Direct measurement of electrical transport through G-quadