Crystal structure at 1.5-.ANG. resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures (original) (raw)
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The crystal structure of the deoxyhexamer, d(CGCICG), has been determined and refined to a resolution of 1.7A. The DNA hexamer crystallises in space group P2 1 2 1 2 1 with unit cell dimensions of a = 18.412 ± .017 A, b = 30.485±.036A, and c = 43.318±.024 A. The structure has been solved by rotation and translation searches and refined to an R-factor of 0.148 using 2678 unique reflections greater than 1.0 a (F) between 10.0-1.7 A resolution. Although the crystal parameters are similar to several previously reported Z-DNA hexamers, this Inoslne containing Z-DNA differs in the relative orientation, position, andcrystal packing Interactions compared to d(CGCGCG) DNA. Many of these differences in the inoslne form of Z-DNA can be explained by crystal packing Interactions, which are responsible for distortions of the duplex at different locations. The most noteworthy features of the inoslne form of Z-DNA as a result of such distortions are: (1) sugar puckers for the inoslnes are of CA'-exo type, (2) all phosphates have the Z, conformation, and (3) narrower minor grove and compression along the helical axis compared to d(CGCGCG) DNA. In addition, the substitution of guanoslne by Inosine appears to have resulted in Watson-Crick type base-pairing between Inoslne and cytidine with a potential bifurcated hydrogen bond between Inoslne N1 and cytidine N3 (2.9 A) and 02 (3.3-3.A). by guest on May 12, 2016 http://nar.oxfordjournals.org/ Downloaded from
Acta Cryst. (2016). D72, 1203-1211, 2016
The self-complementary d(CGCGCG) hexanucleotide was synthesized with both d-2 0-deoxyribose (the natural enantiomer) and l-2 0-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form with C2/c symmetry that diffracted X-rays to 0.78 A ˚ resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to an R factor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg 2+ sites. The crystal structure is comprised of both left-handed (d-form) and right-handed (l-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented d/l-DNA-Mg 2+ structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG) 2 duplex with those of other homochiral and heterochiral Z-DNA structures.
Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs
Nucleic Acids Research, 1988
The left-handed Z-DNA conformatlon has been observed in crystals made f rom the self -complementary DNA hexamer d(CACGTG). This is the first time that a non disordered Z form is found in the crystal structure of an alternating sequence containing AT base pairs without methylated or brominated cytosines.The structure has been determined and refined to an agreement f actor R:22.9X using 746 reflections in the resolution shell 7 to 2.5 A.
Structural Variability and New Intermolecular Interactions of Z-DNA in Crystals of d(pCpGpCpGpCpG)
Biophysical Journal, 1998
We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C222 1 with a ϭ 69.73, b ϭ 52.63, and c ϭ 26.21 Å, and to the space group P2 1 with a ϭ 49.87, b ϭ 41.26, c ϭ 21.91 Å, and ␥ ϭ 97.12°. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes.
Nucleic Acids Research Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs
2020
The left-handed Z-DNA conformatlon has been observed in crystals made f rom the self -complementary DNA hexamer d(CACGTG). This is the first time that a non disordered Z form is found in the crystal structure of an alternating sequence containing AT base pairs without methylated or brominated cytosines.The structure has been determined and refined to an agreement f actor R:22.9X using 746 reflections in the resolution shell 7 to 2.5 A. The overall shape of the molecule is very similar to the Zstructure of the related hexamer d(CG)3 confirming the rigldity of the Z f orm. No solvent molecules were detected In the minor groove of the helix near the A bases. The disruption of the spine of hydration in the AT step appears to be a general fact in the Z form in contrast with the B form. The biological relevance of the structure in relation to the CA genome repeats is discussed.
Structure of the DNA Octanucleotide d(ACGTACGT) 2
Acta Crystallographica Section D Biological Crystallography, 1996
d(ACGTACGT), C78H84N30032PT.20H20 , M r (DNA)= 2170, tetragonal, P43212 (No.96), a = 42.845 (1), b = 42.845 , c = 24.804 (1).A, V = 45532.5 (2) A 3, z = 8,2(MoKo0 = 0.71069 A,#(MoKc0 = 0.10 mm -1 , T = 295K, R = 0.18 for 1994 unique reflections between 5.0 and 1.9 A resolution. The self-complementary octanucleotide d(ACGTACGT)2 has been crystallized and its structure determined to a resolution of 1.9 A,. The asymmetric unit consists of a single strand of octamer with 20 water molecules. It is only the second example of an octanucleotide having terminal A.T base pairs whose structure has been determined by X-ray crystallography. The sequence adopts the modified Atype conformation found for all octanucleotide duplexes studied to date with the helix bent by approximately 15 ° and an average tilt angle of 0 °. Unusually the data collection was carried out using a 3 kW molybdenum sealed-tube source. The conformational details are discussed in comparison with other closely related sequences.
Crystal structure of the DNA sequence d(CGTGAATTCACG)2with DAPI
Acta Crystallographica Section F Structural Biology Communications, 2017
The structure of 4′,6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space groupP212121by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA–DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A–T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.
Acta Crystallographica Section D Structural Biology
The self-complementary L-d(CGCGCG)2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2′-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2′-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K+ cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5′ hydroxyl O atom, and is completed by ...