1. INTRODUCTION:

DNA is now the predominant genetic material in the living world. But which properties of this long polymer favour this ubiquity? Why DNA and not, say, the structurally very similar double-stranded RNA? Just over 60 years ago Watson and Crick published their classic paperon the structure of DNA. In it, they emphasized two principal features of the molecule the complementarity of the base sequences on the two strands and the double-helical nature of the polymer. The base sequence complementarity, with adenine complementary to thymine and guanine complementary to cytosine, provided an elegant molecular expla- nation for the discovery in the previously decade by Avery, McCarty and Macleod that DNA was likely the ‘transforming principle’ that enabled the transfer of genetic information between different strains of bacteria. More, it confirmed Chargaff’s fundamental discovery of the equivalence of A and T and of G and C bases in double-stranded DNA.

Most impor- tantly, the structure implied that the information in the DNA base sequence could possess, by virtue of the complementarity, the ability to be replicated into two identical copies. This insight into the fundamental basis of genetics has underpinned the immense advances in genetic understanding and manipulation over the last 60 years. Today, however, the feature of DNA that defines the molecule is the fact that the two strands are entwined as a right-handed double helix. DNA is ‘the double helix’. Although this double-helical charac- ter is not required by the complementarity per sea simple straight ladder structure would fulfil this function just as well – it does impart crucial physical and chemical properties to the polymer. It is these properties that play a major role in the biological function of DNA. The genetic functions of DNA can thus be understood as the synergism of two properties a tape containing the information store encoding the sequences of proteins and RNA molecules and a poly- mer existing as double-helical string enabling the pack- aging, accessibility and replication of the information store. Crucially, both the coding of proteins and RNA molecules and also the physicochemical properties of the polymer are specified by the base sequence.

2. Physical and Chemical Properties of DNA:

Two helical strands that are wound around the same axis make up DNA. DNA helices are classified as either right-handed or left-handed depending on the direction they are wound. However, right-handed helices DNA is the most stable and benchmark structure. The two helical chains are in opposition to one another. As a result, one strand extends from 5′ to 3′ and the other from 3′ to 5′. The strands are made of four types of nitrogenous bases (A, T, C, and G). These nitrogenous bases serve as genetic information stores and, as a result, encode the amino acids that form proteins.¹

2.1 Solubility:

DNA is polar in nature and thus soluble in water. Its highly charged phosphate-sugar backbone gives it its polarity. However, in the presence of salt and alcohol, it is insoluble.

2.2 Absorption:

At 260 nanometers, the DNA bases can absorb ultraviolet light. A spectrophotometer can measure this absorption. The amount of ultraviolet light absorbed increases with the order of the bases. For example, at 260nm, a single-stranded DNA absorbs 1.37 units, whereas a double-stranded DNA absorbs 1.00 unit at 260 nm.²

2.3 Denaturation and Renaturation:

On heating, both strands denature, and on cooling, they can renature. The melting temperature, which varies depending on the precise DNA sequence, is the temperature at which these strands are permanently separable.In contrast to the region of higher concentration A-T, which is only bonded with two hydrogen bonds, the region of higher concentration of C-G has a higher melting temperature because these bases are bonded with three hydrogen bonds, which require more energy to break.³

3. DNA as an information store:

What is the nature of the genetic information stored in DNA? The distinction between a linear code responsible for specifying the sequences of RNA and protein molecules and also sequence-specific recognition by DNA-binding proteins, and an equally important more continuous structural code, specifying the configuration and dynamics of the polymer extends the informa- tional repertoire of the molecule. Both these DNA information types are intrinsically coupled in the primary sequence organization, but whereas the linear code is, to a first approximation, a direct digital read- out⁴, the structural code is determined not by individual base pairs, but by the additive interactions of successive base steps. The latter code, being locally more continuous, thus has an analogue form.⁵ Importantly, the manifestation of analogue properties is dependent on the length of the DNA sequence. For example, under physiological conditions, DNA unwinding manifested as melting may be restricted to a short sequence (say up to ~ 10 bp), whereas unwind ing in the form of a coiled helical axis may affect hundreds of base pairs. Direct and indirect readout of DNA-recognition sites by proteins is a major determinant of binding selectivity. In direct readout, the individual bases in a binding sequence make direct and specific contacts to the protein surface, whereas in indirect readout, the binding affinity depends on recognition of a structure, such as a DNA bend or bubble, whose formation is influenced by DNA sequence, but does not in general require a protein contacting a specific base.⁶In practice, DNA recognition by proteins effectively spans a continuum from completely digital to completely analogue with many proteins utilizing both modes. For both modes of recognition, the DNA double helix differs from, and is arguably more effective than, the RNA double helix.⁷ Direct readout requires intimate contact between exposed chemical groups on both the protein and nucleic acid surfaces. For DNA recognition, direct readout in most examples takes the form of a DNA-binding motif being inserted into the major groove. In this groove, different exocyclic groups of the bases in a pair are exposed compared with those in the minor groove. Consequently, although A–T and T–A base pairs in a sequence are distinguishable by the position of the thymine methyl group charge pattern in the major groove, in the minor groove, the exposed charge patterns of T–A and A–T base pairs are identical. Similarly, the charge pat- terns of C–G and G–C base pairs in the major groove are distinguishable by the relative position of the 4- amino group of cytosine.⁸ Again, however, there is little difference in the relative spatial arrangements of the charge patterns of C–G and G–C base pairs in the minor groove. The major groove thus provides more sequence information than the minor groove.⁹

