DNA: Difference between revisions

<StructureSection load='B-DNA.pdb' size='450' side='right' scene='DNA/B-dna/7' caption='B-DNA'>

<scene name='User:Adithya_Sagar/Sandbox_DNA/B-dna/4'>DNA</scene> consists of two polynucleotide chains, <scene name='DNA/B-dna/16'>twisted around each other to form a double helix</scene>. The <scene name='10/100853/Nucleotide/2'>nucleotide</scene> in DNA is composed of a <scene name='10/100853/Phosphate/3'>phosphate</scene> bonded to the 5' of <scene name='10/100853/Deoxyribose/2'>D-2'-deoxyribose</scene> which is connected by a beta-glycosidic bond to a purine or a pyrimidine <scene name='10/100853/Base/2'>base</scene>. The <scene name='10/100853/Ribose_pucker/2'>ring pucker</scene> of ribose is a main determinant of which of the [[Forms of DNA]] is present. In this scene, which shows B DNA, the 2' carbon is out of the plane of the other members of the five membered ring.  In <scene name='10/100853/3_endo_a_dna/2'>A form DNA</scene>, the 3' carbon is out of the plane of the ribose ring.

The four types of bases are the two double-ringed purine base <scene name='DNA/B-dna/22'>Adenine (A)</scene> and <scene name='DNA/B-dna/23'>Guanine (G)</scene> and the two single-ringed pyrimidine bases <scene name='DNA/B-dna/28'>Thymine (T)</scene> and <scene name='DNA/B-dna/27'>Cytosine (C)</scene>. Hydrogen atoms on some nitrogen and oxygen atom can undergo tautomeric shifts. The nitrogen atoms that are involved in forming tautomer appear as amino or imino groups and the oxygen atoms are either in keto or enol forms. Using an isolate thymine to illustrate the <scene name='DNA/Thymine_enol/1'>imino/enol tautomer</scene> and the <scene name='DNA/Thymine_keto/3'>amino/keto tautomer</scene>. There is a preference for the amino and keto forms which is very crucial for the biological functioning of DNA as it provides a <scene name='DNA/Amino-glycosidic/1'>ring nitrogen capable of forming a glycosidic bond</scene> with the deoxyribose and it leads to the specificity of hydrogen bonding in base pairing and thus complementarity of the chains.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref> The imino nitrogen can only serve as a donating atom in hydrogen bonding, but the amino nitrogen can also serve as a receiving atom. Each nucleotide in a DNA chain is linked to another via <scene name='DNA/Diester/2'>3',5' phosphodiester bond</scene>. There are four nucleotides in DNA.  The sugar-phosphate backbone of the DNA is very regular owing to the phosphodiester linkage whereas the ordering of bases is highly irregular.<ref name='Watson'> Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner ''Molecular Biology of Gene'' (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8</ref>

Nature 171, 737-738 (1953)</ref> Thus in a strand of DNA the content of adenine is equal to that of thymine  and the guanine content is equal to the cytosine content.  In general DNA with higher GC content is more stable than the one with higher AT content owing to the stabilization due to base stacking interactions.

In a <scene name='DNA/Bdnasf/1'>DNA double helix</scene> the <scene name='DNA/Angled_gylcosidic/5'>beta-glycosyl bonds</scene> of bases which are paired <scene name='DNA/Angled_gylcosidic/7'>do not lie opposite</scene> to each other but are positioned at an angle. This results in unequally spaced sugar-phosphate backbones and gives rise to two grooves: the