Francesco Ricci

Azienda Ospedaliera Santa Maria di Terni · Chirurgia digestiva

We demonstrate here an approach to achieve dynamic and reversible decoration of DNA-based scaffolds. To do this, we employ rationally engineered DNA tiles containing enzyme-responsive strands covalently conjugated to different molecular labels. These strands are designed to be recognized and degraded by specific enzymes (i.e., Ribonuclease H, RNase...

Control over synthetic DNA-based nanodevices can be achieved with a variety of physical and chemical stimuli. Actuation with light, however, is as advantageous as difficult to implement without modifying DNA strands with photo-switchable groups. Herein, we show that DNA nanodevices can be controlled using visible light in photo-switchable aqueous b...

Introduction Recent evidence confirms that the treatment of acute appendicitis is not necessarily surgical, and selected patients with uncomplicated appendicitis can benefit from a non-operative management. Unfortunately, no cost-effective test has been proven to be able to effectively predict the degree of appendicular inflammation as yet, therefo...

Herein, we present a generalizable and versatile strategy to engineer synthetic DNA ligand-binding devices that can be programmed to load and release a specific ligand at a defined temperature. We do so by re-engineering two model DNA-based receptors: a triplex-forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an ATP-b...

Programmable antigen‐conjugated gene circuits which, upon recognition of a target antibody, trigger the cell‐free transcription of an RNA sequence that can be consequently detected with a disposable electrochemical sensor, were designed by Sara Bracaglia, Simona Ranallo, and Francesco Ricci in their Research Article (DOI: 10.1002/anie.202216512). T...

Programmable antigen‐conjugated gene circuits which, upon recognition of a target antibody, trigger the cell‐free transcription of an RNA sequence that can be consequently detected with a disposable electrochemical sensor, were designed by Sara Bracaglia, Simona Ranallo, and Francesco Ricci in their Research Article (DOI: 10.1002/ange.202216512). T...

Dose-limiting toxicity and significant patient-to-patient pharmacokinetic variability often render it difficult to achieve the safe and effective dosing of drugs. This is further compounded by the slow, cumbersome nature of the analytical methods used to monitor patient-specific pharmacokinetics, which inevitably rely on blood draws followed by pos...

We report here the development of an electrochemical cell‐free biosensor for antibody detection directly in complex sample matrices with high sensitivity and specificity that is particularly suitable for point‐of‐care applications. The approach is based on the use of programmable antigen‐conjugated gene circuits that, upon recognition of a specific...

We report here the development of an electrochemical cell‐free biosensor for antibody detection directly in complex sample matrices with high sensitivity and specificity that is particularly suitable for point‐of‐care applications. The approach is based on the use of programmable antigen‐conjugated gene circuits that, upon recognition of a specific...

Here, we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand displacement reactions (SDRs). The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables SD...

Biosensors and bioassays, both of which employ proteins and nucleic acids to detect specific molecular targets, have seen significant applications in both biomedical research and clinical practice. This success is largely due to the extraordinary versatility, affinity, and specificity of biomolecular recognition. Nevertheless, these receptors suffe...

Electrochemical aptamer-based (EAB) sensors utilize the binding-induced conformational change of an electrode-attached, redox-reporter-modified aptamer to transduce target recognition into an easily measurable electrochemical output. Because this signal transduction mechanism is single-step and rapidly reversible, EAB sensors support high-frequency...

We demonstrate here a strategy that allows the programmable and autonomous reorganization of self-assembled DNA polymers using redox chemistry. We have rationally designed different DNA monomers (tiles) that can co-assemble into tubular structures. The tiles can be orthogonally activated/deactivated with disulfide-linked DNA fuel strands that are d...

Here we present a generalizable and versatile strategy to rationally design synthetic DNA ligand-binding devices that can be programmed to load and release a ligand over a specific temperature range. We do so by re-engineering two model DNA-based receptors: a triplex forming bivalent DNA-based receptor that recognizes a specific DNA sequence and an...

The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Ca...

Here we demonstrate a strategy to rationally program a delayed onset of toehold-mediated DNA strand-displacement reactions. The approach is based on blocker strands that efficiently inhibit the strand displacement by binding to the toehold domain of the target DNA. Specific enzymatic degradation of the blocker strand subsequently enables the strand...

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotech...

We demonstrate here the use of DNA repair enzymes to control the assembly of DNA‐based structures. To do so, we employed uracil‐DNA glycosylase (UDG) and formamidopyrimidine DNA glycosylase (Fpg), two enzymes involved in the base excision repair (BER) pathway. We designed two responsive nucleic acid modules containing mutated bases (deoxyuridine or...

We demonstrate here the use of DNA repair enzymes to control the assembly of DNA‐based structures. To do so, we employed uracil‐DNA glycosylase (UDG) and formamidopyrimidine DNA glycosylase (Fpg), two enzymes involved in the base excision repair (BER) pathway. We designed two responsive nucleic acid modules containing mutated bases (deoxyuridine or...

Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste...

We report here the development of a cell-free in vitro transcription system for the detection of specific target antibodies. The approach is based on the use of programmable antigen-conjugated DNA-based conformational switches that, upon binding to a target antibody, can trigger the cell-free transcription of a light-up fluorescence-activating RNA...

Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste...

Real-time detection and nanoscale imaging of human immunodeficiency virus type 1 ribonucleic acid (HIV-1 RNA) in latently infected cells that persist in people living with HIV-1 on antiretroviral therapy in blood and tissue may reveal new insights needed to cure HIV-1 infection. Herein, we develop a strategy combining DNA nanotechnology and super-r...

Cooperativity (homotropic allostery) is the primary mechanism by which evolution steepens the binding curves of biomolecular receptors to produce more responsive input–output behavior in biomolecular systems. Motivated by the ubiquity with which nature employs this effect, over the past 15 years we, together with other groups, have engineered this...

Information processing in living cells results from the communication between DNA, RNA and proteins. Drawing inspiration from these molecular communication systems, in their Research Article (DOI: 10.1002/anie.202115680) Simona Ranallo, Francesco Ricci et al. demonstrate rational design and optimization of an antibody‐responsive, synthetic DNA‐base...

Die Informationsverarbeitung in lebenden Zellen beruht auf der Kommunikation zwischen DNA, RNA und Proteinen. Inspiriert von diesen molekularen Kommunikationssystemen demonstrieren Simona Ranallo, Francesco Ricci et al. in ihrem Forschungsartikel (DOI: 10.1002/anie.202115680) den gezielten Entwurf und die Optimierung einer antikörperresponsiven Fun...

We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the "tran...

We report here the rational design and optimization of an antibody‐responsive, DNA‐based device that enables communication between pairs of otherwise non‐interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “tran...

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Th...

We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “tran...

We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “tran...

We report here the development of a cell-free in-vitro transcription system for the detection of specific target antibodies. The approach is based on the use of programmable antigen-conjugated DNA-based conformational switches that, upon binding to a target antibody, can trigger the cell-free transcription of a light-up fluorescence-activating RNA...

We report here the development of a cell-free in-vitro transcription system for the detection of specific target antibodies. The approach is based on the use of programmable antigen-conjugated DNA-based conformational switches that, upon binding to a target antibody, can trigger the cell-free transcription of a light-up fluorescence-activating RNA...

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We...

DNA nanotechnology offers new biosensing approaches by templating different sensor and transducer components. Here, we combine DNA origami nanoantennas with label-free antibody detection by incorporating a nanoswitch in the plasmonic hotspot of the nanoantenna. The nanoswitch contains two antigens that are displaced by antibody binding thereby elic...

Electrochemiluminescence (ECL) is a powerful transduction technique that has rapidly gained importance as a powerful analytical technique. Since ECL is a surface-confined process, a comprehensive understanding of the generation of ECL signal at a nanometric distance from the electrode could lead to several highly promising applications. In this wor...

Current health emergencies have highlighted the need to have rapid, sensitive, and convenient platforms for the detection of specific antibodies. In response, we report here the design of an electrochemical DNA circuit that responds quantitatively to multiple specific antibodies. The approach employs synthetic antigen-conjugated nucleic acid strand...

Selective configuration control of plasmonic nanostructures using either top-down or bottom-up approaches has remained challenging in the field of active plasmonics. We demonstrate the realization of DNA-assembled reconfigurable plasmonic metamolecules, which can respond to a wide range of pH changes in a programmable manner. This programmability a...

We report the rational design of orthogonal DNA‐based addressable tiles that can re‐organize in a dynamic and reversible way to display well‐defined distributions: homopolymers made of a single tile, random polymers in which different tiles are distributed randomly and block structures in which the tiles are organized in segments. Abstract Nature...

Nature uses the breaking and making of non‐covalent interactions to achieve the reversible formation and structural reconfiguration of biopolymers, a strategy that permits dynamic adaptation in response to external cues and to changes in the environment. Inspired by this observation and taking advantage of the addressability and programmability of...

Taking advantage of the addressability and programmability of DNA/DNA non-covalent interactions we report here the rational design of orthogonal DNA-based addressable tiles that self-assemble into polymer-like structures that can be reconfigured and reorganized by external inputs. The different tiles share the same 5-nucleotide sticky ends responsi...