Fig. 1. Exposure of chemical groups of nucleotide bases in the major and minor grooves of DNA.

How ever, importantly, the wide and shallow morphology of the DNA major groove is in stark contrast to the narrow and deep structure of the RNA major groove. This pattern is reversed for the minor groove. For a protein DNA-binding motif, particularly one containing an a-helix, access to the DNA major groove is more facile than to the minor groove. This fundamental difference between DNA and RNA follows directly from their chemical structures. Whereas DNA can adopt (at least) two forms of right-handed double-heli- cal structures, A-DNA and B-DNA, RNA can only form an A-type double helix because of the steric restrictions imposed by the 2⁰ hydroxyl residue on ribose.¹⁰The B-DNA structure, that proposed by Watson and Crick is most stable at high humid- ity, but converts to the A-form as the water activity is lowered. On this argument, it is the ability to adopt the B-form that facilitates direct access to DNA sequence information. Not only does the A ? B transition affect direct readout, it also changes the physicochemical proper- ties of the polymer. An A-type double helix is, on average, stiffer than a B-type double helix and consequently distortion of A-DNA to a particular bent configuration is energetically less favourable than for the corresponding distortion in B-DNA.¹¹Such differences would be expected to favour B-DNA as the preferred substrate for packaging involving tight DNA bending. Although the formation of a B-type structure is a crucial aspect of DNA functionality the factors which shift the A M B equilibrium are, apart from water activity, poorly understood. One aspect is base-type. In principle, the coding capacity of DNA can be achieved not only by the canonical A–T and G–C base pairs, but also by other possibilities. For example, a DNA polymer with diaminopurine–thymine (DAP–T) and hypoxanthine-cytosine (H–C) base pairs with, respectively, three and two interbase hydrogen bonds would, in principle, present a similar potential for protein recognition and thermal stability.¹² Other variations would be DNA molecules in which all the base pairs contain either two or three hydrogen bonds.¹³ However, not only do the component bases specify a digital code, they also affect the physico- chemical properties of the molecule. For example, DNA molecules with a reversed pattern of hydrogen bonding (DAP–T and H–C base pairs) more readily adopt an A-type conformation than DNA with the canonical base pairs.¹⁴ This is because the properties of the double helix depend not only on the base- pairing capacity of the constituent bases, but also on the stacking interactions between adjacent base pairs. Changing base-pairing interactions by effectively transferring a 2-amino group from guanine to adenine (thereby creating hypoxanthine and diaminopurine) changes the overall stacking because the charged 2- amino group, by being in a different immediate chemical environment, also affects the dipole moments associated with individual base pairs and consequently the stacking interactions between base pairs.¹⁵ In other words, the ability to assume the B- conformation, which confers on DNA an important aspect of its unique genetic role, is itself dependent on base-type and in particular on A–T and G–C base pairs. Although this might constitute a reason for the selection of these base pairs in most DNA molecules no such simple argument can be advanced for the use of A–U and G–C base pairs in RNA, although even in RNA the stability of different base-steps and hence of the double-helix itself is likely dependent on the precise nature of the constituent base pairs.

Fig. 2. (A) Structures of A-DNA and B-DNA. Note the difference in groove width and the relative displacements of the base pairs from the central axis. Reproduced with permission from Arnott¹⁶. (B) A–T and G–C base pairs shown for Watson–Crick pairing (a) and Hoogsteen pairing (b). syn and anti indicated different sugar conformations. Reproduced with permission from Johnson et al.

