“Deoxyribonucleic acid, DNA is the genetic material of us, made up of the deoxy sugar, phosphate and nitrogenous bases.”
The life expectancy of every living entity on earth depends on the DNA, hence, it is as important as water and oxygen.
It is a blueprint of every organism that has all the information on it, in addition, it also transfers the information to consecutive generations.
By doing this DNA inherited the changes and traits from one generation to another for survival.
The structure and function of every biomolecule are encoded by the information present into the DNA.
By building functional proteins such as enzymes, receptors, chaperons and immunoglobulins different biological functions and reactions are regulated.
All the structural and functional proteins are formed only from the DNA (via mRNA intermediate), henceforth, the DNA is a basic unit of a living entity.
In the present articles we will talk only on DNA; its structure, function and location. Furthermore, We will give you some evidence that DNA is genetic material.
- Basic introduction of DNA
- Bonds in DNA
- Function of DNA
- How to write a sequence of DNA?
- Watson and Crick model of DNA
- Evidence: DNA is a genetic material
- Different types of DNA
- Different types of DNA based on their topology
- Different types of DNA based on their location
- How does DNA look?
Basic introduction of DNA:
The DNA is a type of nucleic acid.
A nucleic acid is an alkaline chemical present in a cell nucleus in the form of either ribonucleic acid or deoxyribonucleic acid.
Now let’s decode the terminologies,
The nucleic acid was first isolated by Friedrich Miescher in 1869 and named it as “nuclei”, although the name nucleic acid was given by Richard Altmann in 1889.
The DNA is a deoxyribonucleic acid while the RNA is ribonucleic acid. Both chemicals are information storage unit, DNA in all living organisms and RNA is some viruses.
Besides storing the information, both transfers the information too.
The nucleic acid is a long chain of a nucleotide called polynucleotides a class of biopolymer.
The phosphate or phosphoric acid present on the backbone of it gives it an acidic nature which is neutralized at pH 7.8 to 8.8.
The most abundant nucleic acid- DNA is present in all living organisms (except some viruses) ( it is also present outside the nucleus too, we will discuss it later).
The ribose, a pentose sugar is one of the primary units of the DNA.
Both types of nucleic acid viz DNA and RNA are made up of the pentose sugar. The DNA is made up of deoxyribose, 2’-deoxy D- ribose while the RNA is made up of ribose or D-ribose.
The ribose present in both the nucleic acid are pentose (having five-carbon) and in beta- furanose form ( in a cyclic manner).
The structure of the beta-furanose is given below,
The RNA contains Uracil instead of thymine but that cannot distinguish DNA from RNA.
Even if the DNA contains some uracil, 2’-deoxy D- ribose makes it DNA likewise even if thymine is present in RNA, D-ribose makes it RNA.
The identity of each nucleic acid is because of the difference in the pentose sugar. See the image below,
The backbone of the nucleic acid is made up of phosphate so often called triphosphate because it contains three phosphate molecules.
The monophosphate, diphosphate and triphosphate carry one, two and three phosphate units, respectively.
Four different nitrogenous bases are present on DNA; Adenine, Thymine, Cytosine and guanine. The Uracil is present in place of thymine in RNA.
The nitrogenous bases are classified into two broader groups:
Purines are pyrimidines.
The purines are adenine and Guanine while cytosine, thymine and Uracil are pyrimidines.
The purines and pyrimidines are the aromatic heterocyclic compounds that are weakly basic in nature.
At a neutral pH both are insoluble in water, at acidic pH the water-solubility of both increases. The purines are pyrimidines are hydrophobic in nature.
Do you know?
The thymine was first isolated from the tissues of the thymus that is why it is called it and the guanine from the guano bird manure.
Structurally, the pyrimidines are made up of the six-membered carbon-nitrogen-containing ring having two nitrogens while the purines are made up of Six-membered and a five membered-nitrogen containing carbon-nitrogen ring with four nitrogen atoms.
