RESUMO
The recombinant production of a novel chimeric polyprotein is described. The new protein contains either wild-type beta(2)-microglobulin (beta(2)m) or its truncated variant (DeltaN6 beta(2)m) (see picture). Structural characterization is achieved by means of single-molecule force spectroscopy studies of specific beta(2)m regions which could be involved in amyloidogenesis.
Assuntos
Microglobulina beta-2/química , Amiloidose , Microscopia de Força Atômica , Engenharia de Proteínas , Dobramento de Proteína , Proteínas Recombinantes/química , Espectrometria de FluorescênciaRESUMO
Polynucleotide: adenosine glycosidases (PNAG) are a class of plant and bacterial enzymes commonly known as ribosome-inactivating proteins (RIP). They are presently classified as rRNA N-glycosidases in the enzyme nomenclature [EC 3.2.2.22]. Several activities on nucleic acids, other than depurination, have been attributed to PNAG: in particular modifications induced in circular plasmids, including linearisation and topological changes, and cleavage of guanidinic residues. Here we describe a chromatographic procedure to obtain nuclease-free PNAG by dye-chromatography onto Procion Red derivatized Sepharose((R)). Highly purified enzymes depurinate extensively pBR322 circular, supercoiled DNA at neutral pH and exhibit neither DNase nor DNA glycolyase activities, do not cause topological changes, and adenine is the only base released from DNA and rRNA, even at very high enzyme concentrations. A scanning force microscopy (SFM) study of pBR322 treated with saporin-S6 confirmed that (i) this PNAG binds extensively to the plasmid, (ii) the distribution of the bound saporin-S6 molecules along the DNA chain is markedly variable, (iii) plasmids already digested with saporin-S6 do not appear fragmented or topologically modified. The observations here described demonstrate that polynucleotide:adenosine glycosidase is the sole enzymatic activity of the four ribosome-inactivating proteins gelonin, momordin I, pokeweed antiviral protein from seeds and saporin-S6. These proteins belong to different families, suggesting that the findings here described may be generalized to all PNAG.
Assuntos
DNA/metabolismo , Imunotoxinas , N-Glicosil Hidrolases/isolamento & purificação , N-Glicosil Hidrolases/metabolismo , Cromatografia em Gel/métodos , Corantes , DNA Glicosilases , DNA Super-Helicoidal/metabolismo , Desoxirribonucleases/metabolismo , Concentração de Íons de Hidrogênio , Microscopia de Força Atômica , N-Glicosil Hidrolases/química , Proteínas de Plantas/metabolismo , Plasmídeos/metabolismo , Proteínas Inativadoras de Ribossomos , Proteínas Inativadoras de Ribossomos Tipo 1 , Proteínas Inativadoras de Ribossomos Tipo 2 , Saporinas , Sementes/química , SefaroseRESUMO
They're flexible and sticky: While investigations of the very stiff DNA molecular conformation on surfaces have been made, the equivalent for more typical macromolecules is complicated by their shorter persistance length. A gentle detachment study with a polymer bound to an SFM tip allows the forces between the polymer and surface to be probed; the detachement force required depends on the surface conformation, whether only a small loop or a long tail must be peeled from the surface, as shown by the cartoon.
Assuntos
Substâncias Macromoleculares/química , Microscopia de Força Atômica , Adsorção , Estrutura Molecular , Propriedades de SuperfícieRESUMO
This paper presents a new electronic methodology to detect DNA hybridization for rapid identification of diseases, as well as food and environmental monitoring on a genetic base. The proposed solution exploits a new (electrical) capacitive measurement circuit, not requiring any prior labeling of the DNA (as it is often the case with the commonly employed optical detection). The sensitivity, the reliability, and the reproducibility of this device have been evaluated by experiments performed with a (non-integrated) prototype implementation, easily integrable in IC and/or micro-fabricated lab-on-a-chip.
Assuntos
Técnicas Biossensoriais/instrumentação , Sondas de DNA/química , DNA/análise , DNA/química , Eletroquímica/instrumentação , Análise de Sequência com Séries de Oligonucleotídeos/instrumentação , Adsorção , Técnicas Biossensoriais/métodos , Materiais Revestidos Biocompatíveis , Capacitância Elétrica , Eletroquímica/métodos , Eletrodos , Eletrônica Médica , Desenho de Equipamento , Análise de Falha de Equipamento , Estudos de Viabilidade , Miniaturização , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Projetos Piloto , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Integração de SistemasRESUMO
The addition of poly(ethylene glycol) (PEG) to a DNA solution induces phase separation of droplets of condensed DNA. These droplets possess liquid crystalline properties and their ordering is cholesteric. It was recently proved that daunomycin, by binding to DNA chains, inverts the long-range chirality of their tertiary packing into aggregates. The present paper suggests one possible mechanism by which this inversion can take place. Daunomycin bears a cationic group in its sugar residue. Its intercalation adds a helicoidal distribution of transverse dipoles to DNA chains. By this mechanism, in favourable cases, ionic or strongly polar groups in drugs which bind DNA can induce handedness inversion of the cholesteric ordering of its condensates. This inversion mechanism was tested experimentally using several, charged and uncharged, homologues of daunomycin. All those bearing the cationic ammonium group inverted the long-range chirality of the PEG-induced DNA mesomorphic state. The effects of the uncharged desamino homologues could not be evaluated because of their lower solubility and binding affinity for DNA.
Assuntos
DNA/química , Daunorrubicina/metabolismo , Substâncias Intercalantes/metabolismo , DNA/metabolismo , Polietilenoglicóis/metabolismoRESUMO
Isolation of a His-tagged protein by means of a Ni - nitrilotriacetate-functionalized chromatographic matrix or biosensor was simulated in a single-molecule experiment, and the mechanochemistry-that is, the interplay between mechanical and chemical forces (shown schematically)-was studied with a scanning force microscope.
RESUMO
Individual molecules can be stretched with a scanning force microscope and the forces required to rupture bonds and to mechanically drive their structures towards new conformations and states can be measured. The tailoring of the experiments, the possibility of carrying them out in quasi-equilibrium conditions, the relationships between single molecule force measurements, and macroscopic kinetics or thermodynamic data are discussed. Mechanochemical experiments are expanding chemistry into new realms between biology and material science.
Assuntos
DNA/química , Microscopia de Força Atômica/métodos , Conformação Molecular , Conformação de Ácido Nucleico , TermodinâmicaRESUMO
The effect of daunomycin upon DNA condensed states induced by poly(ethylene glycol) (PEG) was studied by circular dichroism (CD) and circular intensity differential scattering (CIDS). The CD spectra of these aggregates showed psi-type anomalies and intensities 10-100 times greater than those obtained with the dispersed DNA solutions in the absence of PEG. Increasing concentrations of daunomycin, added to the DNA solution prior to its aggregation, led, in the presence of PEG, to CD and CIDS signals which gradually decreased in magnitude and eventually inverted sign. The coincidence of the transition point of both signals and a careful characterization of the CD spectrum at the transition point clearly indicated that the inversion observed corresponds to an inversion of the handedness of the aggregates. The latter result suggests that the structure of the aggregates at the inversion point should resemble that of a nematic liquid-crystalline structure. The characteristic B-DNA spectrum obtained in this case further suggests that the packing process does not affect the secondary structure of the DNA molecules and that small changes in their local structure can induce dramatic changes in their long-range tertiary packing. The results obtained in this study represent a confirmation of a recent theory of psi-type CD in which the anomalous signals are interpreted as a manifestation of the long-range chirality of the aggregates.
Assuntos
DNA/efeitos dos fármacos , Daunorrubicina/farmacologia , Animais , Bovinos , Dicroísmo Circular , DNA/ultraestrutura , Microscopia Eletrônica , Conformação de Ácido Nucleico , Polietilenoglicóis/farmacologia , Timo , Difração de Raios XRESUMO
The deposition of DNA molecules on mica is driven and controlled by the ionic densities around DNA and close to the surface of the substrate. Dramatic improvements in the efficiency and reproducibility of DNA depositions were due to the introduction of divalent cations in the deposition solutions. The ionic distributions on DNA and on mica determine the mobility of adsorbed DNA molecules, thus letting them assume thermodynamically equilibrated conformations, or alternatively trapping them in non-equilibrated conformations upon adsorption. With these prerequisites, mica does not seem like an inert substrate for DNA deposition for microscopy, and its properties greatly affect the efficiency of DNA deposition and the appearance of the molecules on the substrate. In our laboratory, we have some preliminary evidence that mica could also participate in DNA damage, most likely through its heavy metal impurities.
Assuntos
Silicatos de Alumínio , DNA Super-Helicoidal/ultraestrutura , Microscopia de Força Atômica/métodos , Cátions Bivalentes/metabolismo , DNA Super-Helicoidal/química , DNA Super-Helicoidal/metabolismo , Concentração de Íons de Hidrogênio , Conformação de Ácido Nucleico , TermodinâmicaRESUMO
A general approach is developed to interpret linear dichroism (LD) spectra of ubiquinones (Qn) in host bilayers. Information is reported in terms of guest-host mutual orientation and localization. The overall orientational anisotropy of guest ubiquinone molecules is described by a basic set of limiting orientation/localization modes. Assignments of the UV transitions of the ubiquinone chromophore were obtained by the liquid crystal-linear dichroism technique and molecular orbital (CNDO/S) calculations. The LD spectra of Qn in the bilayers provided by the lyotropic nematic mesophase exhibited by water solutions of potassium laurate and decanol were interpreted on the basis of the above assignments. The resulting experimental evidence showed a multisite distribution in the host bilayer for the aromatic heads of all the investigated Qn derivatives except Q0. The orientational distribution suggested by the LD spectra fits the solubilization model recently proposed by G. Lenaz [J. Membrane Biol. (1988) 104:193-209] for ubiquinone in lipid membranes. Within this model Qn molecules are located in the midplane and their headgroups oscillate transversally across the membrane. Q0 instead has a single site location, close to the polar bilayer interface. Experimental evidence that the headgroup carbonyls tend to grasp the polar interface of the host bilayer was also obtained. Orientation and location distributions of Qn guest molecules are therefore likely to result from the tendency of their aromatic heads to grasp the polar heads of the host bilayer and from the concurrent tendency of their chains to settle into the hydrocarbon host interior.
Assuntos
Membrana Celular/química , Bicamadas Lipídicas/química , Ubiquinona/análise , Modelos Biológicos , Análise Espectral , Raios UltravioletaRESUMO
The localization of ubiquinone has been investigated in phospholipid bilayer vesicles in studies of fluorescence quenching of membrane-bound probes by ubiquinone homologs (Qn, where n is the number of the isoprenoid units of the chain). Fluorescence-quenching data obtained by using a set of anthroylstearate probes, having the fluorophore located at different depths, revealed that ubiquinone-3 is located throughout the whole bilayer thickness. From the bimolecular quenching constants in the membrane, lateral diffusion coefficients in two dimensions were calculated to span values of 10(-7)-10(-6) cm2.s-1. This suggests that ubiquinones laterally diffuse in a very fluid environment. On this basis, it is proposed that their translational diffusion in the bilayer takes place in two dimensions, with the quinone ring oscillating between the two bilayer surfaces within a hydrophobic environment not extending beyond the glycerol region. This model implies that the quinonic head is both settled near the polar surface of the bilayer and buried into the host hydrocarbon interior. This two-site distribution was confirmed for all Qn, except Q0, by their linear dichroism spectra in the bilayers provided by disc-like lyotropic nematic liquid crystals. These spectra also provided detailed information on the preferential orientations of the quinonic head of the different derivatives within the two sites. The mechanism by which the localization and orientation of Qn guest molecules inside the host bilayer is modulated by the isoprenoid chain length is discussed on a thermodynamical basis. Being that Qn is expected to be also widely contained in the highly curved cristae of the mitochondrial inner membrane, by using rod-like lyotropic nematic liquid crystals we searched out effects of the curvature of the host bilayer on those Qn distributions. The linear dichroism measurements reveal that Qn guest molecules are no longer obliged to find a partition between two different types of localizations when the host bilayer is highly curved. In this case all Qn, even the longest Q10, were found to stay parallel to the amphiphilic chains with a single site localization of the head near the polar interface. By the same linear dichroism technique, the local ordering of all Qn derivatives was also evaluated. The order parameters were found to be basically the same for all derivatives. This result is justified on the basis of the relaxation, caused by the surface curvature, of the lateral compression of the host chains.
Assuntos
Bicamadas Lipídicas/química , Ubiquinona/química , Fenômenos Químicos , Físico-Química , Fluorescência , Corantes Fluorescentes , Modelos Moleculares , Fosfolipídeos , SolubilidadeRESUMO
The genome of parvovirus B19 is a 5600-base-long single-stranded DNA molecule with peculiar sequence symmetries. Both complementary forms of this single-stranded DNA are contained in distinct virions and they hybridize intermolecularly to double-stranded DNA if extracted from the capsids with traditional methods, thus losing some of their native structural features. A scanning force microscopy analysis of these double-stranded DNA molecules after thermal denaturation and renaturation gave us the chance to study the possible states that this DNA can assume in both its single-stranded and double-stranded forms. A novel but still poorly reproducible in situ lysis experiment that we have conducted on single virions with the scanning force microscope made it possible to image the totally unpaired state that the single-stranded DNA molecule most likely assumes inside the viral particle. Structural considerations on single molecules offer the opportunity for the formulation of plausible hypotheses on the interaction between the DNA and the viral structural proteins that could prove important for the DNA packaging in the capsid and, possibly, the viral infection mechanisms.
Assuntos
DNA de Cadeia Simples/química , DNA de Cadeia Simples/genética , Parvovirus/química , Parvovirus/genética , Capsídeo/química , Capsídeo/genética , DNA de Cadeia Simples/ultraestrutura , Genoma Viral , Processamento de Imagem Assistida por Computador , Microscopia de Força Atômica , Conformação de Ácido Nucleico , Desnaturação de Ácido Nucleico , Parvovirus/ultraestrutura , TermodinâmicaRESUMO
A study of the monomeric chromophore of the oligopeptides netropsin (1), distamycin III (2), and distamycin V (3) by polarization spectroscopy techniques and molecular orbital calculations is reported. Linear dichroism spectra of the monomeric model compounds 1-methyl-2(ethylcarbamoyl)-4-acetamido-pyrrole (4) and 1-methyl-2(ethylcarbamoyl)-pyrrole (5) dissolved and oriented in lyotropic and thermotropic liquid crystals provide, together with the magnetic CD spectra, experimental checks of the theoretical calculations. The polarization directions of the investigated transition obtained by these means in this study allow us to build up in the following paper the exciton states of (1)-(3) and these provide a stereochemical interpretation of the flow linear dichroism spectra of the complexes of DNA with (2) and (3).
Assuntos
DNA , Distamicinas , Pirróis , Modelos Estruturais , Conformação de Ácido Nucleico , Ligação Proteica , Conformação ProteicaRESUMO
The study of the monomeric chromophore of the distamycins reported in Ref. 1 was used here to build up a description of the electronic states of the whole oligopeptide by the exciton theory. Liquid crystal-linear dichroism (LC-LD) spectra of the distamycins were recorded by using as orienting solvents both thermotropic and lyotropic mesomorphic media. The agreement between the LD spectra and the polarization assignments by the exciton treatment is satisfactory. On this basis the flow-LD spectra of the complex between distamycin V and DNA was interpreted in terms of the preferred relative orientations of the guest and host molecules. A single site location of the distamycin within the minor groove does not perfectly match the experimental order parameters. This orientational distribution function could be too simple to explain the experimental data. It may therefore be assumed that a small fraction of the guest molecules are preferentially aligned more parallel to the host chain axis than the minor groove. Alternatively, and probably more likely, the partial mismatch of the experimental data with the minor groove location may be seen as a manifestation of the well-known stiffening and bending effects at the binding sites, which have already been observed by other techniques.
Assuntos
DNA , Distamicinas , Pirróis , Modelos Estruturais , Conformação de Ácido Nucleico , Ligação Proteica , Conformação ProteicaRESUMO
The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a "natural" DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.
Assuntos
DNA Bacteriano/química , Conformação de Ácido Nucleico , Plasmídeos/química , Microscopia de Força Atômica/métodosRESUMO
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.
Assuntos
Cromatina/ultraestrutura , Microscopia de Força Atômica , Cromatina/química , Cromatina/isolamento & purificação , DNA/química , Glutaral/farmacologia , Histonas/química , Processamento de Imagem Assistida por Computador , Microscopia de Força Atômica/instrumentação , Modelos Moleculares , Nucleossomos/ultraestrutura , Conformação ProteicaRESUMO
Calcitonin (CT) inhibits osteoclastic bone resorption and induces calcium uptake from body fluids. A comparative study of the conformational behaviours of therapeutic calcitonins [salmon (s), eel (e), a synthetic eel calcitonin analogue (Elcatonin), porcine (p) and human (h) calcitonins] as a function of solvent polarity and temperature have been performed by circular dichroism spectroscopy. Elements of secondary structure were lacking in H2O but could be observed in 2,2,2-trifluoroethanol and sodium dodecyl sulphate. In particular, similar amounts of alpha-helical content (four alpha-helical turns) were estimated in trifluoroethanol despite the considerable differences in amino acid sequences. The relative ability to form an alpha helix, assessed by trifluoroethanol/H2O titration, was found to be Elcatonin > sCT > pCT > eCT > hCT. In Elcatonin, sCT, pCT and eCT the four alpha-helical turns were promoted almost completely in a single step, between 0 and 35% trifluoroethanol, unlike hCT where helical structure formation has been reported to involve two steps over the whole trifluoroethanol/H2O range [Arvinte, T. & Drake, A. F. (1993) J. Biol. Chem. 268, 6408-6414]. In SDS, which mimics the membrane environment, conformational differences (3-4 helical turns in Elcatonin, sCT, eCT versus one helical turn in pCT, hCT) were observed and correlate well with biological activity (Elcatonin = sCT = eCT > pCT = hCT). Low-temperature studies in a cryogenic solvent mixture showed the formation of high alpha-helix content (similar to that in trifluoroethanol) in Elcatonin, sCT, eCT and pCT, whilst a left-handed extended helix (3(1) helix) was formed in hCT. This is consistent with the hypothesis of 'linear' and 'helical' calcitonin receptors [Nakanuta, H., Orlowski, R. C. & Epand, R. M. (1990) Endocrinology 127, 163-169].
Assuntos
Calcitonina/análogos & derivados , Calcitonina/química , Conformação Proteica , Sequência de Aminoácidos , Animais , Dicroísmo Circular , Feminino , Humanos , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Ovinos , Dodecilsulfato de Sódio , Solventes , Suínos , TemperaturaRESUMO
Reproducible images of pBR322 plasmid molecules have been recorded by scanning force microscopy under 1-propanol. Most of the plasmids were found in a coiled state. The supercoiled molecules of our samples look like branched or unbranched interwound superhelixes. This is consistent with available electron microscopy data on circular DNA molecules. By applying a stratigraphic analysis which takes advantage of the height information contained in the scanning force microscopy images, it is possible to assign the chirality of the local supercoiling of the individual molecules.
Assuntos
DNA Super-Helicoidal/ultraestrutura , Plasmídeos/ultraestrutura , 1-Propanol , DNA Circular/ultraestrutura , Microscopia Eletrônica de Varredura/métodos , Modelos Estruturais , Conformação de Ácido NucleicoRESUMO
Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a scanning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a three-dimensional organization of the fibers. The planar "zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histones H1 and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeling studies, suggest that chromatin fibers may exist as irregular three-dimensional arrays of nucleosomes even at low ionic strength.
Assuntos
Cromatina/ultraestrutura , Animais , Galinhas , Fixadores , Histonas/análise , Microscopia de Força Atômica , Modelos Biológicos , Concentração Osmolar , Cloreto de SódioRESUMO
The binding between Distamycin 3 and the palindromic duplexes d(CGTTTAAACG)2 and d(CGTACGTACG)2 was investigated by two independent techniques: UV-Vis absorption in the Job's plot approach and Induced Circular Dichroism. Both decamers bind two molecules of peptide per duplex, with close overall affinities. This result indicates that a row of six A:T base pairs can accommodate two molecules of drug and that the minimal binding site of Distamycin 3 can consist of just two A:T base pairs.