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<p style="text-align: justify;">DNA is usually formed of two polynucleotide chains twisted each other in an antiparallel manner. One strand is oriented in the 5'&nbsp;<span style="color: #202124; font-family: arial, sans-serif; font-size: 14px; text-align: left; background-color: #ffffff;">&rarr; </span>&nbsp;3' it is and the other in the 3' <span style="color: #202124; font-family: arial, sans-serif; font-size: 14px; text-align: left; background-color: #ffffff;">&rarr;</span> 5' direction. The backbone of each strand of DNA helix is formed of sugar and phosphate residue. Also known as a nucleotide. A nucleotide is the fundamental building block of DNA.</p>
<p style="text-align: justify;">Nucleotide has 3 characteristic components -</p>
<h4 style="text-align: justify;">1. Nitrogenous base</h4>
<h4 style="text-align: justify;">2. Pentose sugars (Ribose deoxyribose)</h4>
<h4 style="text-align: justify;">3. Phosphate group.</h4>
<p><img style="display: block; margin-left: auto; margin-right: auto;" src="https://vediphlie-aws.s3.ap-south-1.amazonaws.com/1_7190568c81.PNG" alt="Structure of pentose sugar of RNA and DNA" /></p>
<p>&nbsp;</p>
<p><img style="display: block; margin-left: auto; margin-right: auto;" src="https://vediphlie-aws.s3.ap-south-1.amazonaws.com/2_b61513c532.PNG" alt="Structure of purine &amp; pyrimidine" /></p>
<p>&nbsp;</p>
<p><img style="display: block; margin-left: auto; margin-right: auto;" src="https://vediphlie-aws.s3.ap-south-1.amazonaws.com/3_399a028a5b.PNG" alt="structure of nitrogenous bases" /></p>
<h2>1. Nitrogenous base -</h2>
<p>They are:-</p>
<p>&bull; Water-insoluble</p>
<p>&bull; Heterocyclic</p>
<p>&bull; Aromatic</p>
<p>&bull; Planar</p>
<p><strong>Nitrogenous bases are of two types :</strong></p>
<p>(i) Pyrimidines</p>
<p>(ii) Purines</p>
<h3>Pyrimidines :</h3>
<p style="text-align: justify;">Major pyrimidines which are commonly found in DNA are thymine (T) and Cytosine (C) cytosine (C) and Uracil (U) is found in RNA. Pyrimidines are derived from the single ring structure known as the pyrimidine ring (2N+4C).</p>
<h3 style="text-align: justify;">Purine :</h3>
<p style="text-align: justify;">Major purines which are commonly found in DNA and RNA are Adenine (A) and Guanine (G). Purines are derived from the two-ring structure known as the purine ring. One rings are pyrimidine (2N+4C) and another is an imidazole ring (2N+3C). Adenine has &ndash;NH<sub>2</sub> group at the C<sub>6</sub> position. Guanine has &ndash;NH<sub>2</sub> group at C<sub>2</sub> position and carbonyl group at the C6 position.</p>
<h4>Sugars:&nbsp; &nbsp; Sugars are of two types :</h4>
<p style="text-align: justify;">(i) Deoxyribose Sugar</p>
<p style="text-align: justify;">(ii) Ribose sugar</p>
<h4 style="text-align: justify;">Deoxy Ribose Sugar :</h4>
<p style="text-align: justify;">This pentose sugar is found in DNA. In this sugar &lsquo;H&rsquo; is present at the C<sub>2</sub> position. So this sugar knows as 2'&ndash;deoxy&ndash;D&ndash;ribose sugar.</p>
<h4 style="text-align: justify;">Ribose Sugar :</h4>
<p style="text-align: justify;">This pentose sugar is found in RNA. In this sugar &lsquo;OH&rsquo; group is present at the 2' position at the place of &lsquo;H&rsquo;. Due to the presence of the &lsquo;OH&rsquo; group at 2'-3,' this sugar is also known as D-ribose sugar.</p>
<h4 style="text-align: justify;">Phosphate :</h4>
<p style="text-align: justify;">Three phosphate groups are present at position C<sub>5</sub> . These phosphate groups are known as a, b, g for the first, second, and third phosphate respectively.</p>
<p style="text-align: justify;"><span style="background-color: #ffffff; color: #282828; font-family: 'Noto Sans', Helvetica, Arial, sans-serif; font-size: 16px;">&beta;</span>-glycosidic bond is formed between 9 nitrogen of Adenine and Guanine and the 1' OH group of is known ribose.</p>
<p style="text-align: justify;">In the pyrimidines, b-glycosidic bonds form between the first nitrogen of their ring at the place of ninth nitrogen and the 1'OH group of deoxyribose. The sugar and base alone know as a nucleoside. Sugar, nitrogenous base, and phosphate to gather are called a nucleotide. The addition of a phosphate group to a nucleoside forms a nucleotide.</p>
<p><img style="display: block; margin-left: auto; margin-right: auto;" src="https://vediphlie-aws.s3.ap-south-1.amazonaws.com/1_7019d4db0d.PNG" alt="Different type of deoxy nucleotide mono phosphate" /></p>
<p style="text-align: center;">Fig.: Different types of deoxynucleotide monophosphate</p>
<h2 style="text-align: left;">2. Phosphodiester bond -</h2>
<p style="text-align: justify;">Many nucleotides are joined to each other through the 3' OH of 2' deoxyribose of one nucleotide and the phosphate attached to the 5' OH group of another nucleotide. This linkage between 3' OH and 5' P is known as the phosphodiester bond. Condensation of two or more nucleotides from polynucleotide.</p>
<h2 style="text-align: justify;">3. Types of DNA structure -</h2>
<h3>(1) Primary structure:</h3>
<p style="text-align: justify;">The linear sequence of nucleotides that are linked by phosphodiester bonds is known as a primary structure of nucleic acid. The primary structure of nucleic acid consists of a Nitrogen base (A, G, C, T), a pentose sugar, and one or more phosphate groups.</p>
<h3 style="text-align: justify;">(2) Secondary structure:</h3>
<p style="text-align: justify;">The formation of hydrogen bonds between two complementary bases of double-helix DNA is known as the secondary structure of DNA. Secondary structure is responsible for the shape of DNA double-ring structure purine always from hydrogen bond with single ring pyrimidine bases.</p>
<p style="text-align: justify;">Adenine forms two Hydrogen bonds with thymine and guanine and three Hydrogen bonds with cytosine.</p>
<p style="text-align: justify;">&nbsp;[A = T, G&nbsp;<span style="color: #202124; font-family: arial, sans-serif; font-size: 14px; text-align: left; background-color: #ffffff;">&equiv;</span><strong style="color: #202124; font-family: arial, sans-serif; font-size: 14px; text-align: left; background-color: #ffffff;"> </strong>C]</p>
<h3 style="text-align: justify;">(3) Tertiary structure:</h3>
<p style="text-align: justify;">The tertiary structure of the DNA is more condensed than the secondary structure of DNA, in which the entire chain of the polynucleotide is folded into a specific three-dimensional shape. In tertiary structure hydrogen bonding and Hydrophobic force, (base stacking force) play an important role.&nbsp;</p>
<h3>(4) Quaternary Structure :</h3>
<p style="text-align: justify;">It is the higher level of organization of DNA. In this structure, DNA interacts with other molecules chromatin is the quaternary structure of DNA in which it interacts with histone proteins.</p>
<h2 style="text-align: justify;">4. Different conformation of DNA -</h2>
<p style="text-align: justify;">Confirmation of DNA depends on the hydrogen level i.e. (if the concentration of water is high, it will be, B form of DNA, and if concentration. of water is low, it will be, A form of DNA), DNA sequence, the concentration of salt and metal ions in solution and modification of the nitrogenous bases.</p>
<h3 style="text-align: justify;">1. B-DNA :</h3>
<p>It is the most abundant form of DNA in cells under normal physical conditions. This form of DNA is observed at a high water concentration (high humidity).</p>
<p>B form of DNA has the following characteristics:-</p>
<p>&bull; Right-handed helix rotation sense.</p>
<p>&bull; More twisted.</p>
<p>&bull; One strand 5'&nbsp;<span style="color: #202124; font-family: arial, sans-serif; font-size: 14px; background-color: #ffffff;">&rarr; </span>3' and other strands 3'&nbsp;<span style="color: #202124; font-family: arial, sans-serif; font-size: 14px; background-color: #ffffff;">&rarr; </span>5' direction oriented.</p>
<p>&bull; The diameter of the helix is 20&Aring;</p>
<p>&bull; The distance between two adjacent base pairs is 0.34 &Aring;</p>
<p>&bull; 10.5 base pair per helical turn.</p>
<h3>2. A-DNA :</h3>
<p style="text-align: justify;">The &lsquo;A&rsquo; form of DNA is observed under low humidity (low water concentration) conditions. B form DNA adopts the &lsquo;A&rsquo; form structure in some DNA-protein complex. &lsquo;A&rsquo; form of DNA has the following characteristics :</p>
<p style="text-align: justify;">&bull; Right-handed</p>
<p style="text-align: justify;">&bull; 11 bp per turn</p>
<p style="text-align: justify;">&bull; Major groove is narrow and much deeper.</p>
<p style="text-align: justify;">&bull; Minor groove is broader and shallower.</p>
<p style="text-align: justify;">&bull; The distance between two adjacent base pairs is 2.3&Aring;.</p>
<p style="text-align: justify;">&bull; 'A' form of DNA is similar to the double-helical RNA.</p>
<h3 style="text-align: justify;">3. Z-DNA :</h3>
<p style="text-align: justify;">It is left-handed DNA. In the B-DNA glycosidic bond is anti conformation at pyrimidine and purine residue. But in the Z-DNA anti confirmation is out only at the pyrimidine residue and syn conformation at purine residue. This syn conformation is responsible for the left-handedness of the helix. The alternating anti-syn confirmation gives the backbone of left-handed DNA a zig-zag look. So this form of DNA is known as the zig-zag or &lsquo;Z&rsquo; form.&nbsp;</p>
