This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1d89

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

A DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNIQUE LATTICE AND EXHIBITS A NEW BEND

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1d89"

Categories: Large Structures | DiGabriele AD | Steitz TA

@@ Line 1: / Line 1: @@
-[[Image:1d89.gif|left|200px]]<br /><applet load="1d89" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1d89, resolution 2.300&Aring;" />
-'''A DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNIQUE LATTICE AND EXHIBITS A NEW BEND'''<br />
-==Overview==
+==A DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNIQUE LATTICE AND EXHIBITS A NEW BEND==
-The structure of d(CGCGAAAAAACG)/d(CGTTTTTTCGCG) was determined at 2.3 A, resolution in order to deduce the local structural features that give rise, to DNA bending by adenine tracts. Whereas all previously reported B-DNA, dodecamers have crystallized isomorphously (spacegroup P2(1)2(1)2(1) with, unit cell dimensions of a = 24.5 A, b = 40.3 A, c = 65.9 A), the duplex, reported here crystallizes in a different lattice (spacegroup P2(1)2(1)2, with unit cell dimensions of a = 44.8 A, b = 66.1 A, c = 42.9 A). The DNA, exhibits a 30 degree bend in the helix axis that is 180 degrees away from, the 20 degree bend exhibited by the adenine tract DNA crystal structures, that have been previously determined. This bend is 90 degrees away from, the bend predicted for an adenine tract by solution and gel experiments., The adenine tract is straight and bending occurs in the G+C-rich regions., Comparison of the various adenine tract DNA crystal structures reveals, that in all cases the adenine tracts have nearly identical structures, even though the overall bends of the helix axes are quite different. This, implies that the structure of the adenine tract is robust, at least under, the conditions of crystallization. The base-pairs in the adenine tracts, exhibit a large propeller twist that leads to the formation of bifurcated, hydrogen bonds and a narrow minor groove. In the crystal structure of, d(CGCGAAAAAACG)/d(CGTTTTTTCGCG), a minor groove spine of hydration is, observed that probably stabilizes the straight structure of the adenine, tract. This straight structure of the A-tract is not consistent with the, results of fiber diffraction, gel experiments, and NMR studies. Although, this may imply that the results of solution experiments need to be, reinterpreted, the conditions under which the crystals were grown are, different from those under which the solution experiments were done. The, possibility remains that the 2-methyl-2,4-pentanediol necessary for, crystal growth may facilitate formation of the spine of hydration that, stabilizes the straight A-tract, although recent NMR results show the, presence of the spine of hydration in aqueous solution. We have also, extended our previously reported observation that non-self-complementary, DNA structures can exist in the crystal lattice in two orientations. A, dodecamer brominated on one strand provides experimental evidence that, d(CGCAAAAAAGCG)/d(CGCTTTTTTG CG) is positioned in two orientations in the, crystal lattice that are related by a 180 degree rotation around the, pseudo-dyad axis of the sequence.(ABSTRACT TRUNCATED AT 400 WORDS)
+<StructureSection load='1d89' size='340' side='right'caption='[[1d89]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1d89]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D89 FirstGlance]. <br>
-D89 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D89 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d89 OCA], [https://pdbe.org/1d89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d89 RCSB], [https://www.ebi.ac.uk/pdbsum/1d89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d89 ProSAT]</span></td></tr>
-==Reference==
+</table>
-A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend., DiGabriele AD, Steitz TA, J Mol Biol. 1993 Jun 20;231(4):1024-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8515463 8515463]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: DiGabriele, A.D.]]
+[[Category: Large Structures]]
-[[Category: Steitz, T.A.]]
+[[Category: DiGabriele AD]]
-[[Category: b-dna]]
+[[Category: Steitz TA]]
-[[Category: double helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:44:47 2007''

1d89

From Proteopedia

Current revision

A DNA DODECAMER CONTAINING AN ADENINE TRACT CRYSTALLIZES IN A UNIQUE LATTICE AND EXHIBITS A NEW BEND

Structural highlights

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox