Biologically occuring polynucleotides in which
the nucleotide sequences are linked in a
specific sequence by phosphoester bonds.
• A nucleotide has three characteristic components: a
nitrogenous base, a pentose, and one or more
phosphates. The molecule without a phosphate group
is called a nucleoside. The nitrogenous bases are
derivatives of two parent compounds, pyrimidine and
purine. The bases and pentoses of the common
nucleotides are heterocyclic compounds.
• In the pentoses of nucleotides and nucleosides the
carbon numbers are given a prime (′) designation to
distinguish them from the numbered atoms of the
• Purine is a heterocyclic aromatic organic compound, consisting of
a pyrimidine ring fused to an imidazole ring.
• Imidazole is a heterocyclic aromatic organic compound. It is further
classified as an alkaloid. Imidazole refers to the parent compound
C3H4N2, while imidazoles are a class of heterocycles with similar ring
structure but varying substituents.
• Pyrimidine is a heterocyclic aromatic organic compound similar
to benzene and pyridine, containing two nitrogen atoms at positions 1 and
3 of the six-member ring.
• Free pyrimidine and purine bases may exist in two or more tautomeric
forms depending on the pH.
• The functional groups of pyrimidines and purines are ring nitrogens,
carbonyl groups, and exocyclic amino groups. Hydrogen bonds involving
the amino and carbonyl groups are the most important mode of
interaction between two (and occasionally three or four) complementary
strands of nucleic acid.
• Tautomers are structural
isomers of chemical
compounds that readily
results in the relocation
of a proton. Tautomerism
is for example relevant to
the behavior of amino
acids and nucleic acids
• The base of a nucleotide is joined covalently
(at N-1 of pyrimidines and N-9 of purines) in
an N-β-glycosyl bond to the 1′ carbon of the
pentose, and the phosphate is esterified to the
5′ carbon. The N-β-glycosyl bond is formed by
removal of the elements of water (a hydroxyl
group from the pentose and hydrogen from
the base), as in O-glycosidic bond formation
2 methyl guanosine 7-methyl guanosine
• The successive nucleotides of both DNA and RNA are
covalently linked through phosphate-group “bridges,”
in which the 5′-phosphate group of one nucleotide unit
is joined to the 3′-hydroxyl group of the next
nucleotide, creating a phosphodiester linkage
• The covalent backbone of DNA and RNA is subject to
slow, nonenzymatic hydrolysis of the phosphodiester
bonds. In the test tube, RNA is hydrolyzed rapidly
under alkaline conditions, but DNA is not; the 2′-
hydroxyl groups in RNA (absent in DNA) are directly
involved in the process.
Nucleic acid structure
• Watson and Crick 1953
• Friedrich Miescher 1868
• Hershey and Chase, 1952
• Franklin and Wilkins
Franklin and Wilkins experiment
• The pattern revealed that DNA
molecules are helical, with two
periodicities along their long
axis, a primary one of 3.4 Å
and a secondary one of 34 Å.
The problem then was to
formulate a three-dimensional
model of the DNA molecule
that could account not only for
the x-ray diffraction data but
also for the specific A = T and
G = C base equivalences
discovered by Chargaff and for
the other chemical properties
Different forms of DNA
• The Watson-Crick structure is also referred to as B-form DNA, or BDNA. The B form is the most
stable structure for a random-sequence DNA molecule under physiological conditions and is
therefore the standard point of reference in any study of the properties of DNA. Two structural
variants that have been well characterized in crystal structures are the A and Z forms.
• The A form is favored in many solutions that are relatively devoid of water. The DNA is still arranged
in a right-handed double helix, but the helix is wider and the number of base pairs per helical turn
is 11, rather than 10.5 as in B-DNA. The plane of the base pairs in A-DNA is tilted about 20° relative
to B-DNA base pairs, thus the base pairs in A-DNA are not perfectly perpendicular to the helix axis.
These structural changes deepen the major groove while making the minor groove shallower. The
reagents used to promote crystallization of DNA tend to dehydrate it, and thus most short DNA
molecules tend to crystallize in the A form.
• Z-form DNA is a more radical departure from the B structure; the most obvious distinction is the
left-handed helical rotation. There are 12 base pairs per helical turn, and the structure appears
more slender and elongated. The DNA backbone takes on a zigzag appearance. Certain nucleotide
sequences fold into left-handed Z helices much more readily than others. Prominent examples are
sequences in which pyrimidines alternate with purines, especially alternating C and G (that is, in
the helix, alternating C≡G and G≡C pairs) or 5-methyl-C and G residues. To form the left-handed
helix in ZDNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the
anti conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow
• Whether A-DNA occurs in cells is uncertain, but there is evidence for some short stretches (tracts)
of Z-DNA in both bacteria and eukaryotes. These Z-DNA tracts may play a role (as yet undefined) in
regulating the expression of some genes or in genetic recombination.
