukaryotes is classified into two categories based on number of copies of the
DNA sequence found in a genome:1.Unique DNA sequences
2.Repetitive DNA sequences
Unique DNA Sequences
 This is also called non-repetitive DNA, contains the bulk of gene that are expressed.
 Structural genes are typically unique sequences of DNA.
 The vast majority of proteins in eukaryotic cells are encoded by genes present in one or a
few copies.
 The length of unique DNA tends to increase with overall genome size:
E. coli - 4.2×106 bp, C. elegans - 6.6×107 bp, D. melanogaster ~ 108 bp,
Mammals ~ 2× 109 bp
 In humans, unique sequences are estimated to make up approximately 55-60% of the
genome
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Repetitive DNA Sequences
 It consists of base sequences, which are present in several to a million copies per genome
 The number of copies of a DNA sequence present in genome is called repetitive
frequency(f)
 If a specific sequences is represented twice in the genome it will have two
complementary sequences
 The proportion of repetitive DNA in the genome varies from one species to the other ;
nematode C. elegans genome has only 17% repetitive DNA, while in rye it constitutes
about 90% of the genome.
 The amount of repetitive DNA varies from ˂ 20% in lower eukaryotes, through ~ 50% in
animal cells to ~ 80% in plants and amphibians
 Repetitive DNA sequences are grouped into the following two classes:
1.Highly repetitive DNA
2.Moderately repetitive DNA
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Moderately Repetitive DNA:
 These DNA are present in 10 to 10,000 copies per genome.
 It can vary from 100-300bp to 5000 bp and can be dispersed throughout the
genome.
 DNA fraction in D. melanogaster is about 12% and in man is about 13% of the
genome
 In few cases, moderately repetitive sequences are multiple copies of the same
gene.
 For example, the genes that encode ribosomol RNA are founds in many copies.
– Ribosomal RNA is necessary for the functioning of ribosomes. Cells need a large
amount of rRNA for making ribosomes, and this is accomplished by having multiple copies of
the genes that encode rRNA.
 Likewise, the histone genes are also found in multiple copies because a large number of
histone proteins are needed for the structure of chromatin.
 This DNA is distributed throughout the genome at variable intervals
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Highly Repetitive DNA :
 About 3% or so of the human genome consists of highly repetitive sequences, referred to as
simple sequence DNA or simple sequence repeats (SSR).
 These sequences are present in more than 105 bp and up to several million copies per genome
long
 It generally consists of very short nucleotide sequences repeated many times in tandem in large
clusters
 These sequences are found in regions of the chromosome such as heterochromatin, centromeres
and telomeres and tend to be arranged as a tandem repeats.
 Both moderately repetitive and highly repetitive DNA sequences are sequences that appear
many times within a genome.
 These sequences can be arranged within the genome in one of two ways:
1. distributed at irregular intervals known as dispersed repeated DNA or interspersed repeated
DNA
2. clustered together so that the sequence repeats many times in a row known as tandemly
repeated DNA.
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• some moderately and highly repetitive sequences are clustered together
in a tandem array, also known as tandem repeats.
• In a tandem array, a very short nucleotide sequence is repeated many
times in a row.
• In Drosophila, for example, 19% of the chromosomal DNA is highly
repetitive DNA found in tandem arrays.
• Depending on the average size of the arrays of repeat units, highly
repetitive noncoding DNA belonging to this class can be grouped into
three subclasses: satellite, minisatellite and microsatellite DNA.
1.Minisatellites (less than 10 bp per repeat),
2. Microsatellites (10-60 bp per repeat)and
3. satellites (up to 100 bp per repeat)
Satellite DNA :
• Human satellite DNA is comprised of very large arrays of tandemly
repeated DNA
• Repeated DNA of this type is not transcribed
• Accounts for the bulk of the heterochromatic regions of the genome,
being notably found in the vicinity of the centromeres. 33

34.
Minisatellite DNA:
 comprises a collection of moderately sized arrays of tandemly repeated DNA
sequences which are dispersed over considerable portions of the nuclear genome
 Like satellite DNA sequences, they are not normally transcribed.
 In humans, 90% of minisatellites are found at the sub-telomeric region of
chromosomes.
 Variation in size (array length) of these regions between individuals in humans was
originally the basis for DNA fingerprinting.
 Hypervariable minisatellite DNA – many of the arrays are found near the telomeres
– 9-64bp repeating unit with array of 0.1–20 kb long.
 Telomeric DNA – 10–15 kb of tandem hexa nucleotide repeat units, especially
TTAGGG, which are added by a specialized enzyme, telomerase
Microsatellites (SSRs, STRs) :
 Also known as Short Tandem Repeat (STR), Simple Sequence length polymorphism
(SSLP) and Simple Sequence Repeat (SSR)
 Repeating sequences of 1-6 base pairs of DNA and can be repeated 10 to 100 times.
 Most common in humans is the (CA)n sequence where n varies from 5 -50 or more.
 Found on average every 10kbp in the human genome
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Euchromatin and heterochromatin
• They are the two structural forms of DNA in the genome, which are found in the
nucleus.
• Euchromatin is the loosely packed form of DNA, found in the inner body of the
nucleus. Found in prokaryotes and eukaryotes
• Heterochromatin is the tightly packed form of DNA, found in the periphery of the
nucleus. Found in eukaryotes
• Around 90% of the human genome consists of euchromatin.
• The main difference between euchromatin and heterochromatin is that euchromatin
consists of transcriptionally active regions of DNA whereas heterochromatin consists of
transcriptionally inactive DNA regions in the genome. Even the crossing over cannot
take place.
• Euchromatin allows genes to be transcribed and genetic variations to occur.
• Heterochromatin maintains the structural integrity of the genome and allows the
regulation of gene expression.
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DNA content variation
 C-value is the total amount of DNA present in the haploid genome of an
organism or Quantity of DNA in an organism per cell, in all cells, is always
constant, for a given species.
 It is a characteristic value for each living species and is represented in base
pairs (bp)
 The list of organisms on this planet, with teaming millions, each have its
own genome whose size varies from one species to the other.
 Variation in genomic content (both qualitatively and quantitatively) within a
phylum or an order or genus is surprisingly large from 105 bp to 1012 bps.
 The lowest C- value (6.6×105 bp )for a living organism is found ,in a
eukaryotes, the unicellular alga Pyronomas salina
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 There is an increase in the C- value with an increase in the complexity of organisms
E.g., Mycoplasma 105 bp, (-) Bacteria 4.2 to 5x 106 bp , (+) Bacteria 2 to
8x106bp, Algae 5 to 8x 107 bp, Worms 7x107 to 2x108 bp, Insects 1.5x 108 to 6x 109
bp, Mammals 3x109 to 5x109 bp
E.g., the unicellular eukaryotes like yeast have only five times as much DNA as
the bacterium E. coli, while the first truly multicellular organisms like C. elegans
show more than 100- times as much DNA as E. coli DNA
 The complexity related to C-value, i.e. In some cases there is not linear relationship
between genome size and organism complexity
Eg. Housefly-8.6×108 , Drosophila 1.4×108 Both are in same group
Eg. Plethodon richmondi has genome size more than Plethodon larsilli.
 In eukaryotes , the total amount of DNA in the genome is very large in comparison
to the amount that would be needed to code for proteins. A large part of this excess
DNA is due to the presence of introns within genes, e.g., about 96% of the average
human genes is due to introns 38

39.
Plants Genome size (Mbp)
Rice 389
Sorghum 818
Maize 2300
Soybean 1115
Cucumber 367
Potato 844
Cabbage 485
Pigeonpea 833
Chickpea 738
Wheat 17000
Barley 5100
Tomato 900
Papaya 372
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DNA content variation in monilophytes and lycophytes:
large genomes that are not endopolyploid
Bainard J. D., et al(2011) 40

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 objectives is to further explore the range of genome sizes in eastern North
American monilophytes and lycophytes and determine if endopolyploidy
exists in the sporophytic tissue of these plants
 Flow cytometry provides a fast and reliable way to determine DNA content
in plants.
Result
 DNA content estimates were obtained for six lycophyte species and 31
monilophyte species , with 1C-values ranging from 2.79 to 26.90 pg.
 Across the different orders, 1Cx-values averaged 4.2 pg in the
Lycopodiales, 18.1 pg for the Equisetales, 5.06 pg for our single
representative of the Ophioglossales, 14.3 pg for the Osmundales, and 7.06
pg for the Polypodiales
 There was no indication of endoreduplication in any of leaf, stem and root
tissue analyzed
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Molecular cytogenetics in the study of repetitive sequences helping
to understand the evolution of heterochromatin in Melipona
(Hymenoptera, Meliponini)
 The eukaryote genome is enriched by different types of repetitive
DNA sequences and is most abundant in heterochromatin regions
 Despite having a constant chromosome number, the genus Melipona
has species with wide variation in heterochromatin content, from 8 to
73%, which is an important feature to be investigated regarding its
origin and evolution.
 In the present study, a repetitive DNA sequence of Melipona
mondury was isolated by restriction enzyme digestion
Pereira J. A. et al.(2021) 42

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