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Biomedical subjects

G R Clark

Publications and source records attributed to G R Clark.

At least 19 recordsLinked to original sources
PubMed2000

Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design.

The DNA photosensitisers m-iodo Hoechst and m-iodo, p-methoxy Hoechst have been co-crystallised with the oligonucleotide d(CGCGAATTCGCG)(2)and their crystal structures determined. The crystals were then subjected to slow dehydration, which reduced their solvent contents from 40 (normal) to 30 (partially dehydrated) and then 20% (fully dehydrated) and caused a reduction in cell volume from 68,000 to 60,000 then 51,000 A(3). The dehydration resulted in a dramatic enhancement of diffraction resolution from approximately 2.6 to beyond 1.5 A. Crystal structures have also been determined for the partially and fully dehydrated states. The fully dehydrated crystals consist of an infinite polymeric network, in which neighbouring dodecamer duplexes are crosslinked through phosphate oxygens via direct bonding to bridging magnesium cations. This unique three-dimensional structure for DNA is described in detail in the following companion paper. The present paper details evidence from the sequence of crystal structures that the DNA is able to breathe locally, allowing the ligand to leave the minor groove, re-orient in the surrounding solvent medium and then re-enter the groove in a different orientation and location. The rearrangement of the minor groove binding ligands during the dehydration process mimics the binding behaviour of these ligands in solution and in vivo. We also present details of the DNA-ligand interactions that are consistent with a hydrogen atom ion mechanism for photocleavage of DNA.

Animals↗
PubMed2000

Intermolecular interactions and water structure in a condensed phase B-DNA crystal.

By controlled dehydration, the unit cells of dodecamer DNA-drug crystals have been shrunk from 68,000 (normal state) to 60,000 (partially dehydrated intermediate state) to 51,000 A(3) (fully dehydrated state), beyond which no further solvent loss occurs. The total solvent content in the normal crystals is approximately 40% by volume, reducing to approximately 20% in the fully dehydrated phase. The 25% reduction in cell volume induced a dramatic enhancement in the resolution of the X-ray diffraction data (from 2. 6 to beyond 1.5 A). We have determined the structures of the normal, partially dehydrated and fully dehydrated crystals. Details of the ligand binding have been presented in the preceding article. The present paper describes the unique features of the structure of the fully dehydrated phase. This structure was refined with 9,015 unique observed reflections to R = 14.9%, making it one of the most reliable models of B -form DNA available. The crystals exist as infinite polymeric networks, in which neighbouring dodecamer duplexes are crosslinked through phosphate oxygens via direct bonding to magnesium cations. The DNA is packed so tightly that there is essentially only a single layer of solvent between adjacent molecules. The details of the crystal packing, magnesium bridging, DNA hydration and DNA conformation are described and compared with other experimental evidence related to DNA condensation.

Animals↗
PubMed1997

Minor groove binding of a bis-quaternary ammonium compound: the crystal structure of SN 7167 bound to d(CGCGAATTCGCG)2.

The X-ray crystal structure of the complex between the synthetic antitumour and antiviral DNA binding ligand SN 7167 and the DNA oligonucleotide d(CGCGAATTCGCG)2 has been determined to an R factor of 18.3% at 2.6 A resolution. The ligand is located within the minor groove and covers almost 6 bp with the 1-methylpyridinium ring extending as far as the C9-G16 base pair and the 1-methylquinolinium ring lying between the G4-C21 and A5-T20 base pairs. The ligand interacts only weakly with the DNA, as evidenced by long range contacts and shallow penetration into the groove. This structure is compared with that of the complex between the parent compound SN 6999 and the alkylated DNA sequence d(CGC[e6G]AATTCGCG)2. There are significant differences between the two structures in the extent of DNA bending, ligand conformation and groove binding.

Antineoplastic Agents↗
PubMed1997

Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.

The crystal structure is reported of a complex between the dodecanucleotide sequence d(CGCGAATTCGCG)2and an analogue of the DNA binding drug Hoechst 33258, in which the piperazine ring has been replaced by an amidinium group and the phenol ring by a phenylamidinium group. The structure has been refined to an R factor of 19.5% at 2.2 A resolution. The drug is held in the minor groove by five strong hydrogen bonds, together with bridging water molecules at both ends. There are few other contacts with the floor of the groove, indicating a lack of isohelicity with the groove and suggesting (i) that the observed high DNA affinity of this drug is primarily due to the array of hydrogen bonds and (ii) that these more than compensate for its poor isohelicity.

Base Sequence↗
PubMed1996

Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2.

An analogue of the DNA binding compound Hoechst 33258, which has the para hydroxyl group altered to be at the meta position, together with the replacement of one benzimidazole group by pyridylimidazole, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The X-ray structure has been determined at 2.2 A resolution and refined to an R factor of 20.1%. The ligand binds in the minor groove at the sequence 5'-AATTC with the bulky piperazine group extending over the CxG base pair. This binding is stabilised by hydrogen bonding and numerous close van der Waals contacts to the surface of the groove walls. The meta-hydroxyl group was found in two distinct orientations, neither of which participates in direct hydrogen bonds to the exocyclic amino group of a guanine base. The conformation of the drug differs from that found previously in other X-ray structures of Hoechst 33258-DNA complexes. There is significant variation between the minor groove widths in the complexes of Hoechst 33258 and the meta-hydroxyl derivative as a result of these conformational differences. Reasons are discussed for the inability of this derivative to actively recognise guanine.

Binding Sites↗
PubMed1996

Targeting the minor groove of DNA: crystal structures of two complexes between furan derivatives of berenil and the DNA dodecamer d(CGCGAATTCGCG)2.

Crystal structures are reported of complexes of two novel furan derivatives of berenil with alkyl benzamidine groups bound to the DNA sequence d(CGCGAATTCGCG)2. They have both been determined to 2.2 A resolution and refined to R factors of 16.9% and 18.6%. In both structures the alkyl substituents, cyclopropyl and isopropyl, are found to be orientated away from the floor of the minor groove. The drugs are located in the minor groove by two strong amidinium hydrogen bonds, to the O2 of the thymines situated at the 5' and 3' ends of the AT-rich region. The isopropyl-substituted derivative has a tight hydrogen-bonded water network in the minor groove at one amidine site, which alters the orientation of the isopropyl substituent. This compound has superior DNA-binding properties and activity against Pneumocystis carinii and Cryptosporidium parvum infections in vivo compared to the cyclopropyl derivative, which in turn is superior to the parent furan compound. We suggest that the nature and extent of the interactions of these compounds in the DNA minor groove play an important role in these activities, possibly in conjunction with a DNA-binding protein. The overall effect of these alkyl benzamidine substitutions is to increase the binding of the drugs to the minor groove.

Crystallography, X-Ray↗
PubMed1996

Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.

The crystal structure is reported of a tris(benzimidazole) analogue of the minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2. The structure has been refined to an R factor of 17.4% at a resolution of 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove width, together with high propeller twists for individual base pairs. The ligand has a highly twisted structure, with an overall twist of 50 degrees between aromatic rings. All three benzimidazole subunits are in register with the DNA, and there is a symmetric group of six hydrogen bonds between ligand and A.T base-pair edges. By contrast, the ligand does not show an optimal isohelical fit to the DNA. The correct phasing of drug and DNA base pairs is ensured by a number of changes to the DNA such that the central 5'-AAATTT region is slightly unwound relative to the structures of other noncovalent minor-groove drug complexes.

Benzimidazoles↗
PubMed1993

Structures of quinone imine metabolites related to the anti-cancer drug amsacrine.

(5): N-(9-Acridinyl)-3-methoxy-1,4-benzoquinone monoimine, C20H14N2O2, M(r) = 314.3, monoclinic, P2(1)/c, a = 13.451 (8), b = 7.007 (4), c = 17.864 (12) A, beta = 117.26 (4) degrees, V = 1497 (2) A3, Z = 4, Dm = 1.36 (1), Dx = 1.395 g cm-3, Mo K alpha, lambda = 0.71069 A, mu = 0.99 cm-1, F(000) = 656, T = 138 (5) K, R = 0.049 for 1556 reflections. (8): N-(9-Acridinyl)-2-methoxy-1,4- benzoquinone monoimine, C20H14N2O2, M(r) = 314.3, triclinic, P1, a = 9.365 (1), b = 13.318 (2), c = 6.918 (3) A, alpha = 96.45 (3), beta = 105.30 (2), gamma = 110.11 (1) degrees, V = 761.6 (4) A3, Z = 2, Dm = 1.35 (1), Dx = 1.371 g cm-3, Mo K alpha, lambda = 0.71069 A, mu = 0.98 cm-1, F(000) = 328, T = 292 (1) K, R = 0.075 for 1009 reflections. (13): N-(9-Acridinyl)-5-dimethylamino-2- methoxy-1,4-benzoquinone monoimine, C22H19N3O2, M(r) = 357.4, triclinic, P1, a = 8.091 (7), b = 10.078 (2), c = 11.716 (3) A, alpha = 108.39 (2), beta = 99.63 (4), gamma = 95.87 (3) degrees, V = 881.4 (9) A3, Z = 2, Dm = 1.33 (1), Dx = 1.347 g cm-3, Mo K alpha, lambda = 0.71069 A, mu = 0.95 cm-1, F(000) = 376, T = 173 (5) K, R = 0.034 for 1460 reflections. The molecular geometries are described and discussed.

Amsacrine↗
PubMed1990

Crystal and solution structures of the oligonucleotide d(ATGCGCAT)2: a combined X-ray and NMR study.

A combined crystal-structure determination and NMR analysis of the octanucleotide d(ATGCGCAT)2 is reported. The X-ray analysis shows that the structure is A-form duplex in crystal state. The NMR study shows that in solution this sequence is B-type. The conformational results from each technique are presented in detail. The implications of these findings in terms of conformational flexibility and ligand binding are discussed.

Base Sequence↗
PubMed1989

Methyl 2-[4-(2-chloroethyl)-2,3-dihydro-7-nitroquinoxalin-1-yl]benzoate from intramolecular cyclization of a nitroaromatic mustard.

C18H18CIN3O4, Mr = 375.81, orthorhombic, P212121, a = 11.000 (3), b = 8.023 (2), c = 19.316 (5) A, V = 1704.68 A3, Z = 4, Dm = 1.46 (1), Dx = 1.417 g cm-3, Mo Kalpha, lambda = 0.71069 A, mu = 1.82 cm-1, F(000) = 760, T = 293 (1) K, R = 0.051 for 985 [I greater than 2.5 sigma(I)] reflections. X-ray analysis confirms that the nitroaromatic mustard methyl N-(2-[bis(2-chloroethyl)amino]- 5-nitrophenyl)anthranilate undergoes rapid intramolecular cyclization, but the product is the 7-nitro rather than the 6-nitro derivative previously reported [Chambers & Denny (1986).

Antineoplastic Agents↗
PubMed1979

The crystal and molecular structure of the polymeric copper (II) complex of inosine 5'-monophosphate. A comparison with the previously reported zinc analogue.

X-ray analysis of [Cu . (5'-IMP) . H2O] has shown a structure containing polymeric chains of composition [Cu.5'-IMP]n in which the copper atom is directly bound to N(7) of the base and to three oxygen atoms of different phosphate groups. Whereas the coordination geometry in the analogous zinc complex resembles a distorted tetrahedrom, that in the copper complex is a distorted square plane with weak axial interactions.

Chemical Phenomena↗
PubMed1979

A prosthetic aid for a developing blind child.

An experimental ultrasonic sonar for use as a sensory aid with blind children is described. Novel signal processing techniques make the aid relatively simple to construct, yet allow many of its parameters to be changed in the field. In particular, the aid has two features, a variable range code and an automatic level control, which make the device very versatile in a wide variety of environments. The ultrasonic tranducers used in the aid are described in some detail.

Blindness↗