Tom Sandbox: Difference between revisions
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===Binding with DNA=== | ===Binding with DNA=== | ||
The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/1'>Major Groove</scene> of the DNA. This causes a | The basic region binding domain of GCN4 inserts itself into the <scene name='Tom_Sandbox/Major_groove/1'>Major Groove</scene> of the DNA. This causes a bend in both the AP-1 and ATF/CREB binding sites of DNA<ref name="bind">PMID:15459288</ref>. AP-1 refers to a group of activator proteins that bind to the same 9 base pair semi-palindromic region for transcription activation. ATF/CREB refers to a fully palendromic region. The AP-1 site sequence is 5′-ATGACTCAT-3′, and the ATF/CREB site is 5′-ATGACGTCAT-3′<ref> Hockings, S. C.; Kahn, J. D.; Crothers, D. M. PNAS February 17, 1998 vol. 95 no. 4 1410-1415 </ref>. The bending mechanism was determined by adding fluorophores to the ends of U shaped manufactured DNA segments with the specific binding sites AP-1 or ATF/CREB inserted into the center. The shift in the fluorophore positioning showed the effect of bending on the DNA due to GCN4 binding. In total, in the complex with GCN4-bZIP, the ATF/CREB site is bent by (25 ± 2)° and the AP-1 site by (20 ± 2)° toward the minor groove.<ref name="bind"/> This is thought to be the mechanism for inducing transcription. | ||
====Heptad Repeat==== | ====Heptad Repeat==== | ||
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'''Image 3: A schematic representation of the Leucine Zipper acting as nano-tweezers under different pH conditions<ref name="ph"/>. | '''Image 3: A schematic representation of the Leucine Zipper acting as nano-tweezers under different pH conditions<ref name="ph"/>. | ||
==See Also== | ==See Also== | ||