- Guanine: 2-amino-6-oxy purine
- Adenine: 6-amino purine
- Thymine: 2,4-dioxy-5-methyl pyrimidine
- Uracil: 2,4-dioxy pyrimidine
- Cytosine: 2-oxy-4-amino pyrimidine
Other than this xanthine and hypoxanthine are two purines and Orotic acid- pyrimidines are also present in nature but not found in DNA or RNA.
A structure having a pentose sugar, a nitrogen-containing base (nitrogenous base) and phosphate is called a nucleotide.
The nucleotide is a structural building block of the DNA. Each nucleotide joint with the nucleotide of another strand with the hydrogen bond and other adjacent nucleotides with the phosphodiester bond.
See the structure below,
By bonding with the hydrogen bonds and phosphodiester bonds, the nucleotides create a helical structure of DNA.
A nucleotide without phosphate is called a nucleoside (deoxyribonucleoside).
The DNA is named deoxyribonucleotide triphosphate because of the presence of three phosphates.
If only single phosphate is present, it is called a deoxyribonucleotide monophosphate, similarly, if two phosphates are present, it is called deoxyribonucleotide diphosphate.
Some methylated nucleotides are also found in nature that helps activate and deactivate the gene expression and protecting genetic information.
Bonds in DNA:
Between the nitrogenous bases of the two strand of DNA, a hydrogen bond occurred.
Like the more electronegative atoms such as nitrogen and oxygen, a weak chemical bond occurred called a hydrogen bond.
The hydrogen bond is actually a temporary bond that stabilizes the DNA and occurred only at the shorter distance.
It can easily break using some of the chemical treatment and heating.
Three weak hydrogen bond between Guanine and cytosine and two weak hydrogen bond between adenine and thymine joined two strands of DNA.
As per the Watson and Crick model, the DNA double helix follows the rules of chargeoff. The number of G and A are equal to the numbers of C and T, respectively into the DNA.
The hydrogen bonds are the key factors in the polymerase chain reaction. As the numbers of hydrogen bond increases, the denaturation temperature further increases.
Furthermore, the higher the total GC content higher the denaturation time and temperature required in the PCR.
In general, 95°C temperature and 5 minutes of denaturation are capable to break all the hydrogen bonds between double-stranded DNA.
Read more on PCR here: The polymerase chain reaction
DNA absorbs UV light with the wavelength of 260nm. A single-stranded DNA absorb more UV light than the double-stranded DNA.
Further to this, a weak Van der Waals forces, Base-stacking interactions and weel hydrophobic effect also occur between the bases that help to stabilize the DNA.
A phosphodiester bond occurs between the 3’ carbon of the one deoxyribose sugar and 5’ carbon of second deoxyribose.
The phosphodiester bond creates the backbone of a DNA.
Once the pyrophosphate is released, the phosphodiester bond forms between the adjacent nucleotides.
The 5’ or 3’ position without the nucleotide is define as an “end” of the DNA. One end of the single strand of DNA containing 3’ and 5’ ends.
“In the nucleic acid (DNA/RNA) all the phosphodiester bonds are in the same orientation along the chain.”
Another important bond besides the phosphodiester bond and hydrogen bond is the glycosidic bond. The glycosidic bond occurred between the pentose sugar and a base.
All the bonds together form a stable, more electronegative, double helical DNA structure.
Function of DNA:
Storing and inheriting information in the consecutive generations is the main function of a DNA molecule.
But how does it happen?
The DNA forms a long chain of amino acid and hence by doing this, it creates different types of protein for different function and structural support.
Three major events happened to do so; replication, transcription and translation.
The replication is a process in which a DNA molecule becomes doubled through the enzymatic reactions.
Briefly, the helicase unwinds the dsDNA, the primase settled RNA primer on the leading strand and a polymerase synthesise a new DNA from it.
From the replicated DNA, a messenger RNA is generated in the process called transcription. The RNA polymerase synthesises an mRNA molecule from the single-stranded DNA and stores all the information for a gene to expression.
Once the mRNA is synthesised, it came out from the nucleus for the process of translation.
In the cytoplasm, using the rRNA and tRNA molecule, an mRNA synthesise a long chain of amino acids.
This will form a specific protein molecule specific to that particular gene.
The DNA does not play a structural role in the cell, as like other molecules.
How to write a sequence of DNA?
This section is something very interesting, you will not get information like this in any other article on the web.
See the figure carefully,
The above figure shows that the DNA molecule shown in the figure is a pentadeoxyribonucleotide and denoted as pT-G-C-T-AOH.
Now let us understand how it has done.
Each deoxyribose is shown by the vertical lines. The top of the line is carbon C1 having a single base on it and the bottom of the carbon is C5 carbon.
P is the symbol used to show the phosphate and each nitrogenous base is denoted as their respective symbols (viz A, T, C and G).
The line passes through the phosphate joined at the bottom is a 5’ end of one sugar and at the middle is a 3’ end of another sugar.
From the above explanation, we can write a DNA molecule as
5’-pT-G-C-T-AOH or pTpGpCpTpAOH
The left end of the DNA is always 5’ and the right end of the DNA is always 3’ in a single-stranded DNA, therefore, it is written as 5’ to 3’.
If the DNA contains six nucleotides it is called as hexadeoxyribonucleotide and so on.
However, in general, up to 50 nucleotides are called as oligonucleotides and more than that are called as polynucleotides.
Before understanding the structure of the DNA, we have to first understand the actual model of DNA structure proposed by Watson and Crick and for doing this we have to collect some of the evidence of DNA.
Watson and Crick model of DNA:
Discovery and evidence of double helix and the actual structure of DNA proposed by Watson and Crick. Their findings were based on previous discoveries. Some of the evidence of it is given below,
Evidence: DNA is the genetic material
The DNA was first isolated by Friedrich Miescher in the year 1868, he called it nuclein.
He said, “a phosphorus-containing substance is present in the cell that is responsible for the inheritance.”
Griffith’s transformation experiment was one of the first evidence of DNA as genetic material.
In the year, 1928, He experimented on mice by infected it with the Streptococcus pneumoniae.
He chose a virulent strain (named it as S) and a non-virulent strain ( named it as R).
(S was for the smooth colony and R was for the rough colony).
When he injected heat-killed virulent cells into the mice, the mice survived.
When he injected a combination of virulent, non-virulent and heat-killed cells in the mice, all the mice died.
From his experiment, he finally concluded that the heat-killed S cells converted the live R strain into the live S strain (virulent strain).
He named it as a process of transformation of genetic material.
See the figure below,
Later on in the year 1940, an experiment conducted by Oswald T. Avery, C. MacLeod and M. McCarty concluded that the DNA was the genetic material.
They had experimented on Streptococcus pneumoniae.
When Avery and coworkers injected into the non-disease causing non-virulent strain from the disease-causing virulent strain, the nonvirulent strains converted into the virulent one.
Their evidence suggests that it was the DNA of a virulent strain that involved in the conversion.
Although, at this point in history, the structure of a DNA is still not discovered.
The scientist was divided into two groups, some believe that protein, not DNA is a genetic material and some believed that it was a DNA nothing else.
However, in the year, 1952, A. Hershey and M. Chase ended all the confusion by experimenting on bacteriophage and concluded strongly that only DNA is a genetic material present in the living entity.
Phosphorus is found in DNA and not in protein while the sulphur is found in protein and not in DNA.
They had incorporated radioisotope of phosphorus (32P) into the phage DNA and sulfur (35S) into the protein of the separated phage particles and infected E.Coli cells with it.
After infection, they had examined that, radioactivity was reported in the E. coli cells infected with the 32P labelled phase.
Whereas radioactivity was not reported in the 35S infected cells.
The evidence clearly indicated that the phage having the DNA (labelled with 32P) infected the cells and entered into the host cell.
Conclusively, they had stated that the DNA is the hereditary material, not the protein. The protein is only a structural unit of the phage.
See the figure below,
Another important evidence was given by Erwin Chargaff and coworker in the year 1940.
The major highlight of their finding was that the number of Adenine is equal to the number of thymine and the number of guanines is equal to the number of cytosines.
Some other findings of their works are enlisted below,
- The overall base composition of an organism is invariant. It can not be changed by changing environmental conditions, age or nutrition.
- The base composition of one species is different from another species.
- The base composition is the same in all the tissues of an organism.
- Also, the total sum of the purines is equal to the total sum of pyrimidines (A + G = T + C).
The above quantitative analysis is also called as the “Chargaff’s rule.”
Chargaff’s rule: The number of adenine is always equal to the number of thymine and the number of cytosines are always equal to the number of guanines and the sum of the total purines are equal to the sum of the total pyrimidines.
One of the most important evidence of the DNA was given by Rosalind Franklin and Raymond Gosling.
In May 1992, (a year before the discovery of the Watson and Crick DNA model), R. Franklin proposed for the first time in the history of genetics, a model of DNA through the X diffraction method.
They had concluded that the bases in the DNA are paired.
Based on all the previous discoveries in the year 1953, James Watson and Francis Crick discovered the structure of DNA and the glims of their discovery are given below,
Watson and Crick model of DNA:
In April 1953, Watson and Crick published a paper on the three-dimensional structure of DNA.
A DNA is a helical structure in which the two helices twisted around each other on the same axis and are right-handed.
The 3’ end of the DNA has the hydroxyl group while the 5’ end of it has the phosphate group.
Both strands are anti-parallel to each other in which the 5′ end of one strand faces the 3’ end of another strand and vice verse.
The nitrogenous bases (purines as well as pyrimidines) are stacked inside the helix whereas the sugar-phosphate creates the backbone of it, situated on the backside of the DNA.
The backbone is hydrophilic while the bases are hydrophobic and the rings of the bases are perpendicular to the long axis.
Chargaff’s rule is strictly followed in the double helix which creates a major groove and minor groove in the dsDNA.
When the backbones are far apart from each other it creates the major groove. When the backbones are close to each other it creates the minor groove.
The major groove is very wide and deep while the minor groove is shallow.
DNA binding proteins and other regulatory proteins will bind to the major and minor groove for performing the replication and transcription.
General four proteins can bind into the major groove and less than four can bind to the minor groove.
Three hydrogen bonds between G and C and two hydrogen bonds between A and T are stabilized the DNA.
Both strands are complementary to each other which means that, whenever a cytosine is present on one strand, guanine must present on the opposite strand.
Also, their findings favour the replication model. The complementary strands can separate from each other and able to synthesize a new daughter strand from it.
Summary of the findings,
- The diameter of DNA: 20Å
- Base pair per helix turn: 10.5bp
- Distance between the adjacent bases: 3.4Å
- The length of the complex helix turn: 34Å
Read more on different types of PCR:
- Real-time PCR: Principle, Procedure, Advantages, Limitations and Applications
- Reverse transcription PCR: Principle, Procedure, Applications, Advantages and Disadvantages
- Inverse PCR: Principle, Procedure, Protocol and Applications
Different types of DNA:
The Watson and Crick model of DNA is a B form DNA which is most prevalent in nature, However, other forms of DNA are also present in nature.
A form of DNA, Z form DNA and C form DNA are also found in nature.
B form DNA:
In any physiological conditions, the B-DNA is more stable than any other forms of DNA. It is the standard form of DNA present in almost all living organisms on earth. In the B-DNA, 10.5 bp per helix tern are present.
A form of DNA:
The form DNA is also arranged right-handed but the helix is wider than the B form DNA.
Also, the number of bases per helical turns are 11 instead of 10.5.
With respect to the axis of the helix, it is tilted 20°.
The base pairing in this form of DNA is not the same as the B form DNA, here the base pairing is not perpendicular to the axis of the helix.
Under the dehydration condition, the DNA is driven into the A form which protects it from the extreme environmental conditions.
Z form DNA:
The rotation of the Z form DNA is left-handed, contains 12 bases per helical turn hence it is wider in length than the B form DNA.
The zigzag type backbone of it gives it elongated and slender appearance.
In the Z form DNA, the purine bases of it switch into the “syn” form conformation which converts the DNA into the left-handed helix.
Notably, the minor groove of the Z form DNA is different, it is deep and narrow as compared to other forms of DNA.
Some short stretches of the Z-DNA are present into the genome of the prokaryotes as well as eukaryotes and it is believed that Z-DNA helps in the recombination and gene expression of several genes, however, it is not proven yet.
The summary of all three forms of DNA is given into the table below,
One other type of DNA form is also present in nature called the C-DNA. It is the combination of many possible double helical structures that can be observed in some conditions such as in the presence of ions like Mg2+.
Different types of DNA based on their topology
Based on the topology of the DNA, three different forms of DNA are present in nature viz the circular DNA, linear DNA and supercoiled DNA.
In the circular DNA, both ends of the dsDNA are joined having a closed loop and no ends.
The circular DNA does not contain any supercoiling (without any twists or writes).
The circular DNA is prevalently present in the prokaryotes as a plasmid.
Also, some of the eukaryotic organelles such as mitochondria and chloroplast contains circular DNA.
When the virus entered inside the nucleus of the host cell, it converted into the special type of circular form called covalently closed circular DNA (cccDNA).
The ends of the linear DNA are free. Some of the short and free DNA fragments present in the cell are in the form of linear DNA.
Some prokaryotes also contain linear DNA.
When the long chain of DNA twist around each other, it creates a complex form of the DNA called supercoiled DNA.
The supercoiled form of DNA is more prevalently found in the eukaryotic genome which helps the long DNA to fit inside the cell nucleus.
Also, the supercoiling helps DNA to arrange it on the chromosome by interacting it with some of the proteins.
The supercoiled form of DNA is the most compact forms of it hence it migrates faster during agarose gel electrophoresis.
Contrary, the circular DNA migrates slower.
Different types of DNA based on their location:
Based on where the DNA is located, two major types of DNA are present in all organisms:
Nuclear DNA and cytoplasmic DNA.
Majority of the total DNA is present inside the nucleus of the cell in all eukaryotes. The nuclear DNA contains all the necessary genes. The total nuclear DNA is located on the metaphase chromosomes.
During the cell division, it divides and inherits to the daughter cell.
Som amount of DNA is also present in the cytoplasm of the cell but only in the membrane bounded-organelles.
The membrane-bound organelles such as mitochondria and chloroplasts contain their own DNA abbreviated as mtDNA and cpDNA respectively.
Both have dedicated machinery for their replication and gene expression.
It is believed that the mitochondria and chloroplasts are the free-living prokaryotes in past.
Cytoplasmic DNA further contains some of the important genes, a mutation in those genes leads to severe lethal conditions.
How does DNA look?
By joining with the hydrogen bonding two single-stranded DNA molecules make a DNA double helix.
DNA under the microscope:
A DNA is a helical structure right!
People think that it looks like the spiral helix, but it is not so.
It helical structure is a hypothetical assumption of it which is proven by the x-ray diffraction image.
Even in the electron microscope you can not able to see it in the spiral form, only a threadlike structure is visible under the microscope.
DNA inside the tube:
DNA is soluble in water and TE buffer, therefore when we extract it, it dissolves in the solution of TE buffer and looks like water, even in this case you can see the spiral helix structure.
DNA can be visualized only by precipitated it. Using the ethanol and salt, DNA can be precipitated into the solid, cotton thread like whitish structure.
This can be visualized by the naked eye but still, you can not see the helical structure.
Under the gel:
Under the gel, a bright and straight bands DNA observed under the UV light.
The bands are sharp and light pink in colour due to the intercalation of EtBr.
- Gene Therapy: Types, Vectors [Viral and Non-Viral], Process, Applications and Limitations
- Transposons: A Jumping Entity and a Foe with Benefits
DNA is genetic material of all, made up of nitrogenous bases, phosphate and sugar. It inherits characters from one generation to another.
Mutation in any of the functional gene leads to abnormality in an organism. Some of the common mutagenic agents are chemicals, environment, UV light and adverse conditions.