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C Bustamante

Publications and source records attributed to C Bustamante.

At least 55 records · Page 3Linked to original sources
PubMed1998

Contributions of linker histones and histone H3 to chromatin structure: scanning force microscopy studies on trypsinized fibers.

Little is known about the mechanisms that organize linear arrays of nucleosomes into the three-dimensional structures of extended and condensed chromatin fibers. We have earlier defined, from scanning force microscopy (SFM) and mathematical modeling, a set of simple structural determinants of extended fiber morphology, the critical parameters being the entry-exit angle between consecutive linkers and linker length. Here we study the contributions of the structural domains of the linker histones (LHs) and of the N-terminus of histone H3 to extended fiber morphology by SFM imaging of progressively trypsinized chromatin fibers. We find that cleavage of LH tails is associated with a lengthening of the internucleosomal center-to-center distance, and that the somewhat later cleavage of the N-terminus of histone H3 is associated with a flattening of the fiber. The persistence of the "zigzag" fiber morphology, even at the latest stages of trypsin digestion, can be attributed to the retention of the globular domain of LH in the fiber.

Animals↗
PubMed1998

Linker histone tails and N-tails of histone H3 are redundant: scanning force microscopy studies of reconstituted fibers.

The mechanisms responsible for organizing linear arrays of nucleosomes into the three-dimensional structure of chromatin are still largely unknown. In a companion paper (Leuba, S. H., et al. 1998. Biophys. J. 74:2823-2829), we study the contributions of linker histone domains and the N-terminal tail of core histone H3 to extended chromatin fiber structure by scanning force microscopy imaging of mildly trypsinized fibers. Here we complement and extend these studies by scanning force microscopy imaging of selectively reconstituted chromatin fibers, which differ in subtle but distinctive ways in their histone composition. We demonstrate an absolute requirement for the globular domain of the linker histones and a structural redundancy of the tails of linker histones and of histone H3 in determining conformational stability.

Animals↗
PubMed1997

Purification and staining of intact yeast DNA chromosomes and real-time observation of their migration during gel electrophoresis.

In the past few years, fluorescence microscopy has been used successfully to characterize the motion of intermediate-size DNA molecules (50-500 kbp) during steady- and pulsed-field gel electrophoresis. However, experimental difficulties had prevented the application of this technique to the direct observation of longer DNA chromosomes (1-2 Mbp). In the present study a particular procedure was followed for the purification and staining of chromosomal yeast DNA to protect it from shear forces. Also, a new highly fluorescent DNA-labelling dye, YOYO-1, was employed to improve brightness and contrast. Finally, the motion of such long DNA molecules (1-2 Mbp) was characterized under steady-field electrophoresis conditions. An accurate description of the molecular mechanisms of motion of such long molecules should provide the basis for a detailed analysis of the mechanisms responsible for DNA trapping.

Base Composition↗
PubMed1997

Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase x sigma 54 holoenzyme by scanning force microscopy.

Scanning force microscopy (SFM) has been used to study transcriptional activation of Escherichia coli RNA polymerase x sigma 54 (RNAP x sigma 54) at the glnA promoter by the constitutive mutant NtrC(D54E,S160F) of the NtrC Protein (nitrogen regulatory protein C). DNA-protein complexes were deposited on mica and images were recorded in air. The DNA template was a 726 bp linear fragment with two NtrC binding sites located at the end and about 460 bp away from the RNAP x sigma 54 glnA promoter. By choosing appropriate conditions the structure of various intermediates in the transcription process could be visualized and analyzed: (1) different multimeric complexes of NtrC(D54E,S160F) dimers bound to the DNA template; (2) the closed complex of RNAP x sigma 54 at the glnA promoter; (3) association between DNA bound RNAP x sigma 54 and NtrC(D54E,S160F) with the intervening DNA looped out; and (4) the activated open promoter complex of RNAP x sigma 54. Measurements of the DNA bending angle of RNAP x sigma 54 closed promoter complexes yielded an apparent bending angle of 49(+/-24) degrees. Under conditions that allowed the formation of the open promoter complex, the distribution of bending angles displayed two peaks at 50(+/-24) degrees and 114(+/-18) degrees, suggesting that the transition from the RNAP x sigma 54 closed complex to the open complex is accompanied by an increase of the DNA bending angle.

Bacterial Proteins↗
PubMed1997

Direct visualization of individual DNA molecules by fluorescence microscopy: characterization of the factors affecting signal/background and optimization of imaging conditions using YOYO.

A new series of high-affinity cyanine dyes was tested for the visualization of the dynamics of single DNA molecules through a fluorescence microscope. In particular, YOYO-1 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)- bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-oxazole)- 2-methylidene]-quinolinium tetraiodide) forms a very stable, highly fluorescent complex with double-stranded DNA and dramatically improves the quality of the images. We have characterized the factors affecting the signal/background in the imaging of single DNA molecules by fluorescence microscopy and compared the results obtained using YOYO-1 with those obtained using standard fluorescent dyes like ethidium bromide or acridine orange.

Acridine Orange↗
PubMed1997

Ionic effects on the elasticity of single DNA molecules.

We used a force-measuring laser tweezers apparatus to determine the elastic properties of lambda-bacteriophage DNA as a function of ionic strength and in the presence of multivalent cations. The electrostatic contribution to the persistence length P varied as the inverse of the ionic strength in monovalent salt, as predicted by the standard worm-like polyelectrolyte model. However, ionic strength is not always the dominant variable in determining the elastic properties of DNA. Monovalent and multivalent ions have quite different effects even when present at the same ionic strength. Multivalent ions lead to P values as low as 250-300 A, well below the high-salt "fully neutralized" value of 450-500 A characteristic of DNA in monovalent salt. The ions Mg2+ and Co(NH3)63+, in which the charge is centrally concentrated, yield lower P values than the polyamines putrescine2+ and spermidine3+, in which the charge is linearly distributed. The elastic stretch modulus, S, and P display opposite trends with ionic strength, in contradiction to predictions of macroscopic elasticity theory. DNA is well described as a worm-like chain at concentrations of trivalent cations capable of inducing condensation, if condensation is prevented by keeping the molecule stretched. A retractile force appears in the presence of multivalent cations at molecular extensions that allow intramolecular contacts, suggesting condensation in stretched DNA occurs by a "thermal ratchet" mechanism.

Cobalt↗
PubMed1997

Folding-unfolding transitions in single titin molecules characterized with laser tweezers.

Titin, a giant filamentous polypeptide, is believed to play a fundamental role in maintaining sarcomeric structural integrity and developing what is known as passive force in muscle. Measurements of the force required to stretch a single molecule revealed that titin behaves as a highly nonlinear entropic spring. The molecule unfolds in a high-force transition beginning at 20 to 30 piconewtons and refolds in a low-force transition at approximately 2.5 piconewtons. A fraction of the molecule (5 to 40 percent) remains permanently unfolded, behaving as a wormlike chain with a persistence length (a measure of the chain's bending rigidity) of 20 angstroms. Force hysteresis arises from a difference between the unfolding and refolding kinetics of the molecule relative to the stretch and release rates in the experiments, respectively. Scaling the molecular data up to sarcomeric dimensions reproduced many features of the passive force versus extension curve of muscle fibers.

Amino Acid Sequence↗
PubMed1997

Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein.

Nitrogen regulatory protein C (NtrC) contacts a bacterial RNA polymerase from distant enhancers by means of DNA loops and activates transcription by allowing polymerase to gain access to the template DNA strand. It was shown that NtrC from Salmonella typhimurium must build large oligomers to activate transcription. In contrast to eukaryotic enhancer-binding proteins, most of which must bind directly to DNA, some NtrC dimers were bound solely by protein-protein interactions. NtrC oligomers were visualized with scanning force microscopy. Evidence of their functional importance was provided by showing that some inactive non-DNA-binding and DNA-binding mutant forms of NtrC can cooperate to activate transcription.

Adenosine Triphosphatases↗
PubMed1997

Escherichia coli RNA polymerase activity observed using atomic force microscopy.

Fluid tapping-mode atomic force microscopy (AFM) was used to observe Escherichia coli RNA polymerase (RNAP) transcribing two different linear double-stranded (ds) DNA templates. The transcription process was detected by observing the translocation of the DNA template by RNAP on addition of ribonucleoside 5'-triphosphates (NTPs) in sequential AFM images. Stalled ternary complexes of RNAP, dsDNA and nascent RNA were adsorbed onto a mica surface and imaged under continuously flowing buffer. On introduction of all four NTPs, we observed some DNA molecules being pulled through the RNAP, some dissociating from the RNAP and others which did not move relative to the RNAP. The transcription rates were observed to be approximately 0.5-2 bases/s at our NTP concentrations, approximately 5 microM. The RNA transcripts were not unambiguously imaged in fluid. However, in experiments using a small single-stranded (ss) circular DNA template, known as a rolling circle, transcripts up to 1 or 2 microns long could be observed with tapping mode AFM once the samples were dried and imaged in air. This confirmed our observations of the transcriptional activity of RNAP adsorbed onto mica. This work illustrates that the development of tapping-mode in fluid has made it possible to use AFM to follow biological processes at the molecular level and get new insights about the variability of activity of individual molecules bound to a surface.

Aluminum Silicates↗
PubMed1997

Visualization and analysis of chromatin by scanning force microscopy.

The use of the scanning force microscope (SFM) to visualize and analyze chromatin fiber structures is presented. Protocols to prepare chromatin fibers for SFM imaging of fibers in air and in buffer are first discussed. Next, the conditions for acquiring high-quality SFM images such as optimal instrumental parameters, appropriate deposition substrates, and adequate procedures of sample deposition are described. It is shown that analysis and quantitation of the SFM images support an irregular, three-dimensional arrangement of nucleosomes in the native chromatin fiber. This structure is lost in linker histone-depleted fibers, which show, instead, a beads-on-a-string structure. Molecular modeling of the chromatin fiber structures and computer simulation of the SFM imaging process indicate that the natural variability of the linker length may be the major determinant of the structural irregularity of the native chromatin fiber. Removal of linker histones (H1/H5) may change the amount of DNA wrapped around the histone octamer, which in turn may induce the transition from a three-dimensional irregular helix to an extended beads-on-a-string structure. Studies of trinucleosomes indicate that both the average successive nucleosome center-to-center distance and the average angle between two successive linkers increase upon the removal of linker histone.

Chromatin↗
PubMed1997

Scanning force microscopy under aqueous solutions.

Merely ten years after its invention, the scanning force microscope is becoming a powerful method to investigate the structure and dynamics of biological molecules under aqueous environments. From the visualization of transcription in real time to the mechanical manipulation of individual proteins, the advances made during the past year open up a vast number of exciting applications of this technique in biology.

Connectin↗
PubMed1996

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

This paper reports a study of the deposition process of DNA molecules onto a mica surface for imaging under the scanning force microscope (SFM). Kinetic experiments indicate that the transport of DNA molecules from the solution drop onto the surface is governed solely by diffusion, and that the molecules are irreversibly adsorbed onto the substrate. A statistical polymer chain analysis has been applied to DNA molecules to determine the deposition conditions that lead to equilibrium and those that result in trapped configurations. Using the appropriate conditions, DNA molecules deposited onto freshly cleaved mica, are able to equilibrate on the surface as in an ideal two-dimensional solution. A persistence length of 53 nm was determined from those molecules. DNA fragments that were labeled on both ends with a horseradish peroxidase streptavidin fusion protein were still able to equilibrate on the surface, despite the additional protein-surface interaction. In contrast, DNA molecules deposited onto glow-discharged mica or H+-exchanged mica do not equilibrate on the surface. These molecules adopt conformations similar to those expected for a simple projection onto the surface plane, suggesting a process of kinetic trapping. These results validate recent SFM application to quantitatively analyze the conformation of complex macromolecular assemblies deposited on mica. Under equilibration conditions, the present study indicates that the SFM can be used to determine the persistence length of DNA molecules to a high degree of precision.

Adsorption↗
PubMed1996

Real-time imaging of the reorientation mechanisms of YOYO-labelled DNA molecules during 90 degrees and 120 degrees pulsed field gel electrophoresis.

Pulsed field gel electrophoresis (PFGE) techniques have been developed to overcome the limitations of conventional electrophoresis and to increase the separation to DNA chromosomes of few megabase pairs in size. Despite of the large success of these techniques, the various separation protocols employed for PFGE experiments have been determined empirically. However, a deep understanding of the molecular mechanisms of motion responsible for DNA separation becomes necessary for the rational optimization of these techniques. This paper shows the first clear observations of individual molecules of DNA during the reorientation process in 90 degrees PFGE and 120 degrees PFGE. Real-time visualization of the DNA dynamics during PFGE was possible with the use of an epi-illumination fluorescence microscope specifically equipped to run these experiments and by staining the DNA with YOYO-1 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-meth yl -2,3-dihydro-(benzo-1,3-oxazole)-2-methyl-idene]-quinolinium tetraiodide). This dye forms a very stable, highly fluorescent complex with double-stranded DNA and dramatically improves the quality of the DNA images. The results of computer simulations used to reproduce the molecular mechanisms of motion as well as the DNA separation features are also discussed.

Benzoxazoles↗
PubMed1996

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.

Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.

Base Composition↗
PubMed1996

Nonlinear enthalpy-entropy compensation for the solubility of phenacetin in dioxane-water solvent mixtures.

The solubility of phenacetin was determined at five temperatures in solvent mixtures of aprotic-amphiprotic mixtures of dioxane and water. Enthalpy-entropy compensation analysis is used to study the effect of changing polarity of the medium on the solute. The apparent heats of solution and free energies of solution are nonlinear functions of the cosolvent (dioxane) ratio. The free energy curve goes through a minimum at 80-90% dioxane in water, whereas the apparent heat of solution displays a maximum at low cosolvent ratio (40% dioxane) and a minimum at high cosolvent ratio (90% dioxane). A plot of delta H against delta G shows a nonlinear compensation effect. Two different mechanisms (entropy and enthalpy) are suggested to be the driving forces to increase solubility. These two mechanisms can be related to the nonlinearity of the compensation effect. The slope changes from positive to negative at 40% dioxane. The overall nonlinear function can also be considered as two linear relationships that intersect at 40% dioxane. The results support the usefulness of enthalpy-entropy compensation analysis for a better understanding of the solubility of drugs in aqueous mixtures as related to the role of cosolvents.

Dioxanes↗
PubMed1996

No adverse impact on protection against pertussis from combined administration of Haemophilus influenza type b conjugate and diphtheria-tetanus toxoid-pertussis vaccines in the same syringe.

To assess whether combining a Haemophilus influenzae type b conjugate vaccine (PRP-T) and diphtheria-tetanus toxoid-pertussis (DTP) vaccine in a single syringe would impact adversely the antibody response and clinical protection conferred by pertussis vaccine, surveillance and a nested serosurvey were conducted among infants in a large-scale evaluation of PRP-T in Santiago. Infants received either combined PRP-T/DTP or DTP only at 2, 4, and 6 months of age. At 8 months, pertussis agglutinin, anti-pertussis toxin, and anti-filamentous hemagglutinin antibody levels in the PRP-T/DTP (137.7, 23.1, and 12.2, respectively) and DTP (142.9, 20.6, and 13.0, respectively) groups were comparable. The incidence of pertussis was similar among infants assigned to health centers administering combined PRP-T/DTP and those administering DTP alone (13.1 vs. 12.2 cases/10(5) child-years). Combined PRP-T/DTP vaccine did not diminish protection against pertussis.

Agglutination Tests↗
PubMed1996

Large scale, postlicensure, selective vaccination of Chilean infants with PRP-T conjugate vaccine: practicality and effectiveness in preventing invasive Haemophilus influenzae type b infections.

BACKGROUND: Haemophilus influenzae type b (Hib) conjugate vaccines have demonstrated an impressive impact in diminishing Hib disease in industrialized countries. However, their high cost prompts nonindustrialized countries to corroborate their effectiveness under local conditions before considering their programmatic implementation. Such a postlicensure evaluation of vaccine effectiveness was undertaken in Chile. METHODS: After its licensure in Chile polyribosylribitol phosphate-tetanus toxoid protein conjugate vaccine (PRP-T), combined with diphtheria-tetanus-pertussis vaccine, was introduced into the Expanded Program on Immunization schedules in 36 health centers throughout metropolitan Santiago for 12 months, whereas 35 similar health centers administered only diphtheria-tetanus toxoid-pertussis vaccine. Bacteriologic surveillance data for invasive Hib cases collected over the ensuing 30 months were analyzed. RESULTS: In an intent-to-vaccinate (effectiveness) analysis, PRP-T provided 90.2% protection (95% confidence interval, 74.5 to 100%) against invasive Hib disease (40 vs. 4 cases, P < 0.001). Vaccine effectiveness was 91.3% against meningitis (22 vs. 2 cases) and 80% against pneumonia and empyema (10 vs. 2 cases, P = 0.039). Vaccine efficacy among infants who received all three doses of PRP-T was 91.7% (95% confidence interval, 64.8 to 100%). CONCLUSIONS: Programmatic use of Hib conjugate vaccine administered in combination with diphtheria-tetanus-pertussis vaccine constitutes a highly effective and practical intervention in Chile, a newly industrializing country.

Bacterial Capsules↗