Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 51
Filtrar
1.
Small ; 19(13): e2202253, 2023 03.
Artigo em Inglês | MEDLINE | ID: mdl-35775957

RESUMO

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.


Assuntos
Nanoestruturas , Nanoestruturas/química , Nanotecnologia , DNA/química , Termodinâmica , Conformação de Ácido Nucleico
2.
Bioconjug Chem ; 34(1): 37-50, 2023 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-36174970

RESUMO

Over the past 40 years, structural and dynamic DNA nanotechnologies have undoubtedly demonstrated to be effective means for organizing matter at the nanoscale and reconfiguring equilibrium structures, in a predictable fashion and with an accuracy of a few nanometers. Recently, novel concepts and methodologies have been developed to integrate nonequilibrium dynamics into DNA nanostructures, opening the way to the construction of synthetic materials that can adapt to environmental changes and thus acquire new properties. In this Review, we summarize the strategies currently applied for the construction of synthetic DNA filaments and conclude by reporting some recent and most relevant examples of DNA filaments that can emulate typical structural and dynamic features of the cytoskeleton, such as compartmentalization in cell-like vesicles, support for active transport of cargos, sustained or transient growth, and responsiveness to external stimuli.


Assuntos
Citoesqueleto , Nanoestruturas , Nanotecnologia , Nanoestruturas/química , Microtúbulos , DNA/química
3.
Nano Lett ; 22(22): 8818-8826, 2022 11 23.
Artigo em Inglês | MEDLINE | ID: mdl-36327970

RESUMO

Synthetic DNA filaments exploit the programmability of the individual units and their predictable self-association to mimic the structural and dynamic features of natural protein filaments. Among them, DNA origami filamentous structures are of particular interest, due to the versatility of morphologies, mechanical properties, and functionalities attainable. We here explore the thermodynamic and kinetic properties of linear structures grown from a ditopic DNA origami unit, i.e., a monomer with two distinct interfaces, and employ either base-hybridization or base-stacking interactions to trigger the dimerization and polymerization process. By observing the temporal evolution of the system toward equilibrium, we reveal kinetic aspects of filament growth that cannot be easily captured by postassembly studies. Our work thus provides insights into the thermodynamics and kinetics of hierarchical DNA origami assembly and shows how it can be mastered by the anisotropy of the building unit and its self-association mode.


Assuntos
Nanoestruturas , Conformação de Ácido Nucleico , Nanoestruturas/química , DNA/química , Termodinâmica , Hibridização de Ácido Nucleico , Nanotecnologia
4.
Nano Lett ; 21(20): 8634-8641, 2021 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-34662130

RESUMO

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrated its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of ∼5% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.


Assuntos
Transferência Ressonante de Energia de Fluorescência , Nanotecnologia , DNA/genética , Corantes Fluorescentes , Potenciais da Membrana , Neurônios
5.
Int J Mol Sci ; 22(16)2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34445704

RESUMO

RNA-binding proteins (RBPs) are essential regulators controlling both the cellular transcriptome and translatome. These processes enable cellular plasticity, an important prerequisite for growth. Cellular growth is a complex, tightly controlled process. Using cancer cells as model, we looked for RBPs displaying strong expression in published transcriptome datasets. Interestingly, we found the Pumilio (Pum) protein family to be highly expressed in all these cells. Moreover, we observed that Pum2 is regulated by basic fibroblast growth factor (bFGF). bFGF selectively enhances protein levels of Pum2 and the eukaryotic initiation factor 4E (eIF4E). Exploiting atomic force microscopy and in vitro pulldown assays, we show that Pum2 selects for eIF4E mRNA binding. Loss of Pum2 reduces eIF4E translation. Accordingly, depletion of Pum2 led to decreased soma size and dendritic branching of mature neurons, which was accompanied by a reduction in essential growth factors. In conclusion, we identify Pum2 as an important growth factor for mature neurons. Consequently, it is tempting to speculate that Pum2 may promote cancer growth.


Assuntos
Fator de Iniciação 4E em Eucariotos/metabolismo , Neurônios/metabolismo , Proteínas de Ligação a RNA/metabolismo , Animais , Fator de Iniciação 4E em Eucariotos/genética , Feminino , Fator 2 de Crescimento de Fibroblastos/metabolismo , Expressão Gênica/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Microscopia de Força Atômica/métodos , Neurogênese/fisiologia , Ligação Proteica/fisiologia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/genética , Transcriptoma/genética
6.
Molecules ; 25(23)2020 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-33255286

RESUMO

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.


Assuntos
DNA/química , DNA/ultraestrutura , Nanoestruturas/química , Conformação de Ácido Nucleico , Sequência de Bases , Isomerismo , Modelos Moleculares , Relação Estrutura-Atividade , Termodinâmica
7.
Molecules ; 24(20)2019 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-31615123

RESUMO

Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.


Assuntos
DNA/química , Enzimas/química , Nanoestruturas/química , Proteínas/química , Pareamento de Bases , Nanotecnologia/tendências , Conformação de Ácido Nucleico
8.
Biol Chem ; 399(7): 773-785, 2018 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-29604202

RESUMO

Natural filaments, such as microtubules and actin filaments, are fundamental components of the cell. Despite their relatively simple linear structure, filaments play a number of crucial roles in living organisms, from scaffolding to cellular adhesion and motility. The mechanical properties of natural filaments mostly rely on the structural features of the component units and on the way they are connected together, thus providing an ideal molecular model for emulation purposes. In this review, we describe the progresses done in this field using DNA for the rational design of synthetic filamentous-like materials with tailored structural and physical characteristics. We firstly survey the strategies that have been adopted until now for the construction of individual DNA building components and their programmable self-assembly into linear oligomeric structures. We then describe the theoretical models of polymer elasticity applied to calculate the bending strength of DNA filaments, expressed in terms of persistence length. Finally, we report some of the most exciting examples of truly biomimetic DNA filaments, which are capable of mimicking not only the sophisticated structural features of their natural counterparts but also their responsiveness to external stimuli, thus resulting in active motion and growing networks between distant loci.


Assuntos
DNA/química , Nanoestruturas/química , DNA/síntese química , Tamanho da Partícula , Propriedades de Superfície
9.
Nat Chem Biol ; 11(11): 862-9, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26436840

RESUMO

Excessive aggregation of proteins has a major impact on cell fate and is a hallmark of amyloid diseases in humans. To resolve insoluble deposits and to maintain protein homeostasis, all cells use dedicated protein disaggregation, protein folding and protein degradation factors. Despite intense recent research, the underlying mechanisms controlling this key metabolic event are not well understood. Here, we analyzed how a single factor, the highly conserved serine protease HTRA1, degrades amyloid fibrils in an ATP-independent manner. This PDZ protease solubilizes protein fibrils and disintegrates the fibrillar core structure, allowing productive interaction of aggregated polypeptides with the active site for rapid degradation. The aggregate burden in a cellular model of cytoplasmic tau aggregation is thus reduced. Mechanistic aspects of ATP-independent proteolysis and its implications in amyloid diseases are discussed.


Assuntos
Peptídeos beta-Amiloides/química , Amiloide/química , Fragmentos de Peptídeos/química , Proteínas Recombinantes de Fusão/química , Serina Endopeptidases/química , Proteínas tau/química , Amiloide/genética , Peptídeos beta-Amiloides/genética , Transporte Biológico , Expressão Gênica , Células HEK293 , Serina Peptidase 1 de Requerimento de Alta Temperatura A , Humanos , Domínios PDZ , Fragmentos de Peptídeos/genética , Agregados Proteicos , Conformação Proteica , Proteólise , Proteínas Recombinantes de Fusão/genética , Serina Endopeptidases/genética , Proteínas tau/genética
10.
Soft Matter ; 13(47): 8894-8902, 2017 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-29130094

RESUMO

DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built from a single type of vertex. Here we use analytic theory and equilibrium and dynamic simulation to show that a model particle, whose rotational properties lie between those of the vertices of the 6.6.6 and 4.8.8 networks, can self-assemble into a network built from three types of vertex. Important in forming this network is the ability of the particle to rotate when bound, thereby allowing the formation of more than one type of binding motif. The network in question is equivalent to a false tiling, a periodic structure built from irregular polygons, and possesses 40 particles in its unit cell. The emergence of this complex structure, whose symmetry properties are not obviously related to those of its constituent particles, highlights the potential for creating new structures from simple variants of existing nanoparticles.


