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O Kennard

Publications and source records attributed to O Kennard.

At least 19 recordsLinked to original sources
PubMed1991

DNA-drug interactions. The crystal structures of d(TGTACA) and d(TGATCA) complexed with daunomycin.

The anticancer drug daunomycin has been co-crystallized with the hexanucleotide duplex sequences d(TGTACA) and d(TGATCA) and single crystal X-ray diffraction studies of these two complexes have been carried out. Structure solution of the d(TGTACA) and d(TGATCA) complexes to 1.6 and 1.7 Angstrom resolution, respectively, shows two daunomycin molecules bound to the DNA hexamer. Binding occurs via intercalation of the drug chromophore at the d(TpG) step, and hydrogen bonding interactions involving the drug, DNA and solvent molecules. The daunomycin sugar is located in the minor groove of the DNA hexamer and is stabilized by hydrogen bonds between the amino group of the sugar and functional groups on the floor of the groove. The amino sugar of the d(TGATCA) duplex interacts directly with the DNA sequence, while in the d(TGTACA) duplex, the interaction is via solvent molecules. Two other complexes d(CGTACG)-daunomycin and d(CGATCG)-daunomycin have previously been structurally characterized. Comparison of the four structures with daunomycin bound to the triplet sequences 5'TGT, 5'TGA, 5'CGT and 5'CGA reveals changes in the conformation of both the DNA hexamer and the daunomycin upon complexation, as well as the hydrogen bonding and van der Waals' interactions.

Binding Sites↗
PubMed1990

Molecular and crystal structure of d(CGCGmo4CG): N4-methoxycytosine.guanine base-pairs in Z-DNA.

The base analogue N4-methoxycytosine (mo4C) is ambivalent in its hydrogen-bonding potential, since it forms stable base-pairs with both adenine and guanine in oligomer duplexes. To investigate the base-pair geometry, the structure of d(CGCGmo4CG) has been determined by single-crystal X-ray diffraction techniques. The d(CGCGmo4CG)2 crystallized in a left-handed double helical structure (Z-type). Refinement using 2559 reflections between 10 and 1.7 A converged with a final R = 0.181 (Rw = 0.130) including 68 solvent molecules. The orthorhombic crystals are in the space group P2(1)2(1)2(1), with cell dimensions a = 18.17 A, b = 30.36 A, c = 43.93 A. The mo4C.G base-pair is of the wobble type, with mo4C in the imino form, and the methoxy group in the syn configuration.

Base Composition↗
PubMed1989

DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin.

The structure of a d(CGATCG)-daunomycin complex has been determined by single crystal X-ray diffraction techniques. Refinement, with the location of 40 solvent molecules, using data up to 1.5 A, converged with a final crystallographic residual, R = 0.25 (RW = 0.22). The tetragonal crystals are in space group P4(1)2(1)2, with cell dimensions of a = 27.98 A and c = 52.87 A. The self-complementary d(CGATCG) forms a distorted right-handed helix with a daunomycin molecule intercalated at each d(CpG) step. The daunomycin aglycon chromophore is oriented at right-angles to the long axis of the DNA base-pairs. This head-on intercalation is stabilized by direct hydrogen bonds and indirectly via solvent-mediated, hydrogen-bonding interactions between the chromophore and its intercalation site base-pairs. The cyclohexene ring and amino sugar substituent lie in the minor groove. The amino sugar N-3' forms a hydrogen bond with O-2 of the next neighbouring thymine. This electrostatic interaction helps position the sugar in a way that results in extensive van der Waals contacts between the drug and the DNA. There is no interaction between daunosamine and the DNA sugar-phosphate backbone. We present full experimental details and all relevant conformational parameters, and use the comparison with a d(CGTACG)-daunomycin complex to rationalize some neighbouring sequence effects involved in daunomycin binding.

Base Sequence↗
PubMed1989

Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions.

Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, space group P4(3)2(1)2, has dimensions a = 42.53 and c = 24.33 A. The asymmetric unit consists of a single strand or four base pairs. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed duplex. This octamer duplex has a mean helix rotation of 32 degrees, 11.3 base pairs per turn, an average rise of 3.1 A, C3'-endo furanose conformations, a shallow minor groove, and a deep major groove. Such averaged parameters suggest classification of the octamer as a member of the A-DNA family. However, the global parameters tend to mask variations in conformational parameters observed at the level of the base pairs. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation. These structural features may be directly related to certain sequence-specific protein-DNA interactions involving nucleases and repressors.

Base Composition↗
PubMed1989

Coexistence of A- and B-form DNA in a single crystal lattice.

It is well known that DNA can exist in a variety of conformations which can be interconverted by relatively mild changes in conditions. The in vivo conformation of DNA is usually thought to be the B form, but there is recent evidence that other conformations may be important in DNA-protein recognition. Different fragments of DNA crystallized under virtually identical conditions can form A, B or Z helices. A fragment that adopted an A conformation in a crystal was found in the B conformation in solution, whereas NMR spectroscopy of A-DNA films revealed the presence of a substantial amount of disordered B-DNA. Until now, however, a DNA fragment of a given sequence has not been crystallized in more than one global conformation. We report here an X-ray diffraction study of crystals of the DNA octamer dGGBrUABrUACC. In addition to a 'framework' of A-DNA, which gives discrete X-ray reflections, there are partially disordered B-DNA helices, recognized by their diffuse scattering features.

Bromodeoxyuridine↗
PubMed1989

Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.

The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7A. The sequence crystallises in space group P6(1), with unit cell dimensions a = b = 45.07, c = 45.49A. The refinement converged with a crystallographic residual R = 0.14 and the location of 81 solvent molecules. The octamer forms an A-DNA duplex with 6 Watson-Crick (G.C) base pairs and 2 inosine-thymine (I.T) pairs. Refinement of the structure shows it to be essentially isomorphous with that reported for d(GGGGCTCC) with the mispairs adopting a "wobble" conformation. Conformational parameters and base stacking interactions are compared to those for the native duplex d(GGGGCCCC) and other similar sequences. A rationale for the apparent increased crystal packing efficiency and lattice stability of the I.T octamer is given.

Base Composition↗
PubMed1989

Binding of actinomycin D to DNA: evidence for a nonclassical high-affinity binding mode that does not require GpC sites.

We have employed a combination of temperature-dependent UV absorption spectroscopy, circular dichroism, and batch calorimetry to characterize the binding of actinomycin D to a series of oligomeric DNA duplexes. We find the duplex [d(CGTCGACG)]2 to be unique in its ability to bind actinomycin D strongly despite the absence of a classic GpC site. We present evidence that this non-GpC-containing duplex binds two actinomycin D molecules in an apparently cooperative manner to form a complex that exhibits aberrant spectroscopic and calorimetric behavior. We propose that these observations are consistent with actinomycin D exhibiting a high-affinity, sequence-dependent DNA-binding mode distinct from its classic binding to isolated GpC sites.

Base Sequence↗
PubMed1988

Crystallization and preliminary analysis of the deoxyoligonucleotide d(CGTAGATCTACG).

Two crystal forms of the self-complementary DNA 12-mer d(CGTAGATCTACG) were grown by the vapour diffusion technique. Form I is in space group C2 with a = 64.8 A, b = 35.4 A, c = 24.4 A and beta = 92.2 (1 A = 0.1 nm). The crystals are grown as monoclinic blocks or hexagonal plates. There are two strands (one duplex) in the asymmetric unit. Form II crystallizes as monoclinic blocks, space group P21 with a = 64.5 A, b = 35.1 A, c = 25.2 A and beta = 91.8 degrees. This form contains four strands (2 duplexes) in the asymmetric unit. Both forms are suitable for high resolution X-ray analysis. The diffraction patterns suggest that the DNA is in a B-type conformation and that the packing in the two forms is very similar.

Crystallization↗
PubMed1987

Inosine.adenine base pairs in a B-DNA duplex.

The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) has been determined by single crystal X-ray diffraction techniques at 2.5A resolution. The refinement converged with a crystallographic residual, R = 0.19 and the location of 64 solvent molecules. The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs.

Adenine↗
PubMed1987

Structural features and hydration of a dodecamer duplex containing two C.A mispairs.

X-ray diffraction techniques have been used to characterise the crystal and molecular structure of the deoxyoligomer d(C-G-C-A-A-A-T-T-C-G-C-G) at 2.5A resolution. The final R factor is 0.19 with the location of 78 solvent molecules. The oligomer crystallises in a B-DNA type conformation with two strands coiled about each other to produce a duplex. This double helix consists of four A.T and six G.C Watson-Crick base pairs and two C.A mispairs. The mismatched base pairs adopt a "wobble" type structure with the cytosine displaced laterally into the major groove, the adenine into the minor groove. We have proposed that the two close contacts observed in the C.A pairing represent two hydrogen bonds one of which results from protonation of adenine. The mispairs are accommodated in the double helix with small adjustments in the conformation of the sugar-phosphate backbone. Details of the backbone conformation, base stacking interactions, thermal parameters and the hydration are now presented and compared with those of the native oligomer d(C-G-C-G-A-A-T-T-C-G-C-G) and with variations of this sequence containing G.T and G.A mispairs.

Base Composition↗
PubMed1987

The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution.

The structure of the deoxyoligomer d(C-G-C-G-A-A-T-T-T-G-C-G) was determined at 2.5-A resolution by single crystal x-ray diffraction techniques. The final R factor is 18% with the location of 71 water molecules. The oligomer crystallizes in a B-DNA-type conformation, with two strands interacting to form a dodecamer duplex. The double helix consists of four A X T and six G X C Watson-Crick base pairs and two G X T mismatches. The G X T pairs adopt a "wobble" structure with the thymine projecting into the major groove and the guanine into the minor groove. The mispairs are accommodated in the normal double helix by small adjustments in the conformation of the sugar phosphate backbone. A comparison with the isomorphous parent compound containing only Watson-Crick base pairs shows that any changes in the structure induced by the presence of G X T mispairs are highly localized. The global conformation of the duplex is conserved. The G X T mismatch has already been studied by x-ray techniques in A and Z helices where similar results were found. The geometry of the mispair is essentially identical in all structures so far examined, irrespective of the DNA conformation. The hydration is also similar with solvent molecules bridging the functional groups of the bases via hydrogen bonds. Hydration may be an important factor in stabilizing G X T mismatches. A characteristic of Watson-Crick paired A X T and G X C bases is the pseudo 2-fold symmetry axis in the plane of the base pairs. The G X T wobble base pair is pronouncedly asymmetric. This asymmetry, coupled with the disposition of functional groups in the major and minor grooves, provides a number of features which may contribute to the recognition of the mismatch by repair enzymes.

Base Sequence↗
PubMed1986

Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C].

The compound Rp-d[Gp(S)CpGp(S)CpGp(S)C], an analogue of the deoxyoligomer d(G-C)3, crystallizes in space group P2(1)2(1)2(1) with a = 34.90 A, b = 39.15 A and c = 20.64 A. The structure, which is not isomorphous with any previously determined deoxyoligonucleotide, was refined to an R factor of 14.5% at a resolution of 2.17 A, with 72 solvent molecules located. The two strands of the asymmetric unit form a right-handed double helix, which is a new example of a B-DNA conformation and brings to light an important and overlooked component of flexibility of the double helix. This flexibility is manifest in the alternation of the backbone conformation between two states, defined by the adjacent torsion angles epsilon and zeta, trans . gauche-(BI) and gauche-. trans (BII). BI is characteristic of classical of B-DNA and has an average C(1') to C(1') separation of 4.5 A. The corresponding separation for BII is 5.3 A. Each state is associated with a distinct phosphate orientation where the plane of the PO2 (or POS) group is alternately near horizontal or vertical with respect to the helix axis. The BI and BII conformations are out of phase on the two strands. As a consequence, on one strand purine-pyrimidine stacking is better than pyrimidine-purine, while the converse holds for the other strand. At each base-pair step, good and bad stacking alternate across the helix axis. The pattern of alternation is regular in the context of a fundamental dinucleotide repeat. Re-examination of the B-DNA dodecamer d(C-G-C-G-A-A-T-T-C-G-C-G) shows that the C-G-C-G regions contain the BI and BII conformations, and the associated dual phosphate orientation and asymmetric base stacking. Different mechanisms are used in the two structures to avoid clashes between guanine residues on opposite strands, a combination of lateral slide, tilt and helical twist in the present structure, and base roll, tilt and longitudinal slide (Calladine rules) in the dodecamer. The flexibility of the phosphate orientations demonstrated in this structure is important, since it offers a structural basis for protein-nucleic acid recognition.

Crystallization↗
PubMed1986

Refined crystal structure of an octanucleotide duplex with G . T mismatched base-pairs.

Single crystal X-ray diffraction techniques have been used to determine the structure of the DNA octamer d(G-G-G-G-C-T-C-C) at a resolution of 2.25 A. The asymmetric unit consists of two strands coiled about each other to produce an A-type DNA helix. The double helix contains six G . C Watson-Crick base-pairs and two G . T mismatched base-pairs. The mismatches adopt a "wobble" type structure in which both bases retain their major tautomer forms. The double helix is able to accommodate this G . T pairing with little distortion of the overall helical conformation. Crystals of this octamer melt at a substantially lower temperature than do those of a related octamer also containing two G . T base-pairs. We attribute this destabilization to disruption of the hydration network around the mismatch site combined with changes in intermolecular packing. Full details are given of conformational parameters, base stacking, intermolecular contacts and hydration involving 52 solvent molecules.

Base Composition↗
PubMed1986

Structural characterisation of the bromouracil.guanine base pair mismatch in a Z-DNA fragment.

The deoxyoligonucleotide d(BrU-G-C-G-C-G) was crystallised at pH 8.2 and its structure analysed by X-ray diffraction. The unit cell, of dimensions a = 17.94, b = 30.85, c = 49.94A contains four DNA duplexes in space group P2(1)2(1)2(1). The duplexes are in the Z conformation, with four Watson-Crick G.C base pairs and two BrU.G base pairs. The structure was refined to an R factor of 0.16 at a resolution of 2.2A with 64 solvent molecules located. The BrU.G base pair mismatch is of the wobble type, with both bases in the major tautomer form and hydrogen bonds linking 0-2 of BrU with N-1 of G and N3 of BrU with 0-6 of G. There is no indication of the presence of ionised base pairs, in spite of the high pH of crystallisation. The results are discussed in terms of the mutagenic properties of 5- bromouracil.

Bromodeoxyuridine↗
PubMed1986

Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations.

The synthetic deoxydodecamer d(C-G-C-G-A-A-T-T-A-G-C-G) was analyzed by x-ray diffraction methods, and the structure was refined to a residual error of R = 0.17 at 2.5-A resolution (2 sigma data) with 83 water molecules located. The sequence crystallizes as a full turn of a B-DNA helix and contains 2 purine X purine (G.A) base pairs and 10 Watson-Crick base pairs. The analysis shows conclusively that adenine is in the syn orientation with respect to the sugar moiety whereas guanine adopts the usual trans orientation. Nitrogen atoms of both bases are involved in hydrogen bonding with the N-1 of guanine 2.84 A from the N-7 of adenine and the N-6 of adenine within 2.74 A of the O-6 of guanine. The C-1'...C-1' separation is 10.7 A close to that for standard Watson-Crick base pairs. The incorporation of the purine.purine base pairs at two steps in the dodecamer causes little perturbation of either the local or the global conformation of the double helix. Comparison of the structural features with those of the G.T wobble pair and the standard G.C pair suggests a rationale for the differential enzymatic repair of the two types of base-pair mismatches.

Chemical Phenomena↗
PubMed1986

Structural features and hydration of d(C-G-C-G-A-A-T-T-A-G-C-G); a double helix containing two G.A mispairs.

Single crystal X-ray diffraction techniques have been used to characterise the molecular structure of the title compound to 2.5A resolution. The structure consists of ten standard Watson-Crick base pairs and two G.A mismatched base pairs. The purine-purine mismatches have guanine in the usual anti orientation with respect to the sugar and adenine in syn orientation. There are two hydrogen bonds formed between the mismatch bases, N-1 and O-6 of guanine with N-7 and N-6 of adenine respectively. The bulky purine-purine mismatches are accommodated with minor perturbation of the sugar-phosphate backbone. There is a slight improvement in base pair overlap at the mismatch sites. Details of the backbone conformation, base stacking interactions and hydration are presented and compared with those of the parent compound d(C-G-C-G-A-A-T-T-C-G-C-G).

Base Composition↗