DNA- Structure, Properties, Types, Forms, Functions

DNA stands for deoxyribonucleic acid, a complex molecule that contains all of the information necessary to build and maintain an organism. DNA is found in all living things, from bacteria and fungi to plants and animals. DNA is located inside the cells of these organisms, usually in a structure called the nucleus.

DNA is composed of two strands of nucleotides that coil around each other to form a double helix. Nucleotides are the building blocks of DNA, and each one consists of three parts: a sugar (deoxyribose), a phosphate group, and a nitrogenous base. There are four types of nitrogenous bases in DNA: adenine (A), thymine (T), guanine (G), and cytosine (C). These bases pair up in a specific way: A with T, and G with C, forming the rungs of the DNA ladder.

The sequence of bases along the DNA strands determines the genetic code, which is the instructions for making proteins. Proteins are essential for the structure and function of all living cells. The genetic code is read by a process called transcription, which produces a messenger RNA (mRNA) molecule that carries the information to the ribosomes, where translation occurs. Translation is the process of assembling amino acids into proteins according to the mRNA sequence.

DNA is also the primary unit of heredity in organisms. This means that DNA is passed down from parents to offspring through reproduction. In sexual reproduction, each parent contributes half of their DNA to their offspring, creating a unique combination of genes. In asexual reproduction, an organism copies its own DNA and produces identical offspring. The transmission of DNA ensures that some traits are inherited from one generation to the next, while also allowing for variation and diversity among living things.

DNA is a remarkable molecule that stores, transmits, and expresses genetic information in all living organisms. It is the basis of life as we know it, and it has been studied extensively by scientists for decades. In this article, we will explore the structure, properties, types, forms, and functions of DNA in more detail.

The structure of DNA was one of the most important scientific discoveries of the 20th century. It revealed how genetic information is stored and transmitted in living organisms, and opened up new possibilities for understanding and manipulating life. The discovery was the result of a collaborative effort by several researchers, who used different methods and approaches to unravel the mystery of DNA.

One of the pioneers of DNA research was Erwin Chargaff, an Austrian biochemist who analyzed the composition of DNA from different sources. He found that the amount of adenine (A) always matched the amount of thymine (T), and the amount of guanine (G) always matched the amount of cytosine (C). This suggested that A and T, and G and C, were somehow paired in DNA.

Another key contributor was Rosalind Franklin, a British biophysicist who used X-ray diffraction to study the structure of DNA. She produced high-quality images of DNA fibers that showed a regular pattern of dark and light bands. She also calculated the dimensions of the DNA molecule and concluded that it had a helical shape.

James Watson and Francis Crick were two young scientists who were interested in finding a model for the structure of DNA. They were inspired by Franklin`s images and Chargaff`s rules, as well as by earlier work by Linus Pauling on protein structures. They used cardboard cutouts of the bases and metal rods to make models of DNA, trying to fit them into the X-ray data. They also consulted with Maurice Wilkins, who was Franklin`s colleague and had access to her unpublished results.

In February 1953, Watson and Crick came up with their famous model of the DNA double helix. They proposed that DNA was made of two strands that ran in opposite directions and were held together by hydrogen bonds between complementary bases: A with T, and G with C. They also suggested that the two strands could separate and serve as templates for copying themselves, thus explaining how genetic information is replicated.

Watson and Crick published their model in the journal Nature in April 1953, along with two papers by Franklin and Wilkins that provided experimental evidence for their structure. Their paper was only one page long, but it had a profound impact on biology and medicine. It was the beginning of a new era of molecular biology, which would reveal how genes control the functions of cells and organisms.

DNA is a double-stranded helix. That is, each DNA molecule is comprised of two biopolymer strands coiling around each other to form a double helix structure. These two DNA strands are called polynucleotides, as they are made of simpler monomer units called nucleotides.

Each strand has a 5′ end (with a phosphate group) and a 3′ end (with a hydroxyl group). The strands are antiparallel, meaning that one strand runs in a 5′ to 3′ direction, while the other strand runs in a 3′ to 5′ direction. The two strands are held together by hydrogen bonds and are complementary to each other.

Basically, the DNA is composed of deoxyribonucleotides. The deoxyribonucleotides are linked together by 3′ – 5′ phosphodiester bonds. The nitrogenous bases that compose the deoxyribonucleotides include adenine, cytosine, thymine, and guanine. The complementarity of the strands is due to the nature of the nitrogenous bases. The base adenine always interacts with a thymine (A-T) on the opposite strand via two hydrogen bonds and cytosine always interacts with guanine (C-G) via three hydrogen bonds on the opposite strand.

The shape of the helix is stabilized by hydrogen bonding and hydrophobic interactions between bases. The diameter of double helix is 2nm and the double helical structure repeats at an interval of 3.4nm which corresponds to ten base pairs.

The structure of DNA can be visualized as follows:

5` P-ATGCATGCATGCATGCATGC-3`
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3` OH-TACGTACGTACGTACGTA-P 5`

The P represents the phosphate group, the OH represents the hydroxyl group, and the letters represent the nitrogenous bases. The vertical lines represent the hydrogen bonds between complementary bases.