Assuntos
DNA/química , Nanopartículas/química , Termodinâmica
11.
Chembiochem ; 17(12): 1063-80, 2016 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-27186937

RESUMO

From atoms to molecules and bio-macromolecules, from organelles to cells, tissues, to the whole living system, nature shows us that the formation of complex systems with emergent properties originates from the hierarchical self-assembly of single components in guided bottom-up processes. By using DNA as a fundamental building block with well-known self-recognition properties, scientists have developed design rules and physical-chemical approaches for the fully programmable construction of highly organized structures with nanosized features. This review highlights the basic principles of hierarchical self-assembly in terms of type and number of distinguishable components and their interaction energies. Such general concepts are then applied to DNA-based systems. After a brief overview of the strategies used until now for the construction of individual DNA units, such as DNA tile motifs and origami structures, their self-association into assemblies of higher order is discussed. Particular emphasis is given to the forces involved in the self-assembly process, understanding and rational combination of which might help to coordinate the single elements of hierarchical structures both in space and time, thus advancing our efforts towards the creation of devices that mimic the complexity and functionality of natural systems.


Assuntos
DNA/química , Nanoestruturas/química , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , Termodinâmica
12.
Angew Chem Int Ed Engl ; 54(41): 12039-43, 2015 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-26306556

RESUMO

Two-dimensional DNA lattices have been assembled from DNA double-crossover (DX) motifs on DNA-encoded surfaces in a site-specific manner. The lattices contained two types of single-stranded protruding arms pointing into opposite directions of the plane. One type of these protruding arms served to anchor the DNA lattice on the solid support through specific hybridization with surface-bound, complementary capture oligomers. The other type of arms allowed for further attachment of DNA-tethered probe molecules on the opposite side of the lattices exposed to the solution. Site-specific lattice assembly and attachment of fluorophore-labeled oligonucleotides and DNA-protein conjugates was demonstrated using DNA microarrays on flat, transparent mica substrates. Owing to their programmable orientation and addressability over a broad dynamic range from the nanometer to the millimeter length scale, such supramolecular architecture might be used for presenting biomolecules on surfaces, for instance, in biosensor applications.


Assuntos
DNA/química , Nanoestruturas/química , Nanoestruturas/ultraestrutura , Nanotecnologia/métodos , Silicatos de Alumínio/química , Corantes Fluorescentes/química , Conformação de Ácido Nucleico , Análise de Sequência com Séries de Oligonucleotídeos , Oligonucleotídeos/química , Propriedades de Superfície
13.
Angew Chem Int Ed Engl ; 54(12): 3592-7, 2015 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-25630797

RESUMO

Today, DNA nanotechnology is one of the methods of choice to achieve spatiotemporal control of matter at the nanoscale. By combining the peculiar spatial addressability of DNA origami structures with the switchable mechanical movement of small DNA motifs, we constructed reconfigurable DNA nanochambers as dynamic compartmentalization systems. The reversible extension and contraction of the inner cavity of the structures was used to control the distance-dependent energy transfer between two preloaded fluorophores. Interestingly, single-molecule FRET studies revealed that the kinetics of the process are strongly affected by the choice of the switchable motifs and/or actuator sequences, thus offering a valid method for fine-tuning the dynamic properties of large DNA nanostructures. We envisage that the proposed DNA nanochambers may function as model structures for artificial biomimetic compartments and transport systems.


Assuntos
DNA/química , Transferência Ressonante de Energia de Fluorescência , Nanoestruturas/química , Materiais Biomiméticos/química , Microscopia de Força Atômica , Estreptavidina/química
14.
Small ; 10(1): 73-7, 2014 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-23861344

RESUMO

A convenient PCR cloning strategy allows one to prepare hundreds of picomoles of circular single-stranded DNA molecules, which are suitable as scaffolds for the assembly of DNA origami structures. The method is based on a combination of site-directed mutagenesis and site- and ligation-independent cloning protocols, with simultaneous insertion of a nicking endonuclease restriction site on a double-stranded plasmid of desired length and sequence.


Assuntos
DNA/química , Mutagênese Sítio-Dirigida , Reação em Cadeia da Polimerase
15.
J Biol Chem ; 287(25): 20931-41, 2012 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-22535953

RESUMO

Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed.


Assuntos
Proteínas do Tecido Nervoso/química , Dobramento de Proteína , Proteólise , Serina Endopeptidases/química , Proteínas tau/química , Encéfalo/metabolismo , Encéfalo/patologia , Regulação Enzimológica da Expressão Gênica , Serina Peptidase 1 de Requerimento de Alta Temperatura A , Humanos , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Neuritos/enzimologia , Neuritos/patologia , Serina Endopeptidases/genética , Serina Endopeptidases/metabolismo , Tauopatias/enzimologia , Tauopatias/patologia , Proteínas tau/genética , Proteínas tau/metabolismo
16.
Nanoscale ; 15(31): 13120-13132, 2023 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-37503690

