User:Karl Oberholser/Sandbox 1

<H2><center>'''Syn and Anti Configurations of Nucleosides and Nucleotides'''</center></H2>

Detailed description of [http://en.wikipedia.org/wiki/Nucleoside nucleosides] and [http://en.wikipedia.org/wiki/Nucleotide nucleotides].

<applet load='Adenosine.pdb' size='300' frame='true' align='right' scene ='User:Karl_Oberholser/Sandbox_1/First_view/1'/> Observe that the adenine ring of adenosine is nearly perpendicular to the furanose ring and that a <scene name='User:Karl_Oberholser/Sandbox_1/Glycosidic_bond/1'>β glycosidic bond</scene> (colored green) connects adenine to ribofuranose. Groups on the ribofuranose, such as the <scene name='User:Karl_Oberholser/Sandbox_1/2_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 have been viewing, but now in <scene name='User:Karl_Oberholser/Sandbox_1/Anti_configuration/2'>spacefill</scene> 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 the anti configuration is favored, but the syn configuration can be formed and actually has a role in the formation of the [http://proteopedia.org/wiki/index.php/Z-DNA Z-DNA], a conformation of DNA double helix.

== 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.

== Examples of Nucleotides ==

AMP <scene name='User:Karl_Oberholser/Sandbox_1/Amp/1'>as ball and stick</scene>; <scene name='User:Karl_Oberholser/Sandbox_1/Amp2/1'>as spacefill</scene>

 

UMP <scene name='User:Karl_Oberholser/Sandbox_1/Ump/1'>as ball and stick</scene>; <scene name='User:Karl_Oberholser/Sandbox_1/Ump2/1'>as spacefill</scene>

 

cAMP <scene name='User:Karl_Oberholser/Sandbox_1/Camp/1'>as ball and stick</scene>; <scene name='User:Karl_Oberholser/Sandbox_1/Camp2/1'>as spacefill</scene>