The structure of DNA was first discovered by James Watson and Francis Crick in 1953, based on the experimental data of Rosalind Franklin and Maurice Wilkins. Their discovery was a landmark achievement in the field of molecular biology and genetics. It revealed how DNA stores and transmits genetic information from one generation to the next. It also paved the way for further studies on the function and regulation of genes and proteins.

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.

The major groove provides more information about the base sequence than the minor groove, because it has more space and more distinctive features. For example, in the major groove, adenine and thymine have one hydrogen bond donor and one hydrogen bond acceptor, while guanine and cytosine have two of each. In contrast, in the minor groove, all four bases have one hydrogen bond donor and one hydrogen bond acceptor.

The major groove also has different patterns of methyl and amino groups that can be distinguished by proteins. For example, adenine has a methyl group on its N6 position, thymine has a methyl group on its C5 position, guanine has an amino group on its N2 position, and cytosine has an amino group on its N4 position. These groups can interact with different amino acids in proteins and affect their binding affinity and specificity.

The minor groove, on the other hand, has less variation and less space for protein interactions. Therefore, proteins that bind to the minor groove usually rely on indirect recognition mechanisms, such as bending or twisting the DNA, or interacting with other proteins that bind to the major groove.

The major and minor grooves of DNA are important for regulating gene expression, DNA replication, DNA repair, and DNA recombination. Different proteins can bind to different grooves and modulate these processes in different ways. For example, transcription factors can bind to the major groove and activate or repress gene expression by interacting with RNA polymerase. Helicases can bind to the minor groove and unwind the DNA strands for replication or repair. Recombinases can bind to both grooves and mediate homologous recombination between DNA molecules.

The major and minor grooves of DNA are also important for understanding how drugs can interact with DNA and affect its function. Some drugs can bind to specific grooves and alter the structure or activity of DNA or its associated proteins. For example, some antibiotics can bind to the minor groove and inhibit bacterial DNA replication. Some anticancer drugs can bind to the major groove and interfere with DNA transcription or repair.

The major and minor grooves of DNA are essential features of its structure and function. They provide information about the base sequence and allow proteins to recognize and regulate DNA in various ways. They also offer potential targets for drug design and therapy.

DNA has several physical and chemical properties that are important for its function and stability. Some of these properties are:

• Solubility: DNA is polar in nature and thus soluble in water. Its highly charged phosphate-sugar backbone gives it its polarity. DNA is also soluble in some organic solvents, such as ethanol and isopropanol, which are used to precipitate DNA from aqueous solutions.
• Absorption: DNA bases can absorb ultraviolet (UV) light most strongly at wavelengths of 254 to 260 nm due to the interaction between UV light and the ring systems of the purines and pyrimidines . This absorption can be measured by a spectrophotometer and used to estimate the concentration and purity of DNA samples.
• Denaturation and renaturation: On heating, the hydrogen bonds between the complementary base pairs of DNA break, causing the two strands to separate. This process is called denaturation or melting of DNA. The temperature at which the two strands separate completely is known as the melting temperature (Tm), which depends on the base composition, length, and salt concentration of the DNA . Higher GC content and longer DNA strands increase the Tm, while higher salt concentration decreases it. On cooling, the separated strands can reassociate or renature by forming hydrogen bonds again. This process is also called annealing or hybridization of DNA.
• Supercoiling: DNA can coil upon itself to form more compact structures called supercoils. Supercoiling can be either positive or negative, depending on the direction of the twist. Negative supercoiling, which is more common in nature, occurs when DNA is twisted in the opposite direction of its helical structure. Positive supercoiling occurs when DNA is twisted in the same direction as its helix . Supercoiling affects the accessibility and function of DNA, as it influences the binding of proteins and enzymes to the DNA.
• Mutation: DNA can undergo changes in its sequence due to errors in replication, recombination, or exposure to mutagens (such as chemicals, radiation, or viruses). These changes are called mutations and can have various effects on the phenotype and fitness of the organism. Some mutations are beneficial, some are neutral, and some are deleterious . The rate of mutation varies depending on the type of DNA (nuclear or mitochondrial), the region of DNA (coding or non-coding), and the species of organism. Mutation is one of the sources of genetic variation and evolution.

Eukaryotic organisms such as animals, plants and fungi, store the majority of their DNA inside the cell nucleus and some of their DNA in organelles such as mitochondria. Based on the location, DNA may be classified into two types: nuclear DNA and mitochondrial DNA.

Nuclear DNA

Nuclear DNA is the DNA that is located within the nucleus of eukaryotic cells. It is usually present in two copies per cell, one inherited from each parent. The structure of nuclear DNA chromosomes is linear with open ends and includes 46 chromosomes containing 3 billion nucleotides in humans. Nuclear DNA is diploid, meaning that it has two sets of chromosomes, one from each parent. Nuclear DNA encodes for most of the genes that determine the traits and functions of an organism. The mutation rate for nuclear DNA is less than 0.3%, which means that it is relatively stable and does not change much over time.