4. Structure of DNA:

A DNA Molecule Consists of Two Complementary Chains of Nucleotides:

A DNA molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits. Each of these chains is known as a DNA chain, or a DNA strand. Hydrogen bonds between the base portions of the nucleotides hold the two chains together (Figure 3). nucleotides are composed of a five-carbon sugar to which are attached one or more phosphate groups and a nitrogen-containing base. In the case of the nucleotides in DNA, the sugar is deoxyribose attached to a single phosphate group (hence the name deoxyribonucleic acid), and the base may be either adenine (A), cytosine (C), guanine (G), or thymine (T). The nucleotides are covalently linked together in a chain through the sugars and phosphates, which thus form a “backbone” of alternating sugar-phosphate-sugar-phosphate (see Figure 3). Because only the base differs in each of the four types of subunits, each polynucleotide chain in DNA is analogous to a necklace (the backbone) strung with four types of beads (the four bases A, C, G, and T). These same symbols (A, C, G, and T) are also commonly used to denote the four different nucleotides—that is, the bases with their attached sugar and phosphate groups. The way in which the nucleotide subunits are lined together gives a DNA strand a chemical polarity. If we think of each sugar as a block with a protruding knob (the 5′ phosphate) on one side and a hole (the 3′ hydroxyl) on the other (see Figure 3), each completed chain, formed by interlocking knobs with holes, will have all of its subunits lined up in the same orientation.¹⁶

The members of each base pair can fit together within the double helix only if the two strands of the helix are antiparallel—that is, only if the polarity of one strand is oriented opposite to that of the other strand (see Figures 4-3 and 4-4). A consequence of these base-pairing requirements is that each strand of a DNA molecule contains a sequence of nucleotides that is exactly complementary to the nucleotide sequence of its partner strand.¹⁸

5. TYPES OF DNA:

There are three different DNA types:

5.1. A-DNA:

It is a right-handed double helix similar to the B-DNA form. Dehydrated DNA takes an A form that protects the DNA during extreme conditions such as desiccation. Protein binding also removes the solvent from DNA, and the DNA takes an A form. It is a right-handed double helix fairly similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are commonly used to form crystals, and many DNA crystal structures are in the A form.[1] The same helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.¹⁹

Biological function:

A-DNA can be derived from a few processes, including dehydration and protein binding. Dehydration of DNA drives it into the A form, which has been shown to protect DNA under conditions such as the extreme desiccation of bacteria. Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of several hyperthermophilic archaeal viruses. SSRV1. It has been proposed that the motors that package double-stranded DNA in bacteriophages exploit the fact that A-DNA is shorter than B-DNA, and that conformational changes in the DNA itself are the source of the large forces generated by these motors. Experimental evidence for A-DNA as an intermediate in viral biomotor packing comes from double dye measurements showing that B-DNA is shortened by 24% in a stalled ("crunched") A-form intermediate. In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the DNA, and the DNA shortening/lengthening cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that moves DNA into the capsid.²⁰

5.2. B-DNA:

This is the most common DNA conformation and is a right-handed helix. The majority of DNA has a B type conformation under normal physiological conditions. B-DNA is generally depicted as a smooth helix; however, specific sequences of bases can distort the otherwise regular structure. For example, short tracts of A residues interspersed with short sections of general sequence result in a bent DNA molecule. Inverted base sequences, on the other hand, produce cruciform structures with four-way junctions that are similar to recombination intermediates. Most of these DNA structures have only been characterized in the laboratory, and their cellular significance is unknown.²¹

5.3. Z-DNA:

Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form. Z-DNA is thought to be one of three biologically active double-helical structures along with A-DNA and B-DNA. The structure of Z-DNA is quite different from the right-handed forms. In fact, Z-DNA is often compared against B-DNA in order to illustrate the major differences. The Z-DNA helix is left-handed and has a structure that repeats every other base pair.²²The major and minor grooves, unlike A- and B-DNA, show little difference in width. Formation of this structure is generally unfavourable, although certain conditions can promote it; such as alternating purine–pyrimidine sequence (especially poly (dGC)2), negative DNA supercoiling or high salt and some cations (all at physiological temperature, 37°C, and pH 7.3–7.4). Z-DNA can form a junction with B-DNA (called a "B-to-Z junction box") in a structure which involves the extrusion of a base pair. The Z-DNA conformation has been difficult to study because it does not exist as a stable feature of the double helix. Instead, it is a transient structure that is occasionally induced by biological activity and then quickly disappears.²³

6. Informational Capacity of DNA:

Although the physicochemical properties of DNA determine its dynamic roles in the context of enzymatic manipulation, how are they integrated with the primary function of DNA as an information store? Like DNA, a fundamental property of RNA is to encode protein sequences, but unlike a DNA genome, an RNA genome must combine both information storage and its functional expression during the translation of the nucleotide sequence into protein. These two requirements are not necessarily wholly compatible. For example, when there are strong selective pressures to maintain the integrity of the genomic nucleotide sequence, the option of regulating translation by modulating the half-life of an RNA molecule is effectively excluded. Perhaps more tellingly, in known present-day biological systems, RNA molecules that function as messengers, and also as genomes (e.g. those of poliovirus and Qb bacteriophage) are, relative to most genomic DNA molecules, very short, comprising only a few thousand nucleotides. An advantage of the separation of responsibilities between the two types of polynucleotide is that the juxtaposition and catenation of individual genes into much longer molecules enhances the potential regulatory repertoire of gene expression. In particular, the coordination of gene expression can be facilitated at the local level by the structural interplay arising from the transcriptional activity of adjacent genes, depending on whether they are organized in tandem or transcription is convergent or divergent. At a higher level of structural organization the continuity afforded by a single DNA double helix in a chromosome permits the organization of genes, and hence the available DNA information, into distinct structural and functional domains comprising many protein coding elements. Apart from these consider- ations, the ability of DNA to accrete more and more packets of information as genes or as regulatory elements into longer and longer chromosomal molecules, is arguably an important factor contributing to increases in organismal complexit.²⁴ Indeed, the postulated usurping of RNA by DNA as the informational store within a cell by itself epitomizes an evolutionary increase in biological complexity; one that enables increased possibilities for information storage such as the differential encoding on complementary strands and processing and hence, provides a substrate for further natural selection. Any increase in the length of chromosomal DNA molecules should be coupled to and possibly limited by mechanisms for the generation and maintenance of genomic integrity. In this context, a relevant biological example is provided by ciliates a group of single celled organisms including the causal agents of malaria and sleeping sickness in which regulation of DNA- directed gene expression is separated from maintenance of the germ line. These organisms contain two types of nuclei. One, the micronucleus, containing the complete diploid genome, serves as the germ line and does not express genes, whereas the second, the polyploid macronucleus contains a highly edited and fragmented version of the genome, and serves as the vehicle controlling gene expression Only the micronucleus undergoes mitotic chromosomal segregation.²⁵

7. Biological Functions:

DNA usually occurs as linear chromosome in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called gene. transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In an alternative fashion, a cell may copy its genetic information in a process called DNA replication.²⁶

7.1. Genes and genomes:

Genomic DNA is tightly and orderly packed in the process called DNA condensation, to fit the small available volumes of the cell. In eukaryotes, DNA is located in the cell nucleus, with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its genotype. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an open reading frame that can be transcribed, and regulatory sequences such as promoters and enhancers, which control transcription of the open reading frame. In many species, only a small fraction of the total sequence of the genome encodes protein. For example, only about 1.5% of the human genome consists of protein-coding exons, with over 50% of human DNA consisting of non-coding repetitive sequences. The reasons for the presence of so much noncoding DNA in eukaryotic genomes and the extraordinary differences in genome size, or C-value, among species, represent a long-standing puzzle known as the "C-value enigma". However, some DNA sequences that do not code protein may still encode functional non-coding RNA molecules, which are involved in the regulation of gene expression.²⁷

7.2. Transcription and translation:

A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides.²⁸

7.3. Replication:

Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.²⁹

7.4. Extracellular nucleic acids:

Naked extracellular DNA (eDNA), most of it released by cell death, is nearly ubiquitous in the environment. Its concentration in soil may be as high as 2μg/L, and its concentration in natural aquatic environments may be as high at 88μg/L. Various possible functions have been proposed for eDNA: it may be involved in horizontal gene transfer; it may provide nutrients; and it may act as a buffer to recruit or titrate ions or antibiotics. Extracellular DNA acts as a functional extracellular matrix component in the biofilms of several bacterial species. It may act as a recognition factor to regulate the attachment and dispersal of specific cell types in the biofilm it may contribute to biofilm formation; and it may contribute to the biofilm's physical strength and resistance to biological stress.³⁰

8. CONCLUSIONS:

Although, quite rightly, the ability of DNA to code for protein sequences is often emphasized, equally important is the encoding of information that enables both the packaging of the polymer and the regulation of the expression and accessibility of the protein-coding information. This latter property depends to a much greater extent on the sequence-dependent physicochemical properties of the molecule and thus on the cumulative properties of a succession of a small number of base pairs. This analogue characteristic contrasts with the digital encoding of protein sequences. A further crucial aspect of DNA function is the dynamic nature of the structural transitions observed during its replication and transcription. These transitions involve both deviations from the canonical double helix and also topological transformations of the trajectory of the double helix facilitating both packaging and regu- lation. Taken together, these properties enable DNA to function as a supremely efficient and versatile coding device.

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Received on 03.05.2023 Modified on 08.06.2023

Asian J. Res. Pharm. Sci. 2023; 13(3):259-266.

DOI: 10.52711/2231-5659.2023.00045