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M Coll

Publications and source records attributed to M Coll.

85 records · Page 5Linked to original sources
PubMed1989

Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.

The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.

Base Composition↗
PubMed1988

Molecular structure of cyclic deoxydiadenylic acid at atomic resolution.

The molecular structure of a small cyclic nucleotide, cyclic deoxydiadenylic acid, has been determined by single-crystal X-ray diffraction analysis and refined to an R factor of 7.8% at 1.0-A resolution. The crystals are in the monoclinic space group C2 with unit cell dimensions of a = 24.511 (3) A, b = 24.785 (3) A, c = 13.743 (3) A, and beta = 94.02 (2) degrees. The structure was solved by the direct methods program SHELXS-86. There are 2 independent cyclic d(ApAp) molecules, 2 hydrated magnesium ions, and 26 water molecules in the asymmetric unit of the unit cell. The two cyclic d(ApAp) molecules have similar conformations within their 12-membered sugar-phosphate backbone ring, but they have quite different appearances due to the different glycosyl torsion angles that make one molecule more compact and the other extended and open. Three of the four deoxyribose rings are in the less common C3'-endo conformation. All four phosphate groups have their phosphodiester torsion angles alpha/zeta in the gauche(+)/gauche(+) conformation. One of the cyclic d(ApAp) molecules associates with another symmetry-related molecule to form a self-intercalated dimer that is a stable structure in solution, as observed in NMR studies. Many interesting intermolecular interactions, including base-base stacking, ribose-base stacking, base pairing, base-phosphate hydrogen bonding, and metal ion-phosphate interactions, are found in the crystal lattice. This structure may be relevant for understanding the conformational potentiality of an endogenous biological regulator of cellulose synthesis, cyclic (GpGp).

Cyclic AMP↗
PubMed1988

Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs.

The left-handed Z-DNA conformation has been observed in crystals made from 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 factor R = 22.9% using 746 reflections in the resolution in the resolution shell 7 to 2.5 A. The overall shape of the molecule is very similar to the Z-structure of the related hexamer d(CG)3 confirming the rigidity of the Z form. 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.

Adenine↗
PubMed1987

A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin.

The crystal structures of d(CGCA3T3GCG) complex to the antitumor drug distamycin and the DNA fragment alone were solved by x-ray diffraction at 2.2 and 2.5 A resolution, respectively. The drug lies in the narrow minor groove near the center of the B-DNA fragment covering 5 of the 6 A.T base pairs. It is bound to the DNA by hydrogen bonding, van der Waals, and electrostatic interactions. In addition, the DNA was found to have an unusual conformation in the (dA)3.(dT)3 regions. These base pairs have a high positive propeller twist so that in the major groove the adenine amino group is located intermediate between the carbonyl O-4 groups of two adjacent thymines of the opposite strand, making bifurcated hydrogen bonds to the two thymine residues. This suggests a model to explain the unusual properties of poly-(dA).poly(dT) in which a modified B conformation is associated with a large propeller twist of the bases and a set of continuous bifurcating hydrogen bonds along the major groove, which may provide incremental stability to these segments. In addition, shorter segments of (dA)3-6.(dT)3-6 may have this conformation in the midst of B-DNA and stabilize bends in the DNA that may be associated with stacking on one of the high propeller-twisted bases at the ends of these segments.

Binding Sites↗
PubMed1987

Crystal and molecular structure of the sodium salt of the dinucleotide duplex d(CpG).

The crystal and molecular structure of the sodium salt of deoxycytidylyl-(3H-5H)-deoxyguanosine has been determined from X-ray diffraction data. The crystal, obtained from an aqueous gamma-butyrolactone solution at pH = 5.3 are orthorhombic, P212121, a = 10.640(2), b = 11.184(2) and c = 44.618(4)A. The structure was refined to an R = 0.041. The d(CpG) structure is similar to the ammonium salt solved by Cruse et al.(1). Both structures form a parallel self base paired mini-double helix. In d(CpG).Na+ one of the two paired cytosines is protonated on N(3). The cytosines form 3 hydrogen bonds while the guanines form only 2. The Na+ ion is coordinated with five groups: two water molecules, O(6) of guanine A, N(7) of guanine B and 0(5') of cytosine B, forming a square pyramid. The hydration shell around the mini-helix is analysed and compared with that of the ammonium salt, d(CpG).Na+ is the second d(CpG) oligonucleotide found with a self base pairing arrangement despite of the fact that the crystallization conditions and counterion were different in both cases. The hypothesis that self base pairing is not only a crystallization artifact but may play a role under physiological conditions as a source of transversion mutations is discussed.

Base Composition↗
PubMed1986

Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs.

The Z-DNA structure has been shown to form in two crystals made from self-complementary DNA hexamers d(CGTDCG) and d(CDCGTG) which contain thymine/2-aminoadenine (TD) base pairs. The latter structure has been solved and refined to 1.3 A resolution and it shows only small conformational changes due to the introduction of the TD base pairs in comparison with the structure of d(CG)3. Spectroscopic studies with these compounds demonstrate that DNA molecules containing 2-aminoadenine residues form Z-DNA slightly more easily than do those containing adenine nucleotides, but not as readily as the parent sequence containing only guanine-cytosine base pairs.

