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Nucleic Acid
Structure
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Dr. Asad Vaisi-Raygani
Associate professor
Department of Clinical Biochemistry,
faculty of Medicine, Kermanshah
University of Medical Sciences
Nucleic Acids /
Bases/Structure
Imidazole
By the attachment of different
groups to the rings, different types
of Py and Pu are generated.
NA / Bases/ Classification
• Purine Bases (pu):
• Major : (A)&(G)
• Minor: Inosine(I) &
methyl guanine(7mG)
• Unnatural :
Mercaptopurine,
Allopurinol &
8-Azaguanine
NA / Bases/ Classification/
Py
Hot spot
• Pyrimidines (py):
• Major : (T), (C) & (U)
•Minor: DHU , 5mC & 5hmC
•Unnatural: Fluorouracil (5FU) &
6-aza cytosine( AZC)
Nucleosides
N-base
Nucleoside
Nucleotide
9
9
1
1
1
Diversity RNA>>>DNA
RNA have Enzyme activity
• The oxo and amino groups
of purines and pyrimidines
exhibit keto-enol and amineimine tautomerism
•but physiologic
conditions strongly
favor the amino
N-glycosidic
bond
• Both therefore exist as syn or
anti conformers (Figure 33–5).
While both conformers occur
in nature, anti conformers
predominate.
Energy carrier ( ATP & GTP)
Regulatory roles:
Group transfer
• Methylated heterocyclic bases of plants include
the
• xanthine derivatives caffeine of coffee,
• theophylline of tea, and theobromine of cocoa
7
1
Coenzymes (NAD, FAD & Co-A)
SYNTHETIC NUCLEOTIDE
ANALOGS
ARE USED IN CHEMOTHERAPY
• The purine analog allopurinol,
used in treatment of hyperuricemia
and gout, inhibits purine
biosynthesis and xanthine oxidase
activity.
• Finally, azathioprine, which is
catabolized to 6-mercaptopurine, is
employed
• during organ transplantation to
suppress immunologic rejection.
Nucleotides Absorb
Ultraviolet Light
• While spectra are pH-dependent,
at pH 7.0 all the common
nucleotides absorb light at a
wavelength close to 260 nm.
• The concentration of nucleotides
and nucleic acids thus often is
expressed in terms of
“absorbance at 260 nm.”
• 1 A260 unit of dsDNA=50 µg/ml H2o
Chemical properties of nucleic acids:
 Nucleic acids show strong UV absorption at 260 nm due to the
conjugated bases. (Detection method.)
POLYNUCLEOTIDES
3’ OH
5’ phosphate
• Phosphodiesterases rapidly
catalyze the hydrolysis of
phosphodiester bonds whose
spontaneous hydrolysis is an
extremely slow process.
• Consequently, DNA persists for
considerable periods and has
been detected even in fossils.
• RNAs are far less stable than
DNA since the 2′-hydroxyl group
of RNA (absent from DNA)
functions as
• a nucleophile during hydrolysis
of the 3′,5′-phosphodiester
bond.
REDUCTION OF RIBONUCLEOSIDE
DIPHOSPHATES FORMS
DEOXYRIBONUCLEOSIDE
DIPHOSPHATES
• Reduction of the 2′-hydroxyl of purine and
pyrimidine ribonucleotides, catalyzed by
the ribonucleotide reductase complex
(Figure 34–5), forms deoxyribonucleoside
diphosphates (dNDPs).
• The enzyme complex is active only when
cells are actively synthesizing DNA.
• Reduction requires thioredoxin,
thioredoxin reductase, and NADPH.
REDUCTION OF RIBONUCLEOSIDE DIPHOSPHATES
FORMS EOXYRIBONUCLEOSIDE DIPHOSPHATES
Nucleic Acid:
1-DNA
2-RNA
DNA
• led Watson, Crick, and Wilkins to
propose in the early 1950s a model
of a double- stranded DNA molecule
• Deoxynucleotide
• (A = T),
• (G = C),
• Because of the phosphate
• moiety, they have acidic
• character (negatively charged
 Rosaline, Wilkins (1950s) ‒ X-ray diffraction pattern of DNA.
• The two strands, in which
opposing bases are held together
by hydrogen bonds, wind around a
central axis in the form of a
double helix.
• Double-stranded DNA exists in at
least six forms (A–E and Z).
• The B form is usually found under
physiologic conditions (low salt,
high degree of hydration).
Chemical properties of nucleic acids:
 Hydrophilic backbone (phosphate and pentose residues) and
hydrophobic bases
⇒ base stacking (van der Waals and dipole-dipole interactions)
• Right handed
because
• clockwise
direction.
•
In the double-stranded
molecule, restrictions
imposed by the rotation
about the hosphodiester
bond,
• the favored anti
configuration of the
glycosidic bond
• and the predominant
tautomers of the four
bases (A, G, T, and C)
• allow A to pair only with T
• and G only with C,.
35.4 A
Structural Stabilization?
1) Electrostatic interactions:
negatively charged phosphate groups
are located at the outer surface where
they can be neutralized by: a) histones,
b) cations (Mg2+), c) polyamines.
2) Base interactions:
a) hydrogen bonds between bases
(dipole-dipole interactions)
b) stacking interaction between the planes
of adjacent base pairs (van der Waals
forces and dipole-dipole)
Different bonds and interactions in
• Covalent:
PDE bonds in the backbone
• Hydrogen:
between complementary bases
Primary or Natural (Watson-Crick)
Secondary or Hoogsteen pairing
(non-Watson-Crick)
• Hyrophobic
(van der Waals)
between the stacked adjacent
base pairs.
DNA / General facts
• Has specific groove (s)
• It is flexible about its long axis It
•
It may be linear or circular
 DNA duplex can exist in
different 3-D forms.
B-form : the Watson-Click
structure, standard form,
most stable under
physiological conditions
A-form : a dehydrated form
Z-form : left handed
A short Z-DNA tracts may
play a role in gene regulation.
template (sense) strand or non coding
template (sense) strand
coding strand (non sense) or non template
The Denaturation (Melting) of
DNA Is Used to Analyze Its
Structure
• Concomitant with this denaturation
of the DNA molecule is an increase
in the optical absorbance of the
purine and pyrimidine bases—a
phenomenon referred
• to as hyperchromicity of
denaturation.
• The midpoint is called the
melting temperature, or Tm.
• The Tm is influenced by the
base composition of the DNA
and by the salt concentration of
the solution.
• DNA rich in G–C pairs, which
have three hydrogen bonds,
melts at a higher temperature
than that rich in A–T pairs,
which have two hydrogen
bonds.
•
THE CHEMICAL NATURE OF
RNA DIFFERS
FROM THAT OF DNA
• Ribonucleic acid (RNA) is
a polymer of purine and
pyrimidine
>90% NA
<10% DNA
• RNA can be hydrolyzed by
alkali to 2′,3′ cyclic diesters of
the mononucleotides,
• compounds that cannot be
formed from alkali-treated
DNA because of the absence
of a 2′-hydroxyl group.
• The alkali liability of RNA is
useful both diagnostically and
analytically.
Kind of RNA
• mRNAs.
• transfer RNAs; tRNAs
• Many other cytoplasmic RNA
molecules (ribosomal RNAs;
rRNAs)
• Some RNA molecules have
intrinsic catalytic activity.
• The activity of these ribozymes
often involves the cleavage of a
nucleic acid.
• In all eukaryotic cells there are
small nuclear RNA (snRNA) species
that are not directly involved in
protein synthesis but play key roles
in RNA processing.
• These relatively small molecules
vary in size from 90 to about 300
nucleotides (Table 35–1).
• small cytoplasmic RNA (scRNA)
• Signal recognition particle
• Concentration rRNA>tRNA> mRNA
• diversity mRNA>tRNA>rRNA
• The heterogeneous nuclear RNA
(hnRNA) molecules may have a
molecular weight in excess of
107,
• whereas the molecular weight
of mRNA molecules is generally
less than 2 ×106.
B. TRANSFER RNA (TRNA)
• tRNA molecules vary in length from
74 to 95 nucleotides.
• The tRNA molecules serve as
adapters for the translation of the
information in the sequence of
nucleotides of the mRNA into
specific amino acids.
• There are at least 20 species of
tRNA molecules in every cell, at
least one (and often several)
corresponding to each of the 20
amino acids required for protein
synthesis.
74-95 nts
• The tRNA-appropriate amino acid is
attached to the 3′-OH group of the A
moiety of the acceptor arm.
• The D, TC, and extra arms help define a
specific tRNA.
• template but must be formed by
processing from a precursor
• Although tRNAs are quite stable in
prokaryotes, they are somewhat less
stable in eukaryotes.
• The opposite is true for mRNAs, which
are quite unstable in prokaryotes but
generally stable in eukaryotic
organisms.
SPECIFIC NUCLEASES DIGEST
NUCLEIC ACIDS
• Those which exhibit specificity for
deoxyribonucleic acid are referred to
as deoxyribonucleases.
• Those which specifically hydrolyze
ribonucleic acids are ribonucleases.
• Within both of these classes are
enzymes capable of cleaving internal
phosphodiester bonds to
• produce either 3′-hydroxyl and 5′phosphoryl terminals or
• 5′-hydroxyl and 3′-phosphoryl
terminals.
• These are referred to as
endonucleases.
• There exist classes of
endonucleases that recognize
specific sequences in DNA; the
majority of these are the
• restriction endonucleases,
• which have in recent years
become important tools in
molecular genetics and medical
• Some nucleases are capable of
hydrolyzing a nucleotide only
when it is present at a terminal
of a molecule;
• these are referred to as
exonucleases.
• Exonucleases act in one
direction (3′ → 5′ or 5′ → 3′)
only.
Histones Are the Most
Abundant Chromatin
Proteins
• Nucleosomes or core histones
• In the nucleosome, the DNA is
supercoiled in a left handed
helix over the surface of the
disk-shaped histone octamer
(Figure 36–2).
Metaphase overall DNA
Transcriptionally inert
10000 fold condence
These four core histones are
subject to at least five types of
covalent modification:
• DNA in active chromatin
contains large regions (about
100,000 bases long) that are
sensitive to digestion by a
nuclease such as DNase I.
• Hypersensitive sites(100-300bp)
often provide the first sign
about the presence and location
of a transcription control
element.
SOME REGIONS OF CHROMATIN ARE
“ACTIVE” & OTHERS ARE “INACTIVE
Euchromatin
[Transcriptionally active]
Chromatin
Structural genes, rRNA
genes, regulatory
regions, etc.
Heterochromatin
[Transcriptionally inactive]
Heterochromatin
[Transcriptionally inactive]
•constitutive and facultative.
constitutive
Centromeric chromatin
Attachment sites to nuclear matrix
telomeres.
• Facultative heterochromatin is
at times condensed,
• but at other times it is actively
transcribed and,
• thus, uncondensed and appears
as euchromatin.
• Chromatin containing active genes
(ie, of the two members of the X
chromosome pair in mammalian
females,
• one X chromosome is almost
completely inactive transcriptionally
and is heterochromatic.
• However, the heterochromatic X
chromosome decondenses during
gametogenesis and becomes
transcriptionally active during early
embryogenesis—thus,
facultative
heterochromatin.
• it is
• The centromere is an adeninethymine (A–T) rich region ranging
in size from 102 (brewers’ yeast)
• to 106 (mammals) base pairs. It
binds several proteins with high
affinity.
• This complex, called the
kinetochore,
• provides the anchor for the
mitotic spindle.
• It thus is an essential structure
for chromosomal segregation
during mitosis.
• The function of the intervening
sequences or introns, is not clear.
24% of the total human genome
• They may serve to separate
functional domains (exons) of coding
information in a form
• that permits genetic rearrangement
by recombination to occur more
rapidly than if
• all coding regions for a given genetic
function were contiguous.
• humans have < 100,000 proteins
• encoded by the ~1.1% of the
human genome that is
composed of exonic DNA.
• This implies that most of the
DNA is noncoding
• The DNA in a eukaryotic genome can
be divided into different “sequence
classes.”
• These are uniquesequence,or
nonrepetitive, DNA and
• These different genes represent
unique DNA sequences that are
present in single copies or at most
only a few copies per genome
•
• repetitive sequence DNA.
• Least 30% of the Genome
• These are divided into two
major classes:
• middle repetitive (<10 copies
per genome)
• highly repetitive (>10 copies per
genome) sequences
• Some middle repetitive DNA consists
of genes that specify
• transfer RNAs,
• ribosomal RNAs,
• or histone proteins that are required
in large amounts in the cell.
• Other middle repetitive DNA
sequences have no known useful
function,
• but may participate in DNA strand
association and
• chromosomal rearrangements during
meiosis.
• The highly repetitive sequences
consist of 5–500 base pair lengths
repeated many times in tandem.
• These sequences are usually
clustered in centromeres and
telomeres of the chromosome
and are present in about 1–10
million copies per haploid
genome.
• These sequences are
transcriptionally inactive
• and may play a structural role in
moderately repetitive
sequences, which are defined as
• The
•
•
•
•
being present in
numbers of less than 106 copies per
haploid genome,
are not clustered but are
interspersed with unique sequences.
In many cases, these long
interspersed repeats are transcribed
by RNA polymerase II and contain
caps indistinguishable from those on
mRNA.
Microsatellite Repeat Sequences
• Satellite DNA consists of
clusters of short, speciesspecific,
• nearly identical sequences that
are tandemly repeated hundreds
of thousands of times.
• AC repeats are very useful in
constructing genetic linkage maps.
• Most genes are associated with one
or more microsatellite markers,
• so the relative position of genes on
chromosomes can be assessed,
• as can the association of a gene
with a disease.
• Using PCR, a large number of family
members can be rapidly screened for
a certain microsatellite
polymorphism.
• These clusters are deficient in
protein-coding genes and are
found principally
• near the centromeres of
chromosomes,
• suggesting that they may
function to align the
chromosomes during
• cell division to
• facilitate recombination
• Trinucleotide sequences that
increase in number (microsatellite
instability) can cause disease.
• The unstable p(CGG)n repeat
sequence is associated with the
• fragile X syndrome.
• Other trinucleotide repeats that
undergo dynamic mutation
(usually an increase) are
associated with
• Huntington’s chorea (CAG),
myotonic dystrophy (CTG),
ONE PERCENT OF
CELLULAR DNA IS IN
MITOCHONDRIA
• An important feature of human
mitochondrial mtDNA is that
because all mitochondria are
• contributed by the ovum during
zygote formation
• it is transmitted by maternal
nonmendelian inheritance.
• Thus, in diseases resulting from
mutations of mtDNA,
• an affected mother would in theory
pass the disease to all of her children
• but only her daughters would transmit
the trait.
• However, in some cases, deletions in
mtDNA occur during oogenesis and
• thus are not inherited from the mother.
• A number of diseases have now been
shown to be due to mutations of
mtDNA.
• These include a variety of myopathies,
• neurologic disorders,
• some cases of diabetes mellitus .