Mitochondrial DNA

Mitochondrial DNA is the DNA that is located in the mitochondria, which are organelles that produce energy for the cell. It is usually present in 100-1,000 copies per cell, depending on the energy demand of the cell. Mitochondrial DNA chromosomes usually have closed, circular structures, and contain for example 16,569 nucleotides in humans. Mitochondrial DNA is haploid, meaning that it has only one set of chromosomes, which is inherited only from the mother. Mitochondrial DNA encodes for some of the genes that are involved in oxidative phosphorylation, which is the process of generating energy from oxygen and nutrients. The mutation rate for mitochondrial DNA is generally higher than nuclear DNA, which means that it changes more frequently over time.

Nuclear DNA and mitochondrial DNA have different roles and characteristics in eukaryotic cells. They also have different origins and evolutionary histories. Nuclear DNA is derived from both parents and reflects the genetic diversity of the population. Mitochondrial DNA is derived only from the mother and reflects the maternal lineage of an individual. By comparing the sequences of nuclear DNA and mitochondrial DNA, scientists can learn more about the ancestry, evolution and health of living organisms.

DNA can adopt different forms depending on the environmental conditions, such as temperature, humidity, salt concentration, and pH. These forms differ in their helical structure, base pairing, and groove dimensions. The most common form of DNA in living cells is B-DNA, which has a right-handed helix with about 10.5 base pairs per turn. However, other forms of DNA have been discovered and characterized by various methods, such as X-ray crystallography and nuclear magnetic resonance (NMR). Some of these forms are:

• A-DNA: This form of DNA is also right-handed, but it has a shorter and wider helix than B-DNA, with about 11 base pairs per turn. It occurs when DNA is dehydrated or in the presence of high salt concentrations. A-DNA is also found in some RNA-DNA hybrids and in some DNA-protein complexes.
• Z-DNA: This form of DNA is left-handed, meaning that it twists in the opposite direction of B-DNA and A-DNA. It has a zig-zag shape and 12 base pairs per turn. It occurs when DNA has alternating purine and pyrimidine bases, such as CGCGCG or ATATAT. Z-DNA can also be induced by negative supercoiling or by some proteins that bind to specific sequences. Z-DNA may play a role in gene regulation, recombination, and immune response.
• C-DNA: This form of DNA is also right-handed, but it has a longer and narrower helix than B-DNA, with about 9.3 base pairs per turn. It occurs when DNA is in the presence of lithium or magnesium ions and at low humidity. C-DNA is similar to A-DNA, but it has a more compact structure and a deeper major groove.
• D-DNA: This form of DNA is rare and has not been observed in vivo. It is right-handed and has 8 base pairs per turn. It occurs when DNA lacks guanine bases, such as poly(A) or poly(T) sequences. D-DNA has a very narrow minor groove and a very wide major groove.
• E-DNA: This form of DNA is also rare and has not been observed in vivo. It is right-handed and has 10 base pairs per turn. It occurs when DNA has an eccentric base stacking, meaning that the bases are not aligned along the helical axis. E-DNA has a very wide minor groove and a very narrow major groove.

These forms of DNA illustrate the structural diversity and adaptability of the genetic material. They may have different biological functions and interactions with other molecules, such as proteins and RNA. Understanding the forms of DNA can help us better appreciate the complexity and versatility of life.

DNA is the information molecule that stores the instructions for making other large molecules, called proteins. These instructions are stored inside each of your cells, distributed among 46 long structures called chromosomes. These chromosomes are made up of thousands of shorter segments of DNA, called genes. Each gene contains the directions for making protein fragments, whole proteins, or multiple specific proteins.

DNA has a crucial role as genetic material in most living organisms. It carries genetic information from cell to cell and from generation to generation. Thus its major functions include:

• Storing genetic information: DNA is a stable molecule that can hold complex information for longer periods of time. The sequence of bases along the DNA molecule encodes for the sequence of amino acids in every protein in all organisms.
• Directing protein synthesis: DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies. This process involves two steps: transcription and translation. Transcription is the copying of a DNA segment into a messenger RNA (mRNA) molecule, which carries the information to the ribosomes. Translation is the decoding of the mRNA sequence into a chain of amino acids, which forms a protein.
• Determining genetic coding: DNA determines the traits and characteristics of an organism by controlling the expression of genes. Gene expression is the process by which the information in a gene is used to make a functional product, such as a protein or a non-coding RNA. Gene expression can be regulated by various factors, such as environmental signals, developmental cues, and epigenetic modifications.
• Directly responsible for metabolic activities, evolution, heredity, and differentiation: DNA is involved in various biological processes that affect the metabolism, adaptation, inheritance, and development of an organism. For example, DNA is responsible for catalyzing some biochemical reactions through enzymes, which are proteins that speed up chemical reactions. DNA is also responsible for generating genetic variation through mutations, which are changes in the DNA sequence that can affect the function or expression of genes. DNA is also responsible for passing on genetic information to offspring through sexual or asexual reproduction, which ensures the continuity of life. DNA is also responsible for directing the differentiation of cells into specialized types and functions during embryonic development and throughout life.

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