2-Aminopurine↗
PubMed1980

Obesity and eating style.

Eating styles of 30 obese women and 37 matched women of normal weight were observed unobtrusively in a fast-food restaurant in the search for an "obese eating style" or other differences between the two groups. The size and character of the food was carefully matched by giving each woman a coupon entitling her to a free meal of either 985 or 1,800 calories. There were only small and inconsistent differences between obese and normal-weight women. No evidence of an "obese eating style" was found.

Feeding Behavior↗
PubMed1980

Food accessibility and food choice. A test of Schachter's externality hypothesis.

A set of naturalistic observations was conducted to examine Schachter's theory that obese individuals are more responsive to external food cues than persons of normal weight. During six days of observation at a large hospital cafeteria, experimenters manipulated the accessibility of high- and low-calorie desserts. No differences in selection by obese, overweight, and normal-weight individuals of meals or desserts were observed. All weight groups were equally responsive to the experimental manipulation of food cues.

Cues↗
PubMed1979

Obesity and food choices in public places.

More than 5,000 food choices were observed at nine eating sites--four where meals were served and five where snacks were served. Caloric content of food choice was strongly affected by eating site and there was great variability in the amount chosen at each site. Men chose somewhat more food than women. Body weight had no overall effect on food choice, although obese people chose somewhat more food than nonobese people at one site--that serving food with the highest caloric content. These findings are consistent with the six earlier studies of food choice, which concluded that the major influence on how much people choose to eat is where they eat, and that there is great variability in the amount they choose at any one site. The presence of obesity is not a major determinant of food choice in public places.

Adult↗
PubMedDate not supplied

Separation of non-ortho polychlorinated biphenyl congeners on pre-packed carbon tubes. Application to analysis in sewage sludge and soil samples.

The analysis of planar (non-ortho) polychlorinated biphenyls (PCB) by HRGC-ECD or HRGC-HRMS requires a fractionation step to avoid the interferences of the bulk of PCB, usually in much higher concentration than the planar ones. In this paper, a new method, based on the fractionation of PCB on SPE commercial tubes pre-packed with Carbopack B, has been developed. After the extract has been applied on the stationary phase, the bulk of PCD are eluted with 15 ml of hexane (fraction I), mono-ortho PCB with 20 ml of hexane/toluene 99:1 (fraction II) and planar PCB with 20 ml of toluene (fraction III) in a station under vacuum. The method has been validated: accuracy (expressed as recovery in %) is >70% and precision (expressed as % RSD) is <20% considering changes of day, analyst and batch of tubes. The method is linear in the range studied. Other advantages are that the method is simple, rapid and it can be easily automated. The application of this separation to the determination of planar PCB in fly-ash extracts from an intercalibration exercise and to sewage sludge, sediment and soil samples has been successful. In addition, this method removes hydrocarbons from the planar PCB fraction and allows its concentration to very small volumes.

Carbon↗
PubMedDate not supplied

Study of evolution of PCDD/F in sewage sludge-amended soils for land restoration purposes.

The evolution of polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF) in sewage sludge-amended soils used in the restoration of degraded lands, like quarries, has been studied. Two experiments were performed: one in the lab, under controlled conditions, and another in a quarry. Two different doses of sewage sludge were applied in both experiments (with two types of application in the quarry experiment) and the evolution of the amended soils were compared with that of the respective control soils (without addition of sewage sludge). The samples were analyzed with a previously validated method by HRGC HRMS after the extraction and the necessary clean-up steps. The results reveal that polluted sewage sludge increases PCDD/F concentration in soils and that these compounds are persistent in the matrix after long periods of time.

Benzofurans↗
PubMedDate not supplied

Effect of temperature and photoperiod on juvenile hormone biosynthesis and sexual maturation in the cotton bollworm, Helicoverpa armigera: implications for life history traits.

The Israeli population of the cotton bollworm, Helicoverpa armigera (Hübner), undergoes a short-day, low-temperature pupal diapause and is also suspected of being a seasonal migrant in the eastern Mediterranean region. H. armigera were reared in the laboratory under several constant temperature and photoperiodic combinations which simulate average conditions encountered in the spring, summer, early-autumn and late-autumn in Israel. Juvenile hormone (JH) biosynthesis, the onset of calling behavior, sex pheromone production and ovarian development were examined in virgin female moths subsequent to eclosion. Allatal maturation, defined as acquisition of competence to synthesize JH, was significantly delayed in moths reared under simulated spring conditions. This was probably the cause for the observed delay in ovarian development and the onset of calling behavior, and to the reduction in sex pheromone biosynthesis. The delay in female sexual maturation, commonly associated with migratory flight, is consistent with presumptive pre-reproductive migration in H. armigera.

Animals↗