161d

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(New page: 200px<br /><applet load="161d" size="450" color="white" frame="true" align="right" spinBox="true" caption="161d, resolution 1.900&Aring;" /> '''A SINGLE 2'-HYDROXY...)
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'''A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUCTURE OF THE DNA-RNA CHIMERIC DECAMER DUPLEX D(CCGGC)R(G)D(CCGG) WITH A NOVEL INTERMOLECULAR G.C BASE-PAIRED QUADRUPLET'''<br />
'''A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUCTURE OF THE DNA-RNA CHIMERIC DECAMER DUPLEX D(CCGGC)R(G)D(CCGG) WITH A NOVEL INTERMOLECULAR G.C BASE-PAIRED QUADRUPLET'''<br />
==Overview==
==Overview==
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We have found that the introduction of a single 2'-hydroxyl group on the, sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it, to A-DNA. Thus, for the first time the X-ray structures of the same, sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer, d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions a = 25.63 A, b = 45.24 A and c = 47.99 A, and, one decamer duplex in the asymmetric unit. The structure was solved by a, rigid body search using the coordinates of the isomorphous structure, d(CCCGGCCGGG) and refined to an R value of 0.136 using 2753 unique, reflections at 1.9 A resolution. The final model contains 406 nucleotide, atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA, geometry, with all the sugars in the C(3')-endo puckering and the, base-pairs inclined and displaced from the helix axis. The 2'-hydroxyl, groups on rG6 and rG16 protrude into the minor groove surface and form, different types of hydrogen bonds; that on strand 1 forms an, intermolecular hydrogen bond with the furanose ring O(4') of a, symmetry-related C1 residue, while that on strand 2 is involved in two, water bridges. Crystal packing forces the G4-G17 base-pair in the top half, of the duplex to slide significantly into the minor groove compared to the, corresponding G7-G14 base-pair in the bottom half, resulting in these, base-pairs exhibiting different base stacking and intermolecular, interactions. The base G4 of the G4-G17 base-pair forms an unorthodox base, "triple", G4*(G10-C11), hydrogen-bonding through its minor groove sites, N(2) and N(3) to the minor groove atoms N(2) and O(2) of both bases of the, G10-C11 base-pair of a symmetry-related molecule. The base G10 of this, triple in turn forms a second similar unorthodox base triple, G10*(G3*C18), with the adjacent base-pair G3-C18 of the duplex, thus G10, is involved in a double triple. On the other hand, in the bottom half of, the duplex, the C7-G14 base-pair is involved only in a single similar, unorthodox base triple with G20, (C7-G14)*G20, while the adjacent, base-pair rG6-C15 is involved in a novel quadruple with C1-G20, (rG6-C15), *(C1-G20), where the latter base-pairs are hydrogen-bonded to each other, via the minor groove sites G(N(2))...C(O(2)).(ABSTRACT TRUNCATED AT 400, WORDS)
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We have found that the introduction of a single 2'-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA. Thus, for the first time the X-ray structures of the same sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions a = 25.63 A, b = 45.24 A and c = 47.99 A, and one decamer duplex in the asymmetric unit. The structure was solved by a rigid body search using the coordinates of the isomorphous structure d(CCCGGCCGGG) and refined to an R value of 0.136 using 2753 unique reflections at 1.9 A resolution. The final model contains 406 nucleotide atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA geometry, with all the sugars in the C(3')-endo puckering and the base-pairs inclined and displaced from the helix axis. The 2'-hydroxyl groups on rG6 and rG16 protrude into the minor groove surface and form different types of hydrogen bonds; that on strand 1 forms an intermolecular hydrogen bond with the furanose ring O(4') of a symmetry-related C1 residue, while that on strand 2 is involved in two water bridges. Crystal packing forces the G4-G17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding G7-G14 base-pair in the bottom half, resulting in these base-pairs exhibiting different base stacking and intermolecular interactions. The base G4 of the G4-G17 base-pair forms an unorthodox base "triple", G4*(G10-C11), hydrogen-bonding through its minor groove sites N(2) and N(3) to the minor groove atoms N(2) and O(2) of both bases of the G10-C11 base-pair of a symmetry-related molecule. The base G10 of this triple in turn forms a second similar unorthodox base triple, G10*(G3*C18), with the adjacent base-pair G3-C18 of the duplex, thus G10 is involved in a double triple. On the other hand, in the bottom half of the duplex, the C7-G14 base-pair is involved only in a single similar unorthodox base triple with G20, (C7-G14)*G20, while the adjacent base-pair rG6-C15 is involved in a novel quadruple with C1-G20, (rG6-C15) *(C1-G20), where the latter base-pairs are hydrogen-bonded to each other via the minor groove sites G(N(2))...C(O(2)).(ABSTRACT TRUNCATED AT 400 WORDS)
==About this Structure==
==About this Structure==
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161D 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=161D OCA].
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161D 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=161D OCA].
==Reference==
==Reference==
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[[Category: double helix]]
[[Category: double helix]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:01:24 2007''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:38:33 2008''

Revision as of 09:38, 21 February 2008

Image:161d.jpg

161d, resolution 1.900Å

Drag the structure with the mouse to rotate

A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUCTURE OF THE DNA-RNA CHIMERIC DECAMER DUPLEX D(CCGGC)R(G)D(CCGG) WITH A NOVEL INTERMOLECULAR G.C BASE-PAIRED QUADRUPLET

Overview

We have found that the introduction of a single 2'-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA. Thus, for the first time the X-ray structures of the same sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions a = 25.63 A, b = 45.24 A and c = 47.99 A, and one decamer duplex in the asymmetric unit. The structure was solved by a rigid body search using the coordinates of the isomorphous structure d(CCCGGCCGGG) and refined to an R value of 0.136 using 2753 unique reflections at 1.9 A resolution. The final model contains 406 nucleotide atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA geometry, with all the sugars in the C(3')-endo puckering and the base-pairs inclined and displaced from the helix axis. The 2'-hydroxyl groups on rG6 and rG16 protrude into the minor groove surface and form different types of hydrogen bonds; that on strand 1 forms an intermolecular hydrogen bond with the furanose ring O(4') of a symmetry-related C1 residue, while that on strand 2 is involved in two water bridges. Crystal packing forces the G4-G17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding G7-G14 base-pair in the bottom half, resulting in these base-pairs exhibiting different base stacking and intermolecular interactions. The base G4 of the G4-G17 base-pair forms an unorthodox base "triple", G4*(G10-C11), hydrogen-bonding through its minor groove sites N(2) and N(3) to the minor groove atoms N(2) and O(2) of both bases of the G10-C11 base-pair of a symmetry-related molecule. The base G10 of this triple in turn forms a second similar unorthodox base triple, G10*(G3*C18), with the adjacent base-pair G3-C18 of the duplex, thus G10 is involved in a double triple. On the other hand, in the bottom half of the duplex, the C7-G14 base-pair is involved only in a single similar unorthodox base triple with G20, (C7-G14)*G20, while the adjacent base-pair rG6-C15 is involved in a novel quadruple with C1-G20, (rG6-C15) *(C1-G20), where the latter base-pairs are hydrogen-bonded to each other via the minor groove sites G(N(2))...C(O(2)).(ABSTRACT TRUNCATED AT 400 WORDS)

About this Structure

161D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

A single 2'-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d(CCGGC)r(G)d(CCGG) with a novel intermolecular G-C base-paired quadruplet., Ban C, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1994 Feb 11;236(1):275-85. PMID:7508984

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