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Simona Ranallo

Bio: Simona Ranallo is an academic researcher from University of Rome Tor Vergata. The author has contributed to research in topics: Nanodevice & DNA. The author has an hindex of 8, co-authored 12 publications receiving 307 citations.

Papers
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Journal ArticleDOI
TL;DR: It is shown here that, by using three different antigens (including one relevant to HIV), it is possible to design different DNA nanomachines regulated by their targeting antibody in a rapid, versatile and highly specific manner.
Abstract: A wide range of molecular devices with nanoscale dimensions have been recently designed to perform a variety of functions in response to specific molecular inputs. Only limited examples, however, utilize antibodies as regulatory inputs. In response to this, here we report the rational design of a modular DNA-based nanomachine that can reversibly load and release a molecular cargo on binding to a specific antibody. We show here that, by using three different antigens (including one relevant to HIV), it is possible to design different DNA nanomachines regulated by their targeting antibody in a rapid, versatile and highly specific manner. The antibody-powered DNA nanomachines we have developed here may thus be useful in applications like controlled drug-release, point-of-care diagnostics and in vivo imaging.

104 citations

Journal ArticleDOI
TL;DR: The versatility of the platform was demonstrated by detecting five bivalent proteins and two monovalent proteins with low nanomolar detection limits and no detectable cross-reactivity.
Abstract: A versatile platform for the one-step fluorescence detection of both monovalent and multivalent proteins has been developed. This system is based on a conformation-switching stem–loop DNA scaffold that presents a small-molecule, polypeptide, or nucleic-acid recognition element on each of its two stem strands. The steric strain associated with the binding of one (multivalent) or two (monovalent) target molecules to these elements opens the stem, enhancing the emission of an attached fluorophore/quencher pair. The sensors respond rapidly (<10 min) and selectively, enabling the facile detection of specific proteins even in complex samples, such as blood serum. The versatility of the platform was demonstrated by detecting five bivalent proteins (four antibodies and the chemokine platelet-derived growth factor) and two monovalent proteins (a Fab fragment and the transcription factor TBP) with low nanomolar detection limits and no detectable cross-reactivity.

91 citations

Journal ArticleDOI
TL;DR: 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.
Abstract: 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 advantageous biomaterial for all the above applications but more specifically for sensing. First, synthetic DNA sequences, especially if of limited length (<100 nucleotides), have highly predictable interactions and thermodynamics. This allows to develop spatio-temporally controlled nanostructures with quasi-Amstrong precision and to engineer supramolecular devices with well controlled secondary structures.17-22 DNA is also quite easy and inexpensive to synthetize: currently the cost of 150 µg of an unmodified single stranded DNA strand of 20 nucleotides is about 8 euros if purchased from one of the many commercial vendors available in the market. Finally, DNA is relatively stable if compared to other biomolecules like enzymes or antibodies. The other important feature of synthetic DNA is the wide range of possibilities that it offers for sensing applications if used as recognition element. Of course the most obvious use of a single stranded synthetic DNA sequence as recognition element is for the detection of a specific target complementary sequence. Countless applications of such use, especially if coupled with PCR, have been reported to date which resulted in many commercially available sensing devices.23,24 Synthetic DNA can also be used as recognition element for targets other than DNA. This is the case, for example, of DNA aptamers, a class of high-affinity nucleic acid ligands, which are selected through alternate cycles in vitro to bind a specific target molecule.25-29 To date, thousands of DNA and RNA aptamers have been selected which bind to specific targets including small molecules, proteins, peptides, bacteria, virus, and live cells.30-32 Other aptamers can bind to surface molecules and membrane proteins of live cells.33-35 A DNA aptamer is usually a short DNA sequence (<100 nucleotides) that can bind with high affinity (nM-µM) and high specificity its specific target. While the affinity of the aptamers is usually not as high as that of other biomolecular recognition elements (i.e. antibodies) there are some advantages connected with their use including the lower cost and the higher stability. Synthetic DNA can also be used as recognition element to detect metal ions through the use of thymine-thymine (T-T) and cytosine-cytosine (C-C) mismatches, which specifically bind mercury(II)36-38 and silver(I)39,40 ions respectively or through the use of copper-dependent DNAzymes.41 Similarly, the use of non-conventional DNA interactions can be used to rationally design pH-sensitive DNA switches that can be used as nanometer scale pH meters.42-44 Such probes typically exploit DNA secondary structures that display pH dependence due to the presence of specific protonation sites. These structures include I-motif,45-50 inter and intra molecular triplex DNA,51-55 DNA tweezers56 and catenanes.57 Recently, we have also reported on the rational design of programmable DNA-based nanoswitches whose closing/opening can be triggered over specific different pH windows by simply changing the relative content of TAT/CGC triplets in the switches.58 Finally, DNA can be employed as convenient recognition element for the detection of transcription factors, proteins that control the transcription of genetic information and that specifically recognize double-stranded or single-stranded DNA and RNA sequences.59-63.

70 citations

Journal ArticleDOI
TL;DR: A rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs is reported.
Abstract: 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 unit that is able to initiate a toehold strand displacement reaction. The effect is rapid and specific and can be extended to different antibodies with the expedient of changing the recognition elements attached to the two split DNA input-strands. Such an antibody-regulated DNA-based circuit has then been employed to control the assembly and disassembly of DNA tubular structures using specific antibodies as inputs. For example, we demonstrate that we can induce self-assembly and disassembly of two distinct DNA tubular structures by using DNA circuits controlled by two different IgG antibodies (anti-Dig and anti-DNP antibodies) in the same solution in an orthogonal way. Antibodies are useful biomarkers and are emerging as powerful therapeutic tools. Here the authors report a rational strategy to orthogonally control assembly and disassembly of DNA-based nanostructures using specific IgG antibodies as molecular inputs.

43 citations

Journal ArticleDOI
TL;DR: Here it is demonstrated that one can rationally and finely control the functionality of different DNA-based nanodevices and nanoswitches using electronic inputs.
Abstract: Here we demonstrate that we can rationally and finely control the functionality of different DNA-based nanodevices and nanoswitches using electronic inputs. To demonstrate the versatility of our approach we have used here three different model DNA-based nanoswitches triggered by heavy metals and specific DNA sequences and a copper-responsive DNAzyme. To achieve electronic-induced control of these DNA-based nanodevices we have applied different voltage potentials at the surface of an electrode chip. The applied potential promotes an electron-transfer reaction that releases from the electrode surface a molecular input that ultimately triggers the DNA-based nanodevice. The use of electronic inputs as a way to finely activate DNA-based nanodevices appears particularly promising to expand the available toolbox in the field of DNA nanotechnology and to achieve a better hierarchical control of these platforms.

36 citations


Cited by
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Journal ArticleDOI
TL;DR: In this article, the electronic structure and bonding characteristics of borophene were investigated by first-principles calculations, and the obtained optical properties exhibited strong anisotropy as well.
Abstract: Borophene (a two-dimensional boron sheet) is a new type of two-dimensional material, which was recently grown successfully on single crystal Ag substrates. In this paper, we investigate the electronic structure and bonding characteristics of borophene by first-principles calculations. The band structure of borophene shows highly anisotropic metallic behaviour. The obtained optical properties of borophene exhibit strong anisotropy as well. Finally, the thermodynamic properties are investigated based on the phonon properties.

321 citations

Journal ArticleDOI
TL;DR: In this paper, a review of recent advances in the development of screen-printed electrode-based biosensors is presented, together with examples of paper-based electrochemical devices, of multiple detections using arrays of screen printed electrodes, and of the most recent developments in the field of wearable sensors.
Abstract: This review addresses recent advances in the development of screen-printed electrode based biosensors modified with different nanomaterials such as carbon nanotubes, graphene, metallic nanoparticles as gold, silver and magnetic nanoparticles, and mediator nanoparticles (Prussian Blue, Cobalt Phthalocyanine, etc.), coupled with biological recognition elements such as enzymes, antibodies, DNA and aptamers to obtain probes with improved analytical features. Examples of clinical applications are illustrated, together with examples of paper-based electrochemical devices, of multiple detections using arrays of screen printed electrodes, and of the most recent developments in the field of wearable biosensors. Also the use of smartphones as final detectors is briefly depicted.

288 citations

Journal ArticleDOI
TL;DR: In this article, the electronic structure and bonding characteristics of borophene were investigated by first-principle calculations, and the thermodynamic properties were investigated based on the phonon properties.
Abstract: Borophene (two-dimensional boron sheet) is a new type of two-dimensional material, which was recently grown successfully on single crystal Ag substrates. In this paper, we investigate the electronic structure and bonding characteristics of borophene by first-principle calculations. The band structure of borophene shows highly anisotropic metallic behaviour. The obtained optical properties of borophene exhibit strong anisotropy as well. The combination of high optical transparency and high electrical conductivity in borophene makes it a promising candidate for future design of transparent conductors used in photovoltaics. Finally, the thermodynamic properties are investigated based on the phonon properties.

245 citations

Journal ArticleDOI
TL;DR: In this paper, the authors present and discuss recent advances in synthesis strategies of assembled graphene-based superstructures of 1D, 2D, and 3D macroscopic shapes in the forms of fibers, thin films and foams/aerogels.
Abstract: Development of next-generation sensor devices is gaining tremendous attention in both academia and industry because of their broad applications in manufacturing processes, food and environment control, medicine, disease diagnostics, security and defense, aerospace, and so forth. Current challenges include the development of low-cost, ultrahigh, and user-friendly sensors, which have high selectivity, fast response and recovery times, and small dimensions. The critical demands of these new sensors are typically associated with advanced nanoscale sensing materials. Among them, graphene and its derivatives have demonstrated the ideal properties to overcome these challenges and have merged as one of the most popular sensing platforms for diverse applications. A broad range of graphene assemblies with different architectures, morphologies, and scales (from nano-, micro-, to macrosize) have been explored in recent years for designing new high-performing sensing devices. Herein, this study presents and discusses recent advances in synthesis strategies of assembled graphene-based superstructures of 1D, 2D, and 3D macroscopic shapes in the forms of fibers, thin films, and foams/aerogels. The fabricated state-of-the-art applications of these materials in gas and vapor, biomedical, piezoresistive strain and pressure, heavy metal ion, and temperature sensors are also systematically reviewed and discussed, and their sensing performance is compared.

192 citations

Journal ArticleDOI
TL;DR: A review of various nucleic acid-based biosensors, the different read-out strategies employed, and their use in chemical and biological sensing and how rational design of such constructs leads to more efficient biosensing platforms.
Abstract: Development of biosensing platforms plays a key role in research settings for identification of biomarkers and in clinical applications for diagnostics. Biosensors based on nucleic acids have taken many forms, from simple duplex-based constructs to stimuli-responsive nucleic acid nanostructures. In this review, we look at various nucleic acid-based biosensors, the different read-out strategies employed, and their use in chemical and biological sensing. We also look at current developments in DNA nanotechnology-based biosensors and how rational design of such constructs leads to more efficient biosensing platforms.

180 citations