309d: Difference between revisions

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A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT

OverviewOverview

The crystal structure of d-CGACGATCGT has been determined to a resolution of 2.6 A. The molecule was synthesized by standard phosphoramidite procedures, and purified by anion-exchange HPLC. Crystals are monolclinic, space group P2(1), with unit cell dimensions, a = 26.45 A, b = 34.66 A, c = 32.17 A, beta = 113.45 degrees and Z = 4, containing a B-DNA double helix in each crystallographic asymmetric unit. The structure was solved using molecular replacement, aided by an isomorphous derivative, in which a bromine atom was attached to the 5 position of cytosine 8. Problems of fit between the search model and the structure ultimately obtained necessitated the use of Patterson correlation procedures between the determination of the orientation and the translation of the molecule. In all, 69 solvent molecules have been identified, and the structure has been refined to an R-factor of 0.214, using the 1421 reflections with F > 2sigma(F), collected at -120 degrees C. The sequence produces a molecule containing eight Watson-Crick base-pairs and a two-nucleotide 5'-sticky end at each end of the duplex. The sticky ends cohere with one another, so the molecules form continuous 10-fold double helices throughout the crystal, with each strand being interrupted by inherent staggered nicks. The relative angular relationships between helices in the structure differ from each other; most of the arrangements differ from Holliday junctions, whose rotational orientations are phased by a crossover and which are modeled to contain double helices that are exactly parallel or antiparallel. However, one helical juxtaposition in this crystal is similar to the alignment of double helices in parallel Holliday junctions. A survey of DNA decamers that also form infinite helices in crystals reveals relationships that approximate both parallel and antiparallel Holliday junction alignments.

About this StructureAbout this Structure

This structure supersedes the now removed PDB entry 273d. Full crystallographic information is available from OCA.

ReferenceReference

A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT., Qiu H, Dewan JC, Seeman NC, J Mol Biol. 1997 Apr 11;267(4):881-98. PMID:9135119 Page seeded by OCA on Sun May 4 20:15:06 2008

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OCA

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- {{Structure
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 '''A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT'''
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 ==About this Structure==
-D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. This structure supersedes the now removed PDB entry 273D. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=309D OCA].
+This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=273d 273d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=309D OCA].
 ==Reference==
 A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT., Qiu H, Dewan JC, Seeman NC, J Mol Biol. 1997 Apr 11;267(4):881-98. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9135119 9135119]
-[[Category: Protein complex]]
 [[Category: Dewan, J C.]]
 [[Category: Qiu, H X.]]
 [[Category: Seeman, N C.]]
-[[Category: b-dna]]
+[[Category: B-dna]]
-[[Category: continuous helix]]
+[[Category: Continuous helix]]
-[[Category: double helix]]
+[[Category: Double helix]]
-[[Category: overhanging base]]
+[[Category: Overhanging base]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:15:06 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:10 2008''