• A segment of a DNA
molecule that contains
required for the
synthesis of a functional
whether protein or
RNA, is called a gene
• A palindrome is a word,
phrase, or sentence that is
spelled identically when
read either forward or
backward; two examples
are ROTATOR and NURSES
RUN. In DNA, the term is
applied to regions of DNA
with inverted repeats, such
that an inverted, self-
complementary sequence in
one strand is repeated in
the opposite orientation in
the paired strand.
• The N-7, O6, and N6 of
purines, the atoms that
participate in the hydrogen
bonding with a third DNA
strand, are often referred to
as Hoogsteen positions, and
pairing is called Hoogsteen
pairing, after Karst
Hoogsteen, who in 1963
first recognized the
potential for these unusual
pairings. Hoogsteen pairing
allows the formation of
• Four DNA strands can also
pair to form a tetraplex
(quadruplex), but this
occurs readily only for
DNA sequences with a
very high proportion of
guanosine residues. The
guanosine tetraplex, or G
tetraplex, is quite stable
over a broad range of
• Solutions of carefully isolated, native DNA are highly viscous at pH 7.0 and room temperature (25
°C). When such a solution is subjected to extremes of pH or to temperatures above 80 °C, its
viscosity decreases sharply
• The close interaction between stacked bases in a nucleic acid has the effect of decreasing its
absorption of UV light relative to that of a solution with the same concentration of free nucleotides,
and the absorption is decreased further when two complementary nucleic acid strands are paired.
This is called the hypochromic effect.
• Denaturation of a double-stranded nucleic acid produces the opposite result: an increase in
absorption called the hyperchromic effect. The transition from double-stranded DNA to the
denatured, single-stranded form can thus be detected by monitoring UV absorption at 260 nm.
• tm; formally, the temperature at which half the DNA is present as separated single strands
• cytosine deamination UV light induces the condensation of two ethylene groups to form a
cyclobutane ring. In the cell, the same reaction between adjacent pyrimidine bases in nucleic acids
forms cyclobutane pyrimidine dimers. This happens most frequently between adjacent thymidine
residues on the same DNA strand. A second type of pyrimidine dimer, called a 6-4 photoproduct, is
also formed during UV irradiation.
• Nitrous acid, Sodium bisulphite
• Alkylating agents
Next Generation sequencing
• Next generation sequencing (NGS), massively parallel or deep sequencing are
related terms that describe a DNA sequencing technology which has
revolutionised genomic research. Using NGS an entire human genome can be
sequenced within a single day. In contrast, the previous Sanger sequencing
technology, used to decipher the human genome, required over a decade to
deliver the final draft. Although in genome research NGS has mostly superseded
conventional Sanger sequencing, it has not yet translated into routine clinical
• Pyrosequencing is a method of DNA sequencing (determining the order
of nucleotides in DNA) based on the "sequencing by synthesis" principle, in which
the sequencing is performed by detecting the nucleotide incorporated by a DNA
polymerase. Pyrosequencing relies on light detection based on a chain reaction
when pyrophosphate is released.
• Illumina dye sequencing is a molecular technique used to determine the series of
base pairs in DNA, also known as DNA sequencing. It was developed by Shankar
Balasubramanian and David Klenerman of Cambridge University, who
subsequently founded Solexa, a company later acquired by Illumina. This
sequencing method is based on reversible dye-terminators that enable the
identification of single bases as they are introduced into DNA strands.
• mRNA: Messenger RNA are those are transcribed
from a DNA template
• Cistrons: In bacteria and archaea, a single mRNA
molecule may code for one or several
polypeptide chains. If it carries the code for only
one polypeptide, the mRNA is monocistronic; if it
codes for two or more different polypeptides,
the mRNA is polycistronic. In eukaryotes, most
mRNAs are monocistronic.
rRNA, snoRNA, snRNA
• rRNA: Ribosomal ribonucleic acid is a type of
non-coding RNA which is the primary
component of ribosomes, essential to all
• snoRNA: Small nucleolar RNAs are a class of
small RNA molecules that primarily guide
chemical modifications of other RNAs, mainly
ribosomal RNAs, transfer RNAs and small
• snRNA: Small nuclear RNA is a class of small
RNA molecules that are found within the
splicing speckles and Cajal bodies of the cell
nucleus in eukaryotic cells. The length of an
average snRNA is approximately 150
• miRNA: microRNA is a small non-coding RNA
molecule found in plants, animals and some
viruses, that functions in RNA silencing and
post-transcriptional regulation of gene
• Hydrolysis of the ester linkage
yields about 14 kJ/mol under
standard conditions, whereas
hydrolysis of each anhydride
bond yields about 30 kJ/mol.
• coenzyme A
• second messengers
• diverse physiological
• processes, including taste,
inflammation, and smooth
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