DNA: Properties, Structure, Composition, Types, Functions
• Deoxyribonucleic acid (DNA) is the heredity material found in humans and all
living organisms. It is a double-stranded molecule and has a unique twisted helical
structure.
• DNA is made up of nucleotides, each nucleotide has three components: a
backbone made up of a sugar (Deoxyribose) and phosphate group and a nitrogen-
containing base attached to the sugar.
• Each strand has many nucleotides or says numerous sugar, a phosphate group, and
nitrogenous bases. These nitrogenous bases are complementary to the other
strand’s nitrogenous base to maintain helical symmetry.
• Each base pairs are bonded through Hydrogen bonding. These nitrogenous bases
are Adenine (A), Guanine (G), Cytosine (C), and Thymine (T), A is
complementary to T, and G to C. These bases are responsible for storing the
genetic information. Most DNA is located at the cell nucleus so is called nuclear
DNA, however, a small amount of DNA is also located in mitochondria, and so is
referred to as mitochondrial DNA.
Properties of DNA (Deoxyribonucleic acid)
• DNA is made up of two helical strands that are coiled around the same axis. If
coiled from right it is known as right-handed helices DNA and if coiled from left
then it is known as left-handed helices. However, the right-handed helices DNA is
the most stable and thus the structure of it is to be referred to as the standard.
• The two chains of helices run antiparallel to each other. Thus, one strand runs 5’ to
3’ and another strand runs from 3’ to 5’.
• Both the strands denature on heating and can renature or say hybridize on cooling.
However, the temperature on which these strands are separately permanently is
referred to as melting temperature and varies according to the specific sequence of
DNA.
• For instance, the region of higher concentration of C-G has a higher melting
temperature cause these bases are bonded with three hydrogen bonds, which
require more energy to break than the region of higher concentration A-T which
are bonded only with two hydrogen bonds.
• These nitrogenous bases store genetic information and thus encode for amino
acids which give rise to proteins.
Structure and Composition of DNA (Deoxyribonucleic acid)
• DNA is made of two helical chains that intertwine with each other to form a
double helix. The most widely accepted structure of DNA is right-handed helix
DNA also known as the B-form of DNA, which is 1.9 nm in diameter.
• These helical chains run anti-parallel to each other, one polynucleotide chain runs
from 5’ to 3’ and the other polynucleotide chain runs from 3’ to 5’. These chains
are connected to each other via nitrogen bases through hydrogen bonding.
• Hydrogen bonding contributes to the specificity of base pairing. Adenine
preferentially pairs with Thymine through 2 hydrogen bonds. Similarly, Cytosine
preferentially pairs with Guanine through 3 hydrogen bonds.
• We can even say, that the base pairing happens when Pyrimidines pair with
Purines because Pyrimidines refers to the single ring structure of Thymine and
Cytosine and Purines refers to double-ring structures, Adenine and Guanine.
• The base pairs A = T and G ≡ C are known as complementary base pairs. Hence,
the amount of Adenine is equal to the amount of Thymine, and the amount of
Guanine is equal to the amount of Cytosine.
• The geometry of the DNA is influenced by the distance between the backbones
and the angle at which the nitrogenous bases are attached to the backbone.
• The major groove occurs when the backbones are far apart from each other and the
minor groove occurs when they are close.
• The regularity of the helical structure forms two repeating and alternating spaces:
Major and Minor grooves.
• These groves act on base-pair recognition and binding sites for protein, the major
groove contains base pair specific information while the minor groove is largely
base-pair nonspecific, caused by protein interactions in the grooves
• The double-helical structure of DNA is highly regular, each turn of the helix
measures approximately 10 base pairs. In addition to hydrogen bonding in
between the bases, the staging of bases also stabilizes the structure, there are pi-pi
interactions between staged aromatic rings of the bases.
• The distance between each turn is 3.4 nm.
• The major groove is 2.2 nm wide and the minor groove is 1.1 nm wide.
Major and Minor Grooves of the DNA
• As a result of the double helical nature of DNA, the molecule has two asymmetric
grooves. One groove is smaller than the other.
• This asymmetry is a result of the geometrical configuration of the bonds between
the phosphate, sugar, and base groups that forces the base groups to attach at 120
degree angles instead of 180 degree.
• The larger groove is called the major groove, occurs when the backbones are far
apart; while the smaller one is called the minor groove, occurs when they are close
together.
• Since the major and minor grooves expose the edges of the bases, the grooves can
be used to tell the base sequence of a specific DNA molecule.
• The possibility for such recognition is critical, since proteins must be able to
recognize specific DNA sequences on which to bind in order for the proper
functions of the body and cell to be carried out.
Types of DNA Conformations
Types of DNA on the basis of forms
1. A-form
• The major difference between the A and B forms of DNA is the conformation of
the deoxyribose sugar ring. For B form, it is in the C2 endoconformation, while in
A form it is in the C3 endoconformation.
• Another important difference between A and B-form is the arrangement or say
placement of nitrogenous base pairs within the duplex.
• In B-form, the base pairs are almost in the center over the helical axis, whereas in
A-form, the base pairs are diverted away from the central axis towards the major
groove.
• The distance between two base pairs is 0.29 nm. One turn of the helix contains 11
base pairs with a length of 2.8 nm
• Shorter than B-form of DNA. However, the helical width is 2.3 nm which is more
than B-form.
• Narrow and deep major groove and wide and shallow minor groove.
• This form of DNA is favored by low hydration and by repeating units of purines
or pyrimidines.
2. B-form
• The standard structure of DNA that is commonly known, was described by
Watson and Crick and is a right-handed double helix.
• The double-helical chains run antiparallel to each other, one running from 5’ to 3’
and another running from 3’ to 5’ and are joined together via complementary
nitrogenous base pairing.
• Based upon Chargaff’s rules, bases coherent with another, only when one purine
of one strand pairs with one pyrimidine of another strand. A with T and G with C
• The pair formed is a keto base pair, with an amino base, a purine with a
pyrimidine.
• The two strands of the DNA molecule are plectonemic coil meaning that these two
strands are coiled around the same axis and are intertwined with each other.
• The consequence of this plectonemic coil is that these two strands can’t be
separated without the DNA rotating.
• The distance between the base pairs is 0.34 nm. One turn of the helix contains 10
base pairs with a length of 3.4 nm.
• This form of DNA is 1.9 nm in diameter, which means the width of the helix is 1.9
nm.
• The wide and shallow major groove of 2.2 nm, making it easily assessable to
proteins, and narrow and minor groove of 1.1 nm.
3. Z-form
• It is a left-handed helix and is a very different structure when compared with the A
and B-form.
• This form of DNA can form when the DNA is in alternating purines-pyrimidines
sequences.
• The backbone is not a smooth helix but an irregular zig-zag, which is resulted
from alternating sequences of purines and pyrimidines.
• The B form DNA can take the Z form when proteins are bound to DNA in one
helical conformation and force the DNA to adopt a different conformation.
• This adoption happens at the G nucleotide, the sugar in this form is of C3
endoconformation and the guanine base is in the synconformation.
• The result of which places the guanine back over the sugar ring, which is unusual
than the B and A form.
• It is long and thin than the B and A forms.
• The helical width is 1.8 nm, being the smallest among the three forms.
• The distance between the base pairs is 0.37 nm. One turn of the helix contains 12
base pairs with a length of 4.56 nm.
• The major groove is flat and the minor groove is narrow and deep.
DNA Sense and Antisense Strands
I. Introduction to DNA Strand Polarity in Transcription
DNA is a double-stranded molecule composed of two antiparallel strands held together
by complementary base pairing. During transcription, only one of these strands is used as
a template to synthesize messenger RNA (mRNA). The choice of strand depends on the
direction of the gene and the action of RNA polymerase. These strands are termed:
1. Sense Strand (also called the Coding Strand)
2. Antisense Strand (also called the Template Strand)
Understanding the distinction between these strands is fundamental for interpreting
genetic sequences, predicting mRNA and protein products, and designing molecular
biology experiments.
II. Structural Features of DNA Relevant to Strand Designation
Double Helix: DNA consists of two polynucleotide chains coiled into a right-handed
helix.
Antiparallel Orientation: One strand runs in the 5′ → 3′ direction; the other runs 3′ → 5′.
Base Pairing: A pairs with T (via 2 H-bonds), and G pairs with C (via 3 H-bonds).
Sense Strand: 5′ — ATG CGT AAG TGA — 3′
Antisense Strand: 3′ — TAC GCA TTC ACT — 5′
III. Definition and Roles
1. Sense Strand (Coding Strand)
Definition: The DNA strand that has the same nucleotide sequence as the mRNA (with
the exception of thymine replaced by uracil in RNA).
Direction: Always written in the 5′ to 3′ direction.
Function:
• Acts as the reference strand when annotating genes.
• Not directly involved in the transcription process.
• Used in bioinformatics tools for gene prediction and annotation.
2. Antisense Strand (Template Strand)
Definition: The DNA strand that serves as a template for RNA polymerase to synthesize
mRNA.
Direction: RNA polymerase reads it in the 3′ to 5′ direction.
Function:
• Provides the complementary sequence to create a copy of the sense strand in RNA
form.
• Ensures that the genetic message is transcribed accurately.
• IV. Mechanism of Transcription Involving the Strands
• Step-by-Step Process
• Initiation:
• RNA polymerase binds to the promoter region on the antisense strand.
• The enzyme determines the transcription start site based on promoter motifs (e.g.,
TATA box).
Elongation:
• The enzyme moves along the antisense strand (3′ → 5′) and builds the mRNA
molecule in the 5′ → 3′ direction.
• Nucleotides are added using complementary base pairing: A with U, T with A, G
with C, C with G.
Termination:
• Transcription stops when a termination signal is encountered.
• The mRNA strand is released, complementary to the antisense strand and identical
to the sense strand (T → U).
Example:
Strand Type Nucleotide Sequence
Sense 5′– ATG CGC TTA – 3′
Antisense 3′– TAC GCG AAT – 5′
mRNA 5′– AUG CGC UUA – 3′ (same as sense,
T→U)
VI. Applications and Advanced Concepts
1. Antisense Technology in Therapeutics
Antisense Oligonucleotides (ASOs):
Short, synthetic strands of DNA designed to bind to mRNA via base pairing.
Can block translation, induce degradation of mRNA (via RNase H), or modify splicing.
Examples:
Spinraza (nusinersen) for Spinal Muscular Atrophy
Exondys 51 for Duchenne Muscular Dystrophy
2. Antisense RNA in Gene Regulation
Natural antisense transcripts (NATs):
Endogenous RNAs transcribed from the opposite DNA strand of a gene.
Play roles in epigenetic regulation, RNA interference, and post-transcriptional silencing.
3. Molecular Biology Tools
PCR Primer Design:
Forward primer matches sense strand.
Reverse primer complements the antisense strand.
Gene Cloning:
Inserts are often synthesized using the sense strand sequence.
RNAi & CRISPR:
Guide RNAs and siRNAs are designed to match or complement sense/antisense targets
depending on strategy.
4. Diagnostic and Research Use
Northern Blot: Uses antisense probes to detect mRNA.
Microarrays: Typically use complementary probes to sense strands.
In Situ Hybridization (ISH): Antisense probes hybridize with target mRNAs in tissues.
Types of DNA on the basis of location
1. Nuclear DNA
• As the name suggests, these DNAs are located inside the nucleus organized in the
chromosome.
• These chromosomes are 43 pairs in humans and are linear with open ends and
contain 3 billion nucleotides.
• Nuclear DNA houses genes that are transcribed into mRNA and ultimately
translated to proteins, that are necessary for the functioning and maintaining the
integrity of the cell.
• It is inherited from both parents, so this is diploid and considered unique to each
individual except for identical twins.
It is usually present in two copy numbers per cell
2. Mitochondrial DNA
• It is located inside the mitochondria.
• It is small and circular in structure
• It is inherited only from the mother, so is a haploid.
• It is present in a much higher copy number. i.e., 100-10,000 per cell.
• It has only 16,500 base pairs and encodes proteins that are specific for
mitochondria. These proteins are vital for producing energy.
• Mitochondrial DNA encoded proteins also play a pivotal role during intracellular
protein transport.
Functions of DNA (Deoxyribonucleic acid)
• DNA stores complete genetic information that requires to specify an organism.
• It is the source of information that is needed in order to synthesize cellular
proteins, and other macromolecules required by an organism.
• It is responsible for identifying and determining the individuality of the given
organism.
• It can also be taken as a targeted element during the diagnosis of a particular
disease.
• It can replicate to give rise to two daughter cells and transfer one copy to the
daughter cells during cell division. Thus, maintaining the genetic materials from
generation to generation.
