275d: Difference between revisions

Revision as of 17:22, 21 February 2008

ALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE AS CANONICAL A-DNA

OverviewOverview

We have solved the single-crystal X-ray structures of two different hexanucleotides: the alternating sequence d(Gm5CGm5CGC), and the non-alternating sequence d(Gm5CCGGC). Both of these hexamers crystallize readily as A-DNA in the orthorhombic space group C222(1). Although hexanucleotides have been previously crystallized as Z-DNA, and in one case as B-DNA, this is the first time hexanucleotides have been crystallized as A-DNA. Both hexamers adopt a typical A-conformation, which is surprisingly more similar to the structure of A-DNA fibers than to other A-DNA single crystals. The structure of d(Gm5CGm5CGC) was solved to a resolution of 2.1 A (R-factor = 19.6%). This structure has all of the features characteristic of canonical A-DNA, including it's helical repeat (11.2 bp/turn), helical rise (2.6 A/bp), base-pair displacement (-4.7 A), base inclination angle (16.9 degrees), and sugar puckers that are predominantly 3'-endo. The lower resolution, non-alternating structure has similar overall average values for these parameters. We observed several sequence-dependent correlations in these parameters, especially in the d(CG) base step. These steps have lower twist and rise values, coupled with high roll angles as compared to d(GC) steps. The molecular interactions involved in crystal packing and the detailed structure of the bound water in the crystals, however, are similar to those of longer 8 and 10 bp A-DNA crystal structures. Although the structural effect of cytosine methylation on A-DNA appears to be minimal, this modification significantly affects the ability of these sequences to crystallize as A-DNA. In conclusion, we present the A-DNA forming class of hexanucleotides, a new crystallographic system for studying DNA structure at near atomic resolution.

About this StructureAbout this Structure

275D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA., Mooers BH, Schroth GP, Baxter WW, Ho PS, J Mol Biol. 1995 Jun 16;249(4):772-84. PMID:7602589

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 ==Overview==
-We have solved the single-crystal X-ray structures of two different, hexanucleotides: the alternating sequence d(Gm5CGm5CGC), and the, non-alternating sequence d(Gm5CCGGC). Both of these hexamers crystallize, readily as A-DNA in the orthorhombic space group C222(1). Although, hexanucleotides have been previously crystallized as Z-DNA, and in one, case as B-DNA, this is the first time hexanucleotides have been, crystallized as A-DNA. Both hexamers adopt a typical A-conformation, which, is surprisingly more similar to the structure of A-DNA fibers than to, other A-DNA single crystals. The structure of d(Gm5CGm5CGC) was solved to, a resolution of 2.1 A (R-factor = 19.6%). This structure has all of the, features characteristic of canonical A-DNA, including it's helical repeat, (11.2 bp/turn), helical rise (2.6 A/bp), base-pair displacement (-4.7 A), base inclination angle (16.9 degrees), and sugar puckers that are, predominantly 3'-endo. The lower resolution, non-alternating structure has, similar overall average values for these parameters. We observed several, sequence-dependent correlations in these parameters, especially in the, d(CG) base step. These steps have lower twist and rise values, coupled, with high roll angles as compared to d(GC) steps. The molecular, interactions involved in crystal packing and the detailed structure of the, bound water in the crystals, however, are similar to those of longer 8 and, 10 bp A-DNA crystal structures. Although the structural effect of cytosine, methylation on A-DNA appears to be minimal, this modification, significantly affects the ability of these sequences to crystallize as, A-DNA. In conclusion, we present the A-DNA forming class of, hexanucleotides, a new crystallographic system for studying DNA structure, at near atomic resolution.
+We have solved the single-crystal X-ray structures of two different hexanucleotides: the alternating sequence d(Gm5CGm5CGC), and the non-alternating sequence d(Gm5CCGGC). Both of these hexamers crystallize readily as A-DNA in the orthorhombic space group C222(1). Although hexanucleotides have been previously crystallized as Z-DNA, and in one case as B-DNA, this is the first time hexanucleotides have been crystallized as A-DNA. Both hexamers adopt a typical A-conformation, which is surprisingly more similar to the structure of A-DNA fibers than to other A-DNA single crystals. The structure of d(Gm5CGm5CGC) was solved to a resolution of 2.1 A (R-factor = 19.6%). This structure has all of the features characteristic of canonical A-DNA, including it's helical repeat (11.2 bp/turn), helical rise (2.6 A/bp), base-pair displacement (-4.7 A), base inclination angle (16.9 degrees), and sugar puckers that are predominantly 3'-endo. The lower resolution, non-alternating structure has similar overall average values for these parameters. We observed several sequence-dependent correlations in these parameters, especially in the d(CG) base step. These steps have lower twist and rise values, coupled with high roll angles as compared to d(GC) steps. The molecular interactions involved in crystal packing and the detailed structure of the bound water in the crystals, however, are similar to those of longer 8 and 10 bp A-DNA crystal structures. Although the structural effect of cytosine methylation on A-DNA appears to be minimal, this modification significantly affects the ability of these sequences to crystallize as A-DNA. In conclusion, we present the A-DNA forming class of hexanucleotides, a new crystallographic system for studying DNA structure at near atomic resolution.
 ==About this Structure==
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 Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA., Mooers BH, Schroth GP, Baxter WW, Ho PS, J Mol Biol. 1995 Jun 16;249(4):772-84. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7602589 7602589]
 [[Category: Protein complex]]
-[[Category: Baxter, W.W.]]
+[[Category: Baxter, W W.]]
-[[Category: Ho, P.S.]]
+[[Category: Ho, P S.]]
-[[Category: Mooers, B.H.]]
+[[Category: Mooers, B H.]]
-[[Category: Schroth, G.P.]]
+[[Category: Schroth, G P.]]
 [[Category: a-dna]]
 [[Category: double helix]]
 [[Category: modified]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:50:14 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:22:03 2008''