260d
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:260d.gif|left|200px]] | [[Image:260d.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_260d", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_260d| PDB=260d | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II''' | '''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=260D OCA]. | |
==Reference== | ==Reference== | ||
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873996 8873996] | Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873996 8873996] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Ban, C.]] | [[Category: Ban, C.]] | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
| - | [[Category: | + | [[Category: A-dna]] |
| - | [[Category: | + | [[Category: Double helix]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:24:15 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 15:24, 3 May 2008
CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II
Overview
The crystal structure of the alternating 5'-purine start decamer d(GCGCGCGCGC) was found to be in the left-handed Z-DNA conformation. Inasmuch as the A.T base pair is known to resist Z-DNA formation, we substituted A.T base pairs in the dyad-related positions of the decamer duplex. The alternating self-complementary decamer d(GCACGCGTGC) crystallizes in a different hexagonal space group, P6(1)22, with very different unit cell dimensions a = b = 38.97 and c = 77.34 A compared with the all-G.C alternating decamer. The A.T-containing decamer has one strand in the asymmetric unit, and because it is isomorphous to some other A-DNA decamers it was considered also to be right-handed. The structure was refined, starting with the atomic coordinates of the A-DNA decamer d(GCGGGCCCGC), by use of 2491 unique reflections out to 1.9-A resolution. The refinement converged to an R value of 18.6% for a total of 202 nucleotide atoms and 32 water molecules. This research further demonstrates that A.T base pairs not only resist the formation of Z-DNA but can also assist the formation of A-DNA by switching the helix handedness when the oligomer starts with a 5'-purine; also, the length of the inner Z-DNA stretch (d(CG)n) is reduced from an octamer to a tetramer. It may be noted that these oligonucleotide properties are in crystals and not necessarily in solutions.
About this Structure
Full crystallographic information is available from OCA.
Reference
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:8873996 Page seeded by OCA on Sat May 3 18:24:15 2008