<p style="text-align: justify;">&lsquo;Z&rsquo; form of DNA has the following characteristics</p>
<p style="text-align: justify;">&bull; Superhelical tension.</p>
<p style="text-align: justify;">&bull; More narrow and more elongated helix.</p>
<p style="text-align: justify;">&bull; Major groove is not really a groove.</p>
<p style="text-align: justify;">&bull; Occurs in the high salt concentration.</p>
<h2 style="text-align: justify;">5. Nucleic acid stability -</h2>
<h3 style="text-align: justify;">1. Base pairing:</h3>
<p style="text-align: justify;">Base pairing holds both of the strands of DNA together like &lsquo;glue&rsquo;. The nitrogenous base of a strand pairs with another strand. Watson Crick base pairing is the more stable of all base pairing in the double helix. It plays a crucial role in the roll instability of DNA.</p>
<h3 style="text-align: justify;">2. Hydrophobic force:</h3>
<p style="text-align: justify;">It is a tendency of water molecules to form a bigger cage around the hydrophobic molecules. In the DNA, pyrimidines and purines are hydrophobic, so water molecules from the hydrophobic interaction with nitrogenous bases. Hydrophobic force plays a central role in determining the nucleic acid structure.</p>
<h3 style="text-align: justify;">3. Base stacking interaction:</h3>
<p style="text-align: justify;">Interaction between two adjacent nitrogenous bases which are out in the plane, in a parallel manner. Different sets of base pairs in a stack have different stacking energies. Stacked G and C bases have greater interaction compared to stacked A and T bases. This force helps to minimize the contact of water with nitrogenous bases.</p>
<h3 style="text-align: justify;">4. Hydrogen bond:</h3>
<p style="text-align: justify;">When a hydrogen atom is present between two electronegative molecules then it forms an extra bond. This extra bond is known as a hydrogen bond. Adenine is always hydrogen-bonded to thymine and guanine is always hydrogen-bonded to cytosine by Watson-crick pairing. The surface atoms in the sugar-fourth and phosphate form a hydrogen bond to water molecules.</p>
<h3 style="text-align: justify;">5. Ionic interaction:</h3>
<p style="text-align: justify;">The phosphate group of the backbone of DNA plays an important role in DNA stability due to their one charge. If we add the positive ions (Na<sup>+</sup> ) in the DNA solution, the melting temperature of duplex DNA increase means the stability of DNA increase because this ion shield the anionic phosphate group and decrease the repulsion.</p>
<h2 style="text-align: justify;">6. Thermal Stability -</h2>
<p style="text-align: justify;">The temperature at which 50% DNA in a given sample becomes denatured, known as melting temperature (Tm). The double-stranded DNA show less absorbance at 260 nm. While the denature DNA shows more absorbance at 260 nm this phenomenon is known as a hyperchromatic effect.</p>
<h3 style="text-align: justify;">Factors affecting T<sub>m</sub></h3>
<h3 style="text-align: justify;">1. Ionic strength:</h3>
<p style="text-align: justify;">When the lower the ionic strength is low it can not completely shield the anionic phosphate. So repulsion makes it energetically more favorable to separate the strands thus Tm temperature becomes lower.</p>
<h3 style="text-align: justify;">2. AT and GC Content:</h3>
<p style="text-align: justify;">GC content has a higher number of Hydrogen bond and base stacking interactions compared to AT content. So the high GC content has higher Tm than DNA with high AT content.</p>
<h3 style="text-align: justify;">3. pH:</h3>
<p style="text-align: justify;">If the pH is greater than 10, the hydrogen bonds of Nitrogenous bases are destroyed and DNA becomes denatured. If the pH is less than 3, it also disrupts the base pairing due to extensive protonation. So very high or very low pH lowers the T<sub>m</sub>.&nbsp;</p>

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 In the DNA Structure topic of Biochemistry; we will cover Nitrogenous base, Phosphodiester bond, Types of DNA structure etc. 

DNA Structure - Types of DNA structure, Different conformation of DNA

DNA is usually formed of two polynucleotide chains twisted each other in an antiparallel manner. In the DNA Structure topic of Biochemistry; we will cover Nitrogenous base, Phosphodiester bond, Types of DNA structure, Different conformation of DNA, Nucleic acid stability, Thermal Stability etc. 

DNA Structure

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