We present a new class of DNA‐based nanoswitches, named folding‐upon‐repair DNA nanoswitches, that upon enzymatic repair could undergo a conformational change mechanism leading to a change in fluorescent signal. The nanoswitches are suitable substrates for different methyltransferases and allow the screening of novel potential methyltransferase inh...

We demonstrate here a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containing O6‐methyl‐guanine (O6‐MeG) nucleobases and labelled with a fluorophore/quencher optical pai...

The function and activity of many proteins is finely controlled by the modulation of the entropic contribution of intrinsically disordered domains that are not directly involved in any recognition event. Inspired by this mechanism, we demonstrate here that we could finely regulate the catalytic activity of a model DNAzyme (i.e., a synthetic DNA seq...

We demonstrate here a homogeneous assay, named NanoHybrid, for monoclonal antibody quantification directly in serum samples in a single step format. NanoHybrid is composed of both synthetic peptide nucleic acids (PNA) and nucleic acid strands conjugated to recognition elements and optical labels and is designed to allow a fast fluorescence quantifi...

We describe a DNA‐based nanodevice that acts as a sulfur switch and can be temporally controlled through redox cycles of a disulfide‐linked allosteric modulator. The system has an unprecedented high tolerance to waste products and displays transient behavior for over 40 cycles without significant loss of efficiency. The approach is reversible and a...

Using proteins to actuate DNA systems is challenging because it requires non‐trivial binding‐induced mechanisms. We demonstrate a strategy to perform DNA‐based molecular operations controlled by DNA‐binding proteins using synthetic DNA translators that convert specific protein‐binding events into trigger inputs through a programmable structural tra...

Integrating dynamic DNA nanotechnology with protein‐controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA‐binding proteins by engineering synthetic DNA translators that convert specific protein‐binding events into trigger inputs through a progra...

Nature employs sulfur switches, i.e. redox‐active disulfides, to kinetically control biological pathways in a highly efficient and reversible way. Inspired by this mechanism we describe here a DNA‐based synthetic nanodevice that acts as a sulfur switch and can be temporally controlled though redox regulation. To do this we rationally designed disul...

Significance Cooperative binding is a property by which biomolecular receptors bind multiple-copy molecules of their targets in a highly concerted fashion, improving their responsiveness to small changes in target concentration. This mechanism is ubiquitous in the cell, where it is used to improve transport efficiency, tighten metabolic regulation,...

DNA nanodevices have been developed as platforms for the manipulation of gene expression, delivery of molecular payloads, and detection of various molecular targets within cells and in other complex biological settings. Despite efforts to translate DNA nanodevices from the test tube (in vitro) to living cells, their intracellular trafficking and fu...

Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a progra...

Kinetisch kontrollierte DNA‐Nanostrukturen wurden durch rein chemische Reaktionen hergestellt. In ihrem Forschungsartikel (DOI: 10.1002/ange.202002180) demonstrieren F. Ricci und Mitarbeiter die transiente Selbstorganisation von DNA‐Nanostrukturen mittels Reduktion/Oxidation von Disulfid‐ bzw. Thiol‐Kontrollsträngen. Inspiriert durch die Redoxsigna...

Kinetically controlled DNA nanostructures were generated through purely chemical reactions. In their Research Article (DOI: 10.1002/anie.202002180), F. Ricci and co‐workers demonstrate transient self‐assembly of DNA‐based nanostructures achieved by reduction/oxidation of disulfide/thiol controllers. Inspired by redox signaling in cells to control c...

Transient self‐assembly of DNA‐based nanostructures is achieved by purely synthetic chemical reactions. Inspired by the redox signalling employed by cells, redox cycles of disulfide‐bond formation/breakage are employed to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion....

In order to ensure maximum specificity, i.e., minimal cross-reactivity with structurally similar analogues to the desired target, most bioassays require careful tuning of the conditions employed (e.g., pH, ionic strength or temperature) to control “stringency.” Willingness to control assay conditions will fall, however, as quantitative, single-step...

Synthetic DNA has emerged as a powerful self‐assembled material for the engineering of nanoscale supramolecular devices and materials. Initial examples were focused on thermodynamically driven self‐assembly of DNA‐based structures with exquisite near‐angstrom control of their geometry. More recently dissipative self‐assembly of DNA‐based supramolec...

Synthetic DNA-based oligonucleotides are loaded into porous silicon nanoparticles (pSiNPs) and incorporated into nanofibers of poly(lactide-co-glycolide) (PLGA), poly-L-lactic acid (PLA), or polycaprolactone (PCL). The resulting hybrid nanofibers are characterized for their ability to release the functional oligonucleotide payload under physiologic...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The ability to control antibody activity by pH has important applications in diagnostics, therapeutic antibody targeting, and antibody-guided imaging. Here, we report the rational design of bivalent peptide–DNA ligands that allow pH-dependent control of antibody activity. Our strategy uses a pH-responsive DNA triple helix to control switching from...

Here we report a rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs. We first demonstrate that the binding of a specific antibody to a pair of antigen-conjugated split DNA input-strands induces their co-localization and reconstitution into a functional uni...

In article number 1900023, Valeria Vetri, Bruno Pignataro, and co‐workers describe a novel inkjet‐printing approach that allows to downscale up to femtoliter‐scale water droplets in oil drops on a chip, triggering the generation of sub‐cellular size artificial compartments with self‐selected submicrometer‐thin molecular and biomolecular shell struc...

The rational regulation of the pKa of an ionisable group in a synthetic device could be achieved by controlling the entropy of the linker connecting the hydrogen bond forming domains. We demonstrate this by designing a set of pH-responsive synthetic DNA-based nanoswitches that share the same hydrogen bond forming domains but differ in the length of...

Silencing of aberrantly expressed microRNAs (miRNAs or miRs) has emerged as one of the strategies for molecular targeted cancer therapeutics. In particular, miR-21 is an oncogenic miRNA overexpressed in many tumors, including ovarian cancer. To achieve efficient administration of anti-miR therapeutics, delivery systems are needed that can ensure lo...

A simple, rapid, and highly controlled platform to prepare life‐inspired subcellular scale compartments by inkjet printing has been developed. These compartments consist of fL‐scale aqueous droplets (few µm in diameter) incorporating biologically relevant molecular entities with programmed composition and concentration. These droplets are ink‐jette...

Allosteric DNA‐based nanodevices can transiently load and release small organic molecules (ATP and cocaine). In their Communication (DOI: 10.1002/anie.201812885), F. Ricci, L. J. Prins, and co‐workers demonstrate that allostery, despite being generally considered as a thermodynamic equilibrium phenomenon, offers a key strategy for the rational desi...

Allosterische DNA‐basierte Nanoeinheiten können niedermolekulare Verbindungen (ATP und Cocain) vorübergehend aufnehmen und wieder freisetzen. F. Ricci, L. J. Prins et al. zeigen in ihrer Zuschrift (DOI: 10.1002/ange.201812885), dass Allosterie – obwohl sie allgemein als ein Phänomen des thermodynamischen Gleichgewichts angesehen wird – eine hervorr...

Bio-catalytic micro- and nanomotors have emerged as a new class of active matter self-propelled through enzymatic reactions. The incorporation of functional nanotools could enable the rational design of multifunctional micromotors for simultaneous real-time monitoring of their environment and activity. Herein, we report the combination of DNA nanot...

Allostery is generally considered as a thermodynamic equilibrium phenomenon. In contrast to this, we show here that this mechanism offers a key strategy to rationally design out‐of‐equilibrium synthetic devices. We demonstrate this by engineering allosteric DNA‐based nanodevices for the transient load and release of small organic molecules. To demo...

Allostery is generally considered as a thermodynamic equilibrium phenomenon. In contrast to this, we show here that this mechanism offers a key strategy to rationally design out‐of‐equilibrium synthetic devices. We demonstrate this by engineering allosteric DNA‐based nanodevices for the transient load and release of small organic molecules. To demo...

DNA nanotechnology employs synthetic nucleic acid strands to design and engineer nanoscale structural and functional systems of increasing complexity that may find applications in sensing,1-7 computing,8-10 molecular transport,11-13 information processing14 and catalysis.15,16 Several features make synthetic DNA a particularly appealing and advanta...

We demonstrate here the rational design of purely entropic domains as a versatile approach to achieve control of the input/output response of synthetic molecular receptors. To do so and to highlight the versatility and generality of this approach we have rationally re-engineered two model DNA-based receptors: a clamp-like DNA-based switch that reco...

We propose an experimental and simulative approach to study the effect of integrating a DNA functional device into a large-sized DNA nanostructure. We selected, as a test bed, a well-known and characterized pH-dependent clamp-switch, based on a parallel DNA triple helix, to be integrated into a truncated octahedral scaffold. We designed, simulated...

Quantitative, experimental studies of the thermodynamics with which biopolymers interact with specific surfaces remain quite limited. In response, here we describe experimental and theoretical studies of the change in folding free energy that occurs when a simple bio-polymer, a DNA stem loop, is site-specifically attached to a range of chemically d...