RESUMO

Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon the application of mechanical forces. Nevertheless, the role of the sequence in this conformational transformation is still unclear. In this work, we address this question by performing a systematic thermodynamic study of three origami domains that have an identical design but different sequence contents. By comparing the thermal stability of the domains in various settings and measuring the extent of isomerization at equilibrium (both at the global and single-molecule levels), we extract the contribution to folding given by the sequence and propose thermal criton maps of the isomers to rationalize our findings. Our data contribute to a deeper understanding of DNA origami assembly by considering both the topological- and thermal-dependent properties of the sites of initial folding. While the former are responsible for the mechanical aspects of the process, the latter justify the observed sequence-dependent conformational preferences, which appear evident in simple origami structures but remain typically undisclosed in large and more intricate architectures.


Assuntos
Nanoestruturas , Nanoestruturas/química , Conformação de Ácido Nucleico , DNA/química , Nanotecnologia , Fenômenos Mecânicos
17.
Small ; 8(19): 3000-8, 2012 Oct 08.
Artigo em Inglês | MEDLINE | ID: mdl-22761085

RESUMO

Miniaturization is an important aspect of device fabrication. Despite the advancements of modern top-down approaches, scaling-down to the sub-nanometer size is still a challenge. As an alternative, bottom-up approaches, such as the use of DNA as an engineering material, are therefore emerging, allowing control of matter at the single-molecule level. A DNA-based self-assembly method for the construction of switchable DNA devices is descrbied here based on G-quadruplex moieties, which are patterned on quasi-planar DNA arrays with nanoscale precision. The reversible switching of the devices is triggered by addition of DNA sequences ('fuels') and translated into linear extension/contractile movements. The conformational change of the devices was visualized by atomic force microscopy and FRET spectroscopy. Steady state fluorescence spectroscopy indicated that scaffolding of the G4 motors to either individual tiles or extended superlattices had no significant impact on the switching and optical performance of the system. However, time-resolved spectroscopy revealed that ordering in the microstructural environment enhances the fraction of molecules subject to FRET. Altogether, our study confirms that DNA superstructures are well-suited scaffolds for accommodation of mechanically switchable units and thus opens the door to the development of more sophisticated nanomechanical devices.


Assuntos
DNA/química , Nanoestruturas , Sequência de Bases , Transferência Ressonante de Energia de Fluorescência , Microscopia de Força Atômica , Conformação de Ácido Nucleico
18.
Chem Soc Rev ; 40(12): 5910-21, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21975573

RESUMO

Proteins possess intrinsic functionalities, which have been optimized in billions of years of natural evolution. The conjugation of proteins with artificial nucleic acids allows one to further functionalize proteins with a synthetically accessible, physicochemically robust tag, which is addressable in a highly specific manner by Watson-Crick hybridization. The resulting DNA-protein conjugates can be advantageously used in a variety of applications, ranging from biomedical diagnostics to DNA-based nanofabrication. This critical review provides an overview on chemical approaches to the synthesis of DNA-protein conjugates and their applications in biomolecular nanosciences (96 references).


Assuntos
DNA/química , DNA/metabolismo , Nanoestruturas , Nanotecnologia/métodos , Proteínas/metabolismo , Proteínas/química
19.
Angew Chem Int Ed Engl ; 51(1): 58-66, 2012 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-22162047

RESUMO

The advent of DNA origami technology greatly simplified the design and construction of nanometer-sized DNA objects. The self-assembly of a DNA-origami structure is a straightforward process in which a long single-stranded scaffold (often from the phage M13mp18) is folded into basically any desired shape with the help of a multitude of short helper strands. This approach enables the ready generation of objects with an addressable surface area of a few thousand nm(2) and with a single "pixel" resolution of about 6 nm. The process is rapid, puts low demands on experimental conditions, and delivers target products in high yields. These features make DNA origami the method of choice in structural DNA nanotechnology when two- and three-dimensional objects are desired. This Minireview summarizes recent advances in the design of DNA origami nanostructures, which open the door to numerous exciting applications.


Assuntos
DNA de Cadeia Simples/química , Nanoestruturas/química , Nanotecnologia , Conformação de Ácido Nucleico
20.
Chem Commun (Camb) ; 58(97): 13479-13482, 2022 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-36383102

RESUMO

We here show a reconfigurable DNA/plasmonic nanodevice with a precisely tunable and DNA-free interparticle gap. The nanodevice comprises two DNA boxes for the size-selective incorporation of nanoparticles in a face-to-face orientation and an underlying switchable DNA platform for the controlled and reversible adjustment of the interparticle distance.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA