Syn and anti nucleosides: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, David Canner, Alexander Berchansky, Angel Herraez

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 == Purine Nucleosides ==
-<applet load='Adenosine.pdb' size='400' frame='true' align='right' scene ='Syn_and_anti_nucleosides/First_view/1'/> Adenosine (<scene name='Syn_and_anti_nucleosides/First_view/1'>Reset Initial scene</scene>) is composed of an adenine bonded to a furanose by a <scene name='Syn_and_anti_nucleosides/Glycosidic_bond/1'>β glycosidic bond</scene> (colored green). Observe that the adenine ring is nearly perpendicular to the furanose ring, but projecting away from the furanose (anti-conformation).  Without hinderance from groups on either ring the adenine ring can rotate about the glycosidic bond, and form the <scene name='Syn_and_anti_nucleosides/Syn-conformation/1'>syn-conformation</scene>.  The two common purines, adenine and guanine, can rotate between the anti- and syn-conformations, but the anti-configuration is favored.  Compare the contact present between the two rings in these two spacfilling representations, anti-conformation and syn-conformation. Groups on the ribofuranose, such as the <scene name='Syn_and_anti_nucleosides/2_hydrogen/1'>hydrogen</scene> on the 2' carbon, sterically hinder the rotation of the adenine about the glycosidic bond.  This lack of ability to rotate results in two possible configurations.  The anti configuration, which you are now viewing, but <scene name='Syn_and_anti_nucleosides/Anti_configuration/1'>spacefill</scene> shows the hinderance more realistically. and the <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration/1'>syn configuration</scene>, <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration2/1'>view of adenine ring on edge</scene>, same view but in <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration3/1'>spacefill</scene>.  With purines, but the syn configuration can be formed and actually has a role in the formation of the [[Z-DNA]], a conformation of DNA double helix.
+<applet load='Adenosine.pdb' size='400' frame='true' align='right' scene ='Syn_and_anti_nucleosides/First_view/1'/> Adenosine (<scene name='Syn_and_anti_nucleosides/First_view/1'>Reset Initial scene</scene>) is composed of an adenine bonded to a furanose by a <scene name='Syn_and_anti_nucleosides/Glycosidic_bond/1'>β glycosidic bond</scene> (colored green). Observe that the adenine ring is nearly perpendicular to the furanose ring, but projecting away from the furanose (anti conformation).  Without hinderance from groups on either ring the adenine ring can rotate about the glycosidic bond, and form the <scene name='Syn_and_anti_nucleosides/Syn-conformation/1'>syn conformation</scene>.  The two common purines, adenine and guanine, can rotate between the anti and syn conformations, but the anti configuration is favored.  Compare the contact present between the two rings in these two spacfilling representations, <scene name='Syn_and_anti_nucleosides/Anti-conformation2/1'>anti conformation</scene> and <scene name='Syn_and_anti_nucleosides/Syn-conformation2/1'>syn conformation</scene>. Even though the anti conformation is favored with the purines the syn configuration can be formed and actually has a role in the formation of the [[Z-DNA]], a conformation of DNA double helix.
+Groups on the ribofuranose, such as the <scene name='Syn_and_anti_nucleosides/2_hydrogen/1'>hydrogen</scene> on the 2' carbon, sterically hinder the rotation of the adenine about the glycosidic bond.  This lack of ability to rotate results in two possible configurations.  The anti configuration, which you are now viewing, but <scene name='Syn_and_anti_nucleosides/Anti_configuration/1'>spacefill</scene> shows the hinderance more realistically. and the <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration/1'>syn configuration</scene>, <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration2/1'>view of adenine ring on edge</scene>, same view but in <scene name='User:Karl_Oberholser/Sandbox_1/Syn_configuration3/1'>spacefill</scene>.
 == Pyrimidine Nucleosides ==
 <scene name='User:Karl_Oberholser/Sandbox_1/Anti_uridine/1'>View</scene> of uridine in the anti conformation.  <scene name='User:Karl_Oberholser/Sandbox_1/Syn_cytidine/1'>View</scene> of cytidine in the syn conformation.  <scene name='User:Karl_Oberholser/Sandbox_1/Syn_cytidine2/4'>View</scene> oxygen at the C-2 position of cytidine invading the space of both hydrogen at C-2' and the oxygen of the furanose ring. Since both pyrimidines found in DNA have an oxygen at the C-2 position, nucleosides and nucleotides of these pyrimidines only adopt the anti conformation and therefore can not be part of Z-DNA.