User:John S. de Banzie/Sandbox 2

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==RNA Stem and Loop Structure==
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==DNA Binding Motifs==
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<StructureSection load='2qh2' size='400' side='right' caption='RNA hairpin loop from human telomerase RNA, [[2qh2]]' scene='59/590622/2qh2stick/3'>
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<StructureSection load='1mdy' size='300' side='right' caption='Helix-Loop-Helix, [[1mdy]]' scene='59/590622/1mdyspacefill/1'>
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Intramolecular hydrogen bonding in RNA molecules results in the formation of stem and loop structures (also known as hairpin loops).
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RNA in the stem of a stem and loop structure forms a double stranded <scene name='59/590622/2qh2stickends/1'>antiparallel</scene> right-handed helix with <scene name='59/590622/2qh2spacefill/1'>major and minor grooves</scene>. However this double helix is not the same as that of [[DNA]]. The most obvious difference is in the tilt of the bases, but there are also differences in the diameter and pitch of the helix<ref>Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Section 27.1, DNA Can Assume a Variety of Structural Forms. Available from: http://www.ncbi.nlm.nih.gov/books/NBK22585/</ref>.
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== Helix-Loop-Helix ==
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This helix-loop-helix protein has <scene name='59/590622/1mdyspacefillsubunit/1'>two subunits</scene>. An <scene name='59/590622/1mdycartoon/1'>alpha helix</scene> in each subunit fits into a major groove in the DNA.
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The RNA shown is 24 nucleotides long. Nucleotides 1 through 8 and 17 through 24 form the stem and nucleotides 9 through 16 form the loop. Note the <scene name='59/590622/2qh2bases/2'>complementary base pairing</scene> in the stem (A: red, C: green, G: orange, T: blue) and the unpaired bases in the loop (white).
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</StructureSection>
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(The stem and loop structure shown is part of the RNA in human telomerase. Telomerase protects chromosomes by restoring DNA that is lost from the ends during DNA replication. The RNA is used as a template and the enzyme is thus an internally-templated RNA-dependant DNA polymerase<ref>Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002. Section 27.4, DNA Replication of Both Strands Proceeds Rapidly from Specific Start Sites. Available from: http://www.ncbi.nlm.nih.gov/books/NBK22587/</ref>.)
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<StructureSection load='9ant' size='300' side='right' caption='Helix-Turn-Helix, [[9ant]]' scene='59/590622/9antspacefill/1'>
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== Helix-Turn-Helix ==
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This helix-loop-helix protein has one subunit. An <scene name='59/590622/9antcartoon/1'>alpha helix</scene> fits into a major groove in the DNA.
</StructureSection>
</StructureSection>
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<StructureSection load='1ysa' size='300' side='right' caption='Leucine Zipper, [[1ysa]]' scene='59/590622/1ysaspacefill/1'>
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== Leucine Zipper ==
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This leucine zipper protein has <scene name='59/590622/1ysaspacefillsubunits/1'>two subunits</scene>. An <scene name='59/590622/1ysacartoon/1'>alpha helix</scene> in each subunit fits into a major groove in the DNA. Interactions between <scene name='59/590622/1ysaleucines/1'>leucyl R groups</scene> help hold the subunits together.
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</StructureSection>
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<StructureSection load='1mey' size='300' side='right' caption='Leucine Zipper, [[1mey]]' scene='59/590622/2qh2stick/3'>
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== Zinc Finger ==
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This zinc finger protein has one subunit. Three zinc finger motifs fit into a major groove in the DNA.
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</StructureSection>
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== References ==
== References ==
<references/>
<references/>

Revision as of 18:31, 13 June 2014

DNA Binding Motifs

Helix-Loop-Helix, 1mdy

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Helix-Turn-Helix, 9ant

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Leucine Zipper, 1ysa

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Leucine Zipper, 1mey

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References

Proteopedia Page Contributors and Editors (what is this?)

John S. de Banzie

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