160d: Difference between revisions

Revision as of 12:38, 21 February 2008

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS

OverviewOverview

The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in the asymmetric unit. The structure was solved by molecular replacement and refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related molecule results in distortion of the backbone bonds of the fifth residue G(5), P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their favored gauche- and gauche+ conformations, respectively. In this close encounter the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11)) triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove, causing a toll on the backbone conformation of the adjacent residue G(5). A similar triplet base-pairing interaction with somewhat weaker hydrogen bonds occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20), does not perturb the backgone alpha and gamma torsions of G(15). Both the novel base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17) base-pair jolts the global helical base-pair parameters, inclination, tilt, roll, tip, etc. quite markedly. Therefore a better description of the helix parameters is obtained by splitting the duplex and calculating the local helix axis for the top half consisting of the first three base-pairs, and the lower half consisting of the last six base-pairs, omitting the fourth base-pair. The two half duplexes are bent by only 10 degrees. This structure further demonstrates that crystal packing interactions, which can also be governed by base sequence, play a dominant role in determining DNA conformation.

About this StructureAbout this Structure

160D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G*(G.C) triplets., Ramakrishnan B, Sundaralingam M, J Mol Biol. 1993 May 20;231(2):431-44. PMID:8510155

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-[[Image:160d.gif|left|200px]]<br /><applet load="160d" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="160d, resolution 1.650&Aring;" />
 '''HIGH RESOLUTION CRYSTAL STRUCTURE OF THE A-DNA DECAMER D(CCCGGCCGGG): NOVEL INTERMOLECULAR BASE-PAIRED G*(G.C) TRIPLETS'''<br />
 ==Overview==
-The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group, P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a, duplex in the asymmetric unit. The structure was solved by molecular, replacement and refined to an R factor of 18.5% using 6033 reflections at, 1.65 A resolution. The decamer duplex adopts an A-DNA conformation. The, abrupt dislocation of the duplex at the fourth base-pair G(4).C(17) by an, abutting symmetry related molecule results in distortion of the backbone, bonds of the fifth residue G(5), P-O(5')(alpha) and C(4')-C(5')(gamma), to, the trans conformations from their favored gauche- and gauche+, conformations, respectively. In this close encounter the terminal, G(10).C(11) base-pair of the symmetry related molecule hydrogen bonds to, the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11)), triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To, facilitate this hydrogen bonding the G(4).C(17) base-pair slides into the, minor groove, causing a toll on the backbone conformation of the adjacent, residue G(5). A similar triplet base-pairing interaction with somewhat, weaker hydrogen bonds occurs at the pseudo dyad related C(7).G(14), base-pair with G(20) of another symmetry related duplex. This pseudo, triplet interaction (C(7).G(14))*G(20), does not perturb the backgone, alpha and gamma torsions of G(15). Both the novel base triplets are, non-planar. The abrupt dislocation/bend at the G(4).C(17) base-pair jolts, the global helical base-pair parameters, inclination, tilt, roll, tip, etc. quite markedly. Therefore a better description of the helix, parameters is obtained by splitting the duplex and calculating the local, helix axis for the top half consisting of the first three base-pairs, and, the lower half consisting of the last six base-pairs, omitting the fourth, base-pair. The two half duplexes are bent by only 10 degrees. This, structure further demonstrates that crystal packing interactions, which, can also be governed by base sequence, play a dominant role in determining, DNA conformation.
+The DNA decamer d(CCCGGCCGGG) crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 24.88, b = 44.60 and c = 46.97 A containing a duplex in the asymmetric unit. The structure was solved by molecular replacement and refined to an R factor of 18.5% using 6033 reflections at 1.65 A resolution. The decamer duplex adopts an A-DNA conformation. The abrupt dislocation of the duplex at the fourth base-pair G(4).C(17) by an abutting symmetry related molecule results in distortion of the backbone bonds of the fifth residue G(5), P-O(5')(alpha) and C(4')-C(5')(gamma), to the trans conformations from their favored gauche- and gauche+ conformations, respectively. In this close encounter the terminal G(10).C(11) base-pair of the symmetry related molecule hydrogen bonds to the G(4).C(17) base-pair forming a novel base-paired G(4)*(G10).C(11)) triplet, where G(4) is hydrogen bonded to both G(10) and C(11). To facilitate this hydrogen bonding the G(4).C(17) base-pair slides into the minor groove, causing a toll on the backbone conformation of the adjacent residue G(5). A similar triplet base-pairing interaction with somewhat weaker hydrogen bonds occurs at the pseudo dyad related C(7).G(14) base-pair with G(20) of another symmetry related duplex. This pseudo triplet interaction (C(7).G(14))*G(20), does not perturb the backgone alpha and gamma torsions of G(15). Both the novel base triplets are non-planar. The abrupt dislocation/bend at the G(4).C(17) base-pair jolts the global helical base-pair parameters, inclination, tilt, roll, tip, etc. quite markedly. Therefore a better description of the helix parameters is obtained by splitting the duplex and calculating the local helix axis for the top half consisting of the first three base-pairs, and the lower half consisting of the last six base-pairs, omitting the fourth base-pair. The two half duplexes are bent by only 10 degrees. This structure further demonstrates that crystal packing interactions, which can also be governed by base sequence, play a dominant role in determining DNA conformation.
 ==About this Structure==
-D 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=160D OCA].
+D 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://oca.weizmann.ac.il/oca-bin/ocashort?id=160D OCA].
 ==Reference==
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 [[Category: double helix]]
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