Yossi Weizmann

Yossi Weizmann
Ben-Gurion University of the Negev | bgu · Department of Chemistry

Ph.D. Chemistry

About

78
Publications
8,238
Reads
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6,468
Citations
Additional affiliations
June 2008 - June 2011
Massachusetts Institute of Technology
Position
  • PostDoc Position

Publications

Publications (78)
Article
Nucleic acid amplification techniques have been amongst the most powerful tools for biological and biomedical research, and the vast majority of the bioassays rely on thermocycling that uses time-consuming and expensive Peltier-block heating. Here, we introduce a plasmonic photothermal method for quantitative real-time PCR, using gold bipyramids an...
Article
The realization of complex topologies at the molecular level represents a grand challenge in chemistry. This necessitates the manipulation of molecular interactions with high precision. Here we show that single-stranded DNA (ssDNA) knots and links can be created by utilizing the inherent topological properties that pertain to the DNA four-way junct...
Article
Full-text available
Much of the interest in noble metal nanoparticles is due to their plasmonic resonance responses and local field enhancement, both of which can be tuned through the size and shape of the particles. However, both properties suffer from the loss of monodispersity that is frequently associated with various morphologies of nanoparticles. Here we show a...
Article
Recent advances in RNA research have posed new directives in biology and chemistry to uncover the complex roles of ribonucleic acids in cellular processes. Innovative techniques to visualize native RNAs, particularly, short, low-abundance RNAs in live-cells, can dramatically impact current research on the roles of RNAs in biology. Herein, we report...
Article
Full-text available
Surface encoding of colloidal nanoparticles with DNA is fundamental for fields where recognition interaction is required, particularly controllable material self-assembly. However, regioselective surface encoding of nanoparticles is still challenging because of the difficulty associated with breaking the identical chemical environment on nanopartic...
Article
The design and screening of electrocatalysts for gas evolution reactions suffer from little understanding of multiphase processes at the electrode-electrolyte interface. Due to the complexity of the multiphase interface, it is still a great challenge to capture gas evolution dynamics under operando conditions to precisely portray the intrinsic cata...
Article
Bacterial infection is rising as a threatening health issue. Because of the present delay in early diagnosis of bacterial diseases as well as the abuse of antibiotics, it has become a vital issue in the development of in-time detection and therapy of bacterial infections. Herein, we designed a multifunctional nanotheranostics platform based on the...
Article
The long non-coding RNA (lncRNA) MALAT1 acts as an oncogene. RNA interference (RNAi) is an effective method to control the expression of specific genes and can be used for the treatment of tumors, but an effective and safe carrier system is a significant obstacle to gene therapy. Herein, we explored the possibility of constructing an in situ bio-re...
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Full-text available
Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable on...
Article
The increasing emergence of pathogenic bacterial infection have been regarded as urgent threats. Notwithstanding, developing simplified and effective means for accurate bacterial target diagnosis and therapy remains a considerable challenge. Here we report a reasonable method for accurate and rapid theranostic of bacteria by in situ self-assembly s...
Preprint
Full-text available
p>Though advances in nanotechnology have enabled the construction of synthetic nucleic acid based nanoarchitectures with ever-increasing complexity for various applications, high-resolution structures are lacking due to the difficulty of obtaining good diffracting crystals. Here we report the design of RNA nanostructures based on homooligomerizable...
Article
Full-text available
The synthesis of discrete nanoparticle self-assemblies has challenged the nanotechnology field for decades and has limited the study of nanoparticle interactions and the advance of nanomachinery. Here, we describe the preparation of discrete nanoparticle dimers from spherical gold nanoparticles and gold nanorods with stimuli-responsive optical prop...
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Full-text available
Background MicroRNA (miRNA) therapeutics are a promising approach to cancer treatment. However, this method faces considerable challenges to achieve tissue-specific, efficient, and safe delivery of miRNAs in vivo. Methods Herein, we developed a miRNA delivery system based on the in situ self-assembly of Au-miRNA nanocomplexes (Au-miRNA NCs). Withi...
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Full-text available
In biological systems, large and complex structures are often assembled from multiple simpler identical subunits. This strategy—homooligomerization—allows efficient genetic encoding of structures and avoids the need to control the stoichiometry of multiple distinct units. It also allows the minimal number of distinct subunits when designing artific...
Article
Cancer remains one of the most challenging diseases to treat. For accurate cancer diagnosis and targeted therapy, it is important to assess the localization of the affected area of cancers. The general approaches for cancer diagnostics include pathological assessments and imaging. However, these methods only generally assess the tumor area. In this...
Article
Despite all the efforts to develop an ideal technology for cancer treatment, vital parameters, such as reducing the adverse effects and improving treatment efficiency, still require significant improvement. For this purpose, the rational design of a smart stimuli-responsive and fully biodegradable delivery system is of great significance. By using...
Preprint
div>This study presents a robust homooligomeric self-assembly system based on RNA and DNA tiles that are folded from a single-strand of nucleic acid and assemble via a novel artificially designed branched kissing-loops (bKL) motif. By adjusting the geometry of individual tiles, we have constructed a total of 16 different structures that demonstrate...
Article
Full-text available
Trinucleotide repeat (TNR) instability is associated with over 42 neurodegenerative diseases and cancer, for which the molecular mechanisms remain to be elucidated. We have shown that the DNA base excision repair (BER) pathway and its central component, DNA polymerase β (pol β), in particular, its polymerase activity plays an active role in regulat...
Article
DNA condensation is a facile method to construct DNA nanostructure with high biostability and low cost, which is mainly used in DNA separation and gene transfection. The recent emerging condensed DNA nanostructures from the rolling circle amplification (RCA), i.e., the complexes between RCA products and magnesium pyrophosphate (RCA-MgPPi), have qui...
Article
Full-text available
Programmed self-assembly of nucleic acids is a powerful approach for nano-constructions. The assembled nanostructures have been explored for various applications. However, nucleic acid assembly often requires chemical or in vitro enzymatical synthesis of DNA or RNA, which is not a cost-effective production method on a large scale. In addition, the...
Article
RNA nanotechnology seeks to exploit the structural and functional properties of the RNA molecule in order to rationally design RNA nanoparticles and devices for applications in biotechnology and medicine, among others. Compared to DNA, RNA can adopt a larger diversity of structural motifs that allows the construction of more complicated nanoparticl...
Article
Extension of the Maxwell-Faraday law of electromagnetic induction to optical frequencies requires spatially appropriate materials and optical beams to create resonances and excitations with curl. Here we employ cylindrical vector beams with azimuthal polarization to create electric fields that selectively drive magnetic responses in dielectric core...
Article
Figure 1. The Origin, Design, and Operation of the First Crystalline DNA Device
Data
Supplementary Figures, Supplementary Tables and Supplementary References.
Article
Full-text available
Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontr...
Article
Human bone marrow mesenchymal stem cells (hBMSCs) and their exosomes can suppress immune reaction and deliver small RNAs. Thus, they may improve islet transplantation by delivering small RNAs for promoting islet function and inhibiting immune rejection. Here, we proposed an hBMSC and its exosome-based therapy to overcome immune rejection and poor i...
Article
Thin gold films offer intriguing material properties for potential applications including fuel cells, supercapacitors, electronic and photonic devices. We describe here an ambient filtration method that provides a simple and novel way to rapidly generate porous and thin gold films without the need for sophisticated instruments, clean-room environme...
Article
We report the construction of periodic DNA nanoribbons (DNRs) by a modified DNA origami method. Unlike the conventional DNA origami, the DNR scaffold is a long, single-stranded DNA of tandem repeats, originating from the rolling circular amplification (RCA). Consequently, the number of folding staple strands tremendously decreases from hundreds to...
Article
Full-text available
The exciting applications of gold nanoparticles (AuNPs) in bio-diagnostics are not limited to use as signal transduction probes; the fascinating effect of AuNPs on enhancing the reactions of nucleic acids has also been increasingly recognized. Herein, we explored the power of AuNPs and their enhancing effect on isothermal amplification reactions. T...
Article
Chemiresistive sensor arrays for cyclohexanone and nitromethane are fabricated using single-walled carbon nanotubes (SWCNTs) that are covalently functionalized with urea, thiourea, and squaramide containing selector units. Based on initial sensing results and 1H NMR binding studies, the most promising selectors are chosen and further optimized. The...
Article
As a crucial piece in the puzzle of cancer and human ageing, telomeres and telomerase play an indispensable role in modern biology. Herein, we describe a novel Exponential Isothermal Amplification of Telomere Repeat (EXPIATR) assay, which is a sensitive, simple, and reliable in vitro method for measuring telomerase activity in cell extracts. Throug...
Article
The ability to detect biological analytes in a rapid, sensitive, operationally simple, and cost-effective manner will impact human health and safety. Hybrid biocatalyzed-carbon nanotube (CNT) nanowire-based detection methods offer a highly sensitive and specific platform for the fabrication of simple and effective conductometric devices. Here, we r...
Article
Despite many advances in carbon nanotube (CNT) research, several issues continue to plague the field with regard to the construction of well-defined hybrid CNT materials. Regiospecific covalent functionalization, nonspecific surface absorption, and carbon nanotube aggregation/bundling present major difficulties when working with these materials. In...
Article
The synthesis of precisely defined nanoscale hybrid materials remains a challenge at the frontier of chemistry and material science. In particular, the assembly of diverse high-aspect ratio one-dimensional materials such as gold nanorods and carbon nanotubes into functional systems is of ever increasing interest due to their electronic and sensing...
Article
Full-text available
The ability of DNA to self-assemble into one-, two- and three-dimensional nanostructures, combined with the precision that is now possible when positioning nanoparticles or proteins on DNA scaffolds, provide a promising approach for the self-organization of composite nanostructures. Predicting and controlling the functions that emerge in self-organ...
Article
DNA strands consisting of programmed sequence-specific domains were synthesized by the rolling circle amplification (RCA) process. The spatial positioning of glucose oxidase (GOx) and of horseradish peroxidase (HRP) on the RCA-synthesized DNA template via hybridization enabled the activation of the bienzyme cascade. The GOx-catalyzed oxidation of g...
Article
A method for the amplified analysis of a gene sequence by a Fok I/DNA machine is described. A tailored nucleic acid that includes a recognition sequence for the analyzed gene and a hybridized sequence of the gene itself acting as the "fuel" substrate of the "machine". Upon recognition of the gene by the "fuel" substrate, the autonomous Fok I-induce...
Article
Alpha and beta conjugated bis-aptamers against thrombin act as bidentate "glue" for the self-assembly of thrombin nanowires; mixing the bidentate aptamer with a tripodal tridentate alpha aptamer construct yields branched thrombin nanowire structures.
Article
The amplified detection of DNA or of single-base mismatches in DNA is achieved by the use of nucleic acid-functionalized magnetic particles that separate the recognition duplexes and, upon amplification, yield chemiluminescence-generating DNAzymes as reporter units. The analysis of M13 phage ssDNA is achieved by the hybridization of the analyte to...
Article
Full-text available
A unique DNA scaffold was prepared for the one-step self-assembly of hierarchical nanostructures onto which multiple proteins or nanoparticles are positioned on a single template with precise relative spatial orientation. The architecture is a topologically complex ladder-shaped polycatenane in which the “rungs” of the ladder are used to bring toge...
Article
Mit einer Druckwalze konnen lange periodische Muster aufgetragen werden. Ahnlich funktioniert auch die biochemische Amplifizierung am rollenden Ring (rolling-circle amplification, RCA), in der eine cyclische Oligonucleotidsequenz als Matrize beim Aufbau einer komplementaren Einzelstrang-DNA wirkt. Werden DNA-Ketten mit Aptameren fur ein Protein wie...
Article
Die biochemische Amplifizierung am rollenden Ring (rolling-circle amplification, RCA) beruht auf Protein-Aptamer-Wechselwirkungen auf DNA-Gerüsten. Dieses Prinzip wurde genutzt, um hierarchische eindimensionale DNA-Protein/DNA-Protein-Nanopartikel-Aggregate zu erhalten. Die Konjugate können selbst als Matrizen zur Immobilisierung von Goldnanopartik...
Article
An aptamer-based machine is used for the amplified detection of the low-molecular-weight analyte, cocaine. The aptamer sequence recognizing cocaine, 1, is blocked to an inactive structure through its hybridization with 1a. In the presence of cocaine, 2, the blocked aptamer is folded to form the cocaine-aptamer complex 3, while releasing 1a. In the...
Article
An autonomous DNA-based machine that amplifies DNA biorecognition by the generation of a nucleic acid product that induces aggregation of Au nanoparticles (NPs) was analyzed. The colorimetric imaging of the DNA machine functions and the optical readout of the biosensing event was done by optical features of the Au NP aggregates. The DNA machine rev...
Article
Full-text available
Circular DNA is used as a template for the amplified detection of M13 phage ssDNA by a rolling circle amplification (RCA) process that synthesizes DNAzyme chains, thus enabling the colorimetric or chemiluminescent detection of the analyte.
Article
Hochempfindlich: Zur Analyse viraler DNA (M13-Phage) eignet sich eine DNA-basierte Maschine, die durch dNTPs angetrieben wird und DNAzym-Reportereinheiten synthetisiert. Die DNAzyme imitieren Peroxidase und führen zu einem Auslesen der analysierten DNA mithilfe von Kolorimetrie oder Chemilumineszenz.
Article
The preparation of nucleotide-functionalized CdS nanoparticles (NP) and their assembly on Au electrodes was discussed. The base C monolayer was assembled on the Au electrode by the covalent coupling of C to a cysteamine-functionalized Au electrode that resulted in layered H-bonded assembly of C-G hydrogen bonds following the layer-by-layer depositi...
Article
(Figure Presented) Fuel for a DNA machine: A Fokl enzyme/DNA scission machine is triggered by the hybridization of its DNA hairpin structure with a target nucleic acid. The machine is fueled by a secondary fluorophore (F)- and quencher (Q)-functionalized nucleic acid 2. Scission of 3 leads to replication of the machinery cutter 1 and yields a fluor...
Article
Gold-nanoparticle-functionalized enzymes act as "biocatalytic inks" for the generation of metallic nanowires via dip-pen nanolithography. Deposition of nanoparticle-modified oxidases or a phosphatase followed by development with their respective substrates and metal salts results in nanowires (see figure). This concept may be extended to the genera...
Article
Full-text available
Here we describe a protocol for the amplified detection of a target DNA using a DNA/FokI-based replicating cutting machine. The protocol is based on the design of a sensing hairpin oligonucleotide that is opened upon hybridization with the analyte DNA. The endonuclease FokI binds to the double-stranded complex and cleaves it to a "cutter" unit. The...
Article
The endonuclease scission of magnetic particles functionalized with sequence-specific DNAs, which are associated on cantilevers, is followed by the magnetic force-amplified readout of the reactions by the nano-mechanical deflection/retraction of the cantilevers. The systems are employed to develop AND or OR logic gates and to detect single base mis...
Article
Biorecognition and biocatalytic reactions of DNA monolayers, such as hybridization, polymerization, and hydrolytic digestion, were followed in situ by chronocoulometry and Faradaic impedance spectroscopy. Hydrophobic magnetic nanoparticles attracted to, and retracted from, the electrode surface by an external magnetic field were used to activate an...
Article
Thiolated nucleic acids 1 or 2 are immobilized on Au-coated cantilevers and hybridized with the complementary nucleic acids 1a or 2a associated with magnetic particles. The duplexes 1/1a or 2/2a include specific sequences for the scission by Apa I or Mse I, respectively. The cantilevers positioned in a flow cell are subjected to an external magneti...
Article
The synthesis of conductive nanowires or patterned conductive nanoelements is a challenging goal for the future fabrication of nanoscale circuitry. Similarly, the realization of nanoscale mechanics might introduce a new facet to the area of nanobiotechnology. Here we report on the design of conductive and patterned actin-based gold nanowires, and o...
Article
A highly sensitive telomerase detection method that involves amplified telomerase analysis and the use of rotating magnetic particles has been developed. Magnetic particles, functionalized with a primer (1) that is recognized by telomerase, are mixed with a nucleotide mixture that includes biotinylated-dUTP, and telomerase-induced elongation of the...
Article
The reconstitution of glucose oxidase on a flavin-adenine-dinucleotide (FAD)-functionalized single-walled carbon nanotube (SWCNT) associated with an Au electrode yields an electrically contacted biocatalyst (see picture). The efficiency of the electrical contact is controlled by the length of the SWCNT.
Article
Telomers are single-stranded DNA consisting of constant repeat units that are generated by the ribonucleoprotein telomerase present in cancer cells (e.g., HeLa cancer cells). Two methods for using telomer templates for the preparation of Au nanowires are presented. By one method, telomerization is performed in the presence of aminoallyl-functionali...
Article
The ultra-sensitive magneto-mechanical detection of DNA, single-base-mismatches in nucleic acids, and the assay of telomerase activity are accomplished by monitoring the magnetically induced deflection of a cantilever functionalized with magnetic beads associated with the biosensing interface. The analyzed M13phi DNA hybridized with the nucleic aci...
Article
CdSe-ZnS core-shell quantum dots (QDs) act as photochemical centers for lighting-up the dynamics of telomerization or DNA replication.
Article
The intercalation of doxorubicin into double-stranded DNA stimulates the electocatalyzed oxidation of aniline to polyaniline and its winding on the DNA template.
Article
Taking DNA analysis for a spin: Amplified detection of viral DNA and single-base mutations in nucleic acids is accomplished by the thermally cycled incorporation of biotin labels into DNA replica associated with magnetic particles, by the electrocatalyzed biochemiluminescence transduction of the DNA recognition events, and by the rotation of the ma...
Article
Amplified chemiluminescent detection of DNA-complementary DNA or of antigen-antibody interactions is accomplished in the presence of rotating functionalized magnetic particles.
Article
A crop of gold circles and lines: Psoralen-functionalized Au nanoparticles incorporated into DNA, and Au-nanoparticle-functionalized poly-L-lysine, yield linear and circular nanowires, respectively, on mica surfaces (see atomic force microscopy images).
Article
A crop of gold circles and lines: Psoralen‐functionalized Au nanoparticles incorporated into DNA, and Au‐nanoparticle‐functionalized poly‐L‐lysine, yield linear and circular nanowires, respectively, on mica surfaces (see atomic force microscopy images).
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Vergoldete Nanodrähte: Durch Einschluss von Psoralen‐funktionalisierten Au‐Nanopartikeln in DNA und durch Funktionalisierung von Poly‐L‐lysin mit Au‐Nanopartikeln werden lineare bzw. kreisförmige Nanodrähte auf Glimmer gebildet (siehe rasterkraftmikroskopische Aufnahmen).
Article
Three different methods for the amplified detection of a single-base mismatch in DNA are described using microgravimetric quartz-crystal-microbalance as transduction means. All methods involve the primary incorporation