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L D Williams

Publications and source records attributed to L D Williams.

At least 55 records · Page 3Linked to original sources
PubMed1992

Variable temperature infrared spectroscopy of cytosine-guanine base pairs: tautomerism versus polarization.

This report describes an infrared (IR) spectroscopic study of a model cytosine-guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O6-methylguanosine (O6MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35,724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw,J.Am.Chem.Soc. 112,829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent, but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C = O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O6-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.

Base Composition↗
PubMed1991

Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution.

We describe the three-dimensional X-ray structure of a complex of spermine bound to a Z-DNA duplex, [d(CGCGCG)]2, in the absence of any inorganic polyvalent cations. We have crystallized the DNA hexamer d(CGCGCG) in the exclusion of magnesium and other polyvalent ions and solved its structure at 1.0-A resolution. In the crystal of this pure-spermine form of Z-DNA, the relative orientation, position, and interactions of the DNA differ from the arrangement uniformly observed in over a dozen previously reported Z-DNA hexamers. Moreover, the conformation of the Z-DNA hexamer in this structure varies somewhat from those found in earlier structures. The DNA is compressed along the helical axis, the base pairs are shifted into the major groove, and the minor groove is more narrow. The packing of spermine-DNA complexes in crystals suggests that the molecular basis for the tendency of spermine to stabilize compact DNA structures derives from the capacity of spermine to interact simultaneously with several duplexes. This capacity is maximized by both the polymorphic nature and the length of the spermine cation. The length and flexibility of spermine and the dispersion of charge-charge, hydrogen-bonding, and hydrophobic bonding potential throughout the molecule maximize the ability of spermine to interact simultaneously with different DNA molecules.

Base Sequence↗
PubMed1991

Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex.

Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)]2. The DNA in the complex with ditercalinium is kinked (by 15 degrees) and severely unwound (by 36 degrees) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix.

Base Sequence↗
PubMed1991

DNA-nogalamycin interactions.

The anthracycline antibiotic nogalamycin differs from the more common daunomycin-type anthracyclines by substitution on both ends of the intercalating chromophore, giving nogalamycin the approximate shape of a dumbbell. The chromophore of daunomycin is substituted on only one end. In nogalamycin, the positively charged amino sugar substituent of daunomycin is replaced by an uncharged nogalose sugar and a methyl ester group. The other end of nogalamycin, where daunomycin is unsubstituted, is fused to a bicyclo amino sugar with a positively charged dimethylamino group. Much larger DNA fluctuations are required for intercalative entry of nogalamycin than for entry of daunomycin. This report describes the X-ray crystal structure of the complex between nogalamycin and the self-complementary DNA hexamer d(me5CGTsAme5CG). The DNA contains cytosines methylated at the 5-positions and a phosphorothioate linkage at the TpA step. Nogalamycin intercalates at the terminal CpG steps and interacts with both strands in both grooves of the DNA. Large conformational adjustments in both nogalamycin and the DNA are necessary to form a stable, intercalative complex. The interactions of the bases with the nogalamycin substituents lead to sliding of bases relative to each other along the normal to Watson-Crick hydrogen bonds. The planarities of base pairs surrounding the intercalation site are distorted. The backbones of the two strands are distorted asymmetrically by nogalamycin with large deviations from standard B-DNA geometry. The complex between nogalamycin and DNA illustrates the conformational flexibility of DNA. The hydrogen-bonding interactions between nogalamycin and DNA do not suggest a sequence-specific binding of the drug, although additional secondary effects might lead to differences between various intercalation sites.

Crystallography↗
PubMed1991

Implications and concepts of polyamine-nucleic acid interactions.

Modeling, x-ray diffraction, and solution studies have contributed to the understanding of interactions between polyamines and nucleic acids. Polyamines stabilize a variety of unusual DNA structures and conformations in vitro, including both the left-handed Z and the right-handed A DNA. In addition, polyamines condense DNA and may be important in bending specific sequences. Investigations into the mechanisms of these effects provide support for both specific and nonspecific interactions between polyamines and DNA. Although exact relationships between the binding of polyamines and conformational changes in nucleic acids are still being clarified, polyamines remain important candidates for regulators of DNA conformation in vivo.

Crystallography↗
PubMed1991

Preparation of long-acting superoxide dismutase using high molecular weight polyethylene glycol (41,000-72,000 daltons).

Superoxide dismutase (SOD) has demonstrated therapeutic potential for treating a variety of conditions including radiation injury, oxygen toxicity, reperfusion injury, and inflammation, especially arthritis. However, the native enzyme's short half-life in plasma (6 minutes in mice, 25 minutes in man) limits the enzyme's effectiveness in many applications, or requires infusion of large doses. High doses of SOD derived from either natural or rDNA sources may increase the potential for immunologic sensitization. One effective use of native SOD is intra-articular administration for treatment of arthritis, where injection of SOD into joints retards elimination (15 hour terminal half-life), allowing the effective use of lower doses. To overcome the limitations resulting from rapid clearance, various researchers have increased the persistence of SOD by cross-linking SOD or by attaching polymeric substances, including dextrans, albumin, Ficoll, polyvinyl alcohol or polyethylene glycol (PEG). PEG is relatively safe; however, the amount of modification by PEG, is the MW range 1,900-5,000 daltons, which is necessary to optimally increase serum persistence and reduce immunogenicity, results in the loss of much of the enzymatic activity. In this report we describe the preparation of SOD adducts containing 1 to 4 strands of high MW PEG (41,000-72,000 daltons). The MW range of these adducts, measured by steric exclusion HPLC based on protein standards, is 200,000 to over 1,000,000 daltons. The number of PEG strands attached per SOD dimer (32,000 daltons) was measured by HPLC. Because of the low degree of protein modification required to produce very high MW products, these PEG-SODs retain 90%-100% of the SOD activity of the native enzyme. Additionally, these very large adducts demonstrate longer persistence and lower immunogenicity and antigenicity compared to the more highly modified PEG-SODs containing low MW PEG (i.e., 7-16 strands of 5,000 dalton methoxy-PEG).

Chromatography, Ion Exchange↗
PubMed1990

Ternary interactions of spermine with DNA: 4'-epiadriamycin and other DNA: anthracycline complexes.

The recently developed anthracycline 4'-epiadriamycin, an anti-cancer drug with improved activity, differs from adriamycin by inversion of the stereochemistry at the 4'-position. We have cocrystallized 4'-epiadriamycin with the DNA hexamer d(CGATCG) and solved the structure to 1.5 A resolution using x-ray crystallography. One drug molecule binds at each d(CG) step of the hexamer duplex. The anthracycline sugar binds in the minor groove. A feature of this complex which distinguishes it from the earlier DNA:adriamycin complex is a direct hydrogen bond from the 4'-hydroxyl group of the anthracycline sugar to the adenine N3 on the floor of the DNA minor groove. This hydrogen bond results directly from inversion of the stereochemistry at the 4'-position. Spermine molecules bind in the major groove of this complex. In anthracycline complexes with d(CGATCG) a spermine molecule binds to a continuous hydrophobic zone formed by the 5-methyl and C6 of a thymidine, C5 and C6 of a cytidine and the chromophore of the anthracycline. This report discusses three anthracycline complexes with d(CGATCG) in which the spermine molecules have different conformations yet form extensive van der Waals contacts with the same hydrophobic zone. Our results suggest that these hydrophobic interactions of spermine are DNA sequence specific and provide insight into the question of whether DNA:spermine complexes are delocalized and dynamic or site-specific and static.

Antibiotics, Antineoplastic↗
PubMed1990

Structure of 11-deoxydaunomycin bound to DNA containing a phosphorothioate.

The anthracyclines form an important family of cancer chemotherapeutic agents with a strong dependence of clinical properties on minor differences in chemical structure. We describe the X-ray crystallographic solution of the three-dimensional structure of the anthracycline 11-deoxydaunomycin plus d(CGTsACG). In this complex, two drug molecules bind to each hexamer duplex. Both the drug and the DNA are covalently modified in this complex in contrast with the three previously reported DNA-anthracycline complexes. In the 11-deoxydaunomycin complex the 11 hydroxyl group is absent and a phosphate oxygen at the TpA step has been replaced by a sulfur atom leading to a phosphorothioate with absolute stereochemistry R. Surprisingly, removal of a hydroxyl group from the 11 position does not alter the relative orientation of the intercalated chromophore. However, it appears that the phosphorothioate modification influenced the crystallization and caused the 11-deoxydaunomycin-d(CGTsACG) complex to crystallize into a different lattice (space group P2) with different lattice contacts and packing forces than the non-phosphorothioated DNA-anthracycline complexes (space group P4(1)2(1)2). In the minor groove of the DNA, the unexpected position of the amino-sugar of 11-deoxydaunomycin supports the hypothesis that in solution the position of the amino sugar is dynamic.

DNA↗
PubMed1990

Chemical reactivity of potassium permanganate and diethyl pyrocarbonate with B DNA: specific reactivity with short A-tracts.

We have examined the reactivity of B DNA with two chemical probes of DNA structure, potassium permanganate (KMnO4; thymine specific) and diethyl pyrocarbonate (DEPC; purine specific, A greater than G). The DNA probed is from the beta-lactamase promoter region of the vector pBR322, and from the 3' noncoding region of a chicken embryonic myosin heavy chain gene. The chemical probes display variable reactivity with the susceptible bases in these fragments, suggesting that modification of these bases by KMnO4 and DEPC is quite sequence dependent. In contrast, these probes react with the short A-tracts present in these DNA fragments in a reproducible fashion, generating two related patterns of reactivity. In the majority of the A-tracts, all but the 3'-terminal thymine are protected from KMnO4 attack, while DEPC reacts significantly with all but the 3'-terminal adenine of the A-tracts. Some A-tracts also display a very high DEPC reactivity at the adenine adjacent to the 3'-terminal unreactive adenine. Little qualitative difference in the KMnO4 reactivity of the A-tracts was found between 12 and 43 degrees C. However, at lower temperatures the elevated KMnO4 reactivity at the 3'-terminal A-tract thymine is sometimes lost. Raising the temperature of the KMnO4 reaction can cause relatively large increases in the reactivity of some single thymines, suggesting that significant local changes in stacking occur at these thymines at elevated temperatures. The data presented suggest that many short A-tracts embedded in long fragments of DNA can assume a number of related structures in solution, each of which possess distinct junctions with the flanking DNA. This result is consistent with high-resolution structural studies on oligonucleotides containing short A-tracts. The relevance of these results to current models of A-tract structure and DNA bending is discussed. Our data also indicate that KMnO4 and DEPC are potentially useful reagents for the study of sequence-dependent variations in B DNA structure.

Adenine↗
PubMed1990

Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin.

The anticancer drugs adriamycin and daunomycin have each been crystallized with the DNA sequence d(CGATCG) and the three-dimensional structures of the complexes solved at 1.7- and 1.5-A resolution, respectively. These antitumor drugs have significantly different clinical properties, yet they differ chemically by only the additional hydroxyl at C14 of adriamycin. In these complexes the chromophore is intercalated at the CpG steps at either end of the DNA helix with the amino sugar extended into the minor groove. Solution of the structure of daunomycin bound to d(CGATCG) has made it possible to compare it with the previously reported structure of daunomycin bound to d(CGTACG). Although the two daunomycin complexes are similar, there is an interesting sequence dependence of the binding of the amino sugar to the A-T base pair outside the intercalation site. The complex of daunomycin with d(CGATCG) has tighter binding than the complex with d(CGTACG), leading us to infer a sequence preference in the binding of this anthracycline drug. The structures of daunomycin and adriamycin with d(CGATCG) are very similar. However, there are additional solvent interactions with the adriamycin C14 hydroxyl linking it to the DNA. Surprisingly, under the influence of the altered solvation, there is considerable difference in the conformation of spermine in these two complexes. The observed changes in the overall structures of the ternary complexes amplify the small chemical differences between these two antibiotics and provide a possible explanation for the significantly different clinical activities of these important drugs.

Amino Sugars↗
PubMed1990

Structure of nogalamycin bound to a DNA hexamer.

The anthracycline antibiotic nogalamycin, which binds to DNA, is composed of a planar aglycone substituted on each end to form an unusual dumbbell-shaped molecule. At one end nogalamycin contains an uncharged nogalose sugar and a methyl ester. At the other end nogalamycin contains a positively charged bicyclo amino sugar. We report the crystal structure of nogalamycin bound to the self-complementary DNA hexamer d(m5CGTsAm5CG). In this complex, the cytosines are methylated at the 5 position and the DNA contains a phosphorothioate linkage at the TpA step. Two nogalamycin molecules bind to the 6-base-pair fragment of double-helical DNA. The drug has threaded between the phosphodiester backbones with three aromatic rings intercalated within the DNA. In the major groove, the bicyclo amino sugar forms two direct hydrogen bonds to span a CG base pair and interacts indirectly with the next base pair of the duplex via a water-mediated hydrogen bond. In the minor groove, a carbonyl oxygen of nogalamycin forms a hydrogen bond directly to N2 of a guanine. The DNA base pairs are severely buckled by up to 26 degrees and are also distorted in directions perpendicular to the Watson-Crick hydrogen bonds. This complex illustrates the deformable nature of DNA.

Base Sequence↗
PubMed1990

Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid.

Cyclic diguanylic acid acts as a regulator for cellulose synthase activity in the bacterium Acetobacter xylinum. We report the x-ray crystal structure of the regulator at atomic resolution. The structure contains two independent molecules that adopt almost identical conformations. The two molecules form self-intercalated units that are stacked on each other. Two different G.G base-pairing modes occur between the stacks. The more stable one has two or possibly three hydrogen bonds between two guanines and is related to the type of hydrogen bonding that is believed to exist between G-rich strands at the ends of chromosomes.

Acetobacter↗
PubMed1989

The Bender-Gestalt as a method of personality assessment with adolescents.

Normative data are presented for two Bender-Gestalt scoring systems with a sample of "normal" controls (n = 150), emotionally disturbed (n = 140), and mentally retarded/neurologically impaired (MR/NI) adolescents (n = 47), aged 12 to 17 years. The results failed to support the use of Hutt's (1985) Psychopathology Scale and Adolescent Configuration in differentiating the "normal" and emotionally disturbed groups, but did support their use in differentiating the MR/NI group from the other two. The Hutt scores also were found to be related inversely to age and IQ. By contrast, the Koppitz scores differentiated the three groups from each other and were not related significantly to IQ. The results supported limited use of Koppitz's (1975) Emotional Indicators as a "sign" approach to brief screening for emotional disturbance in adolescents.

Adjustment Disorders↗
PubMed1988

Specific binding of o-phenanthroline at a DNA structural lesion.

DNA intercalators are found to recognize a DNA lesion as a high affinity receptor site. This lesion-specific binding is observed when one strand of a DNA double helix contains an extra, unpaired nucleotide. Our assay for binding controls for the effects of sequence with a series of oligodeoxynucleotide duplexes which are identical except for the location of the lesion, an extra cytidine. Scission of the series of oligodeoxynucleotides by the cuprous complex of ortho-phenanthroline (OP-Cu) indicates that OP-Cu binds at the lesion-specific stable intercalation site, suggesting that OP-Cu intercalates into DNA. The dispersion of OP-Cu scission sites over three residues is consistent with scission via a diffusible intermediate. The location of the scission sites, directly on the 3' side of the lesion, is consistent with minor groove binding in B DNA.

Base Sequence↗
PubMed1988

Selective strand scission by intercalating drugs at DNA bulges.

A bulge is an extra, unpaired nucleotide on one strand of a DNA double helix. This paper describes bulge-specific strand scission by the DNA intercalating/cleaving drugs neocarzinostatin chromophore (NCS-C), bleomycin (BLM), and methidiumpropyl-EDTA (MPE). For this study we have constructed a series of 5'-32P end labeled oligonucleotide duplexes that are identical except for the location of a bulge. In each successive duplex of the series, a bulge has been shifted stepwise up (from 5' to 3') one strand of the duplex. Similarly, in each successive duplex of the series, sites of bulge-specific scission and protection were observed to shift in a stepwise manner. The results show that throughout the series of bulged duplexes NCS-C causes specific scission at a site near a bulge, BLM causes specific scission at a site near a bulge, and MPE-Fe(II) causes specific scission centered around the bulge. In some sequences, NCS-C and BLM each cause bulge-specific scission at second sites. Further, bulged DNA shows sites of protection from NCS-C and BLM scission. The results are consistent with a model of bulged DNA with (1) a high-stability intercalation site at the bulge, (2) in some sequences, a second high-stability intercalation site adjacent to the first site, and (3) two sites of relatively unstable intercalation that flank the two stable intercalation sites. On the basis of our results, we propose a new model of the BLM/DNA complex with the site of intercalation on the 3' side (not in the center) of the dinucleotide that determines BLM binding specificity.(ABSTRACT TRUNCATED AT 250 WORDS)

Antibiotics, Antineoplastic↗
PubMed1988

Suppression of cytotoxic responses by a supernatant factor derived from Mycoplasma hyorhinis-infected mammalian cell lines.

A class of interleukin-2-dependent T-cell clones, isolated from a murine fetal thymus, was previously shown to suppress the induction of cytotoxic responses to alloantigens (H.-S. Teh, M. Ho, and W. R. McMaster, J. Immunol. 135:1582-1588, 1985). In that article, the immunosuppressive properties of these T-cell clones were shown to be a direct consequence of infection by Mycoplasma hyorhinis. Suppression of cytotoxic responses was mediated by both the mycoplasmas and a 200-kilodalton factor present in supernatants of infected cultures. This factor was sensitive to proteases but was resistant to heating to 60 degrees C for 1 h and to incubation on ice at pH 2 or pH 14 for 4 h. The production of suppressor factor in infected cultures was independent of the viability or the protein synthesis capability of the mammalian cells, suggesting that it was produced by M. hyorhinis. The factor was most suppressive when it was added during the early stages of the cytotoxic response. Its suppressive effects on cytotoxic responses were not reversed by the addition of an excess of recombinant interleukin-2. This factor also suppressed mitogenic responses to lipopolysaccharide. However, it is not a growth inhibitor since it did not affect the proliferation of tumor cell lines. A simple method for detecting M. hyorhinis in the infected T-cell clones and for eliminating it is described.

Animals↗
PubMed1988

Antigen-independent activation of cytotoxic T cells by lymphokines.

Supernatants from phorbol myristate acetate (PMA)-stimulated EL4.IL2 cells (EL4.PMA), but not recombinant IL-2 (rIL-2), induced the production of cytotoxic T lymphocytes (CTL) in low density murine spleen cell cultures. CTL induction in these cultures was completely abrogated by treatment with anti-Thy-1 or anti-Lyt-2 antibody plus complement but not by anti-L3T4 antibody plus complement. Fractionation of EL4.PMA on a Sephadex G-150 column demonstrated that the CTL-inducing activity in EL4.PMA eluted with an apparent molecular weight of about 44,000 and was partially separated from IL-2. This 44,000 MW material was shown to contain insignificant amounts of PMA. Following a 3-day culture period with the partially purified factor, C57BL/6J thymocytes could proliferate and differentiate into cytotoxic cells in response to rIL-2, whereas there was no proliferation or generation of cytotoxic cells when the thymocytes were cultured in rIL-2 alone. The number of IL-2 receptor-positive cells in C57BL/6J thymocytes also increased from 1.1% to 22.8% after 3 days of culture in the partially purified factor. Recombinant IL-4 (BSF-1) and IL-5 (TRF), when used alone or in combination with rIL-2, were unable to induce a cytotoxic response under similar culture conditions. These findings are consistent with the interpretation that EL4.PMA contains a novel lymphokine that directly, or indirectly, induces the expression of IL-2 receptors on resting CTL precursors without intentional stimulation by specific antigen. In the presence of IL-2, these precursors may then differentiate into effector CTL.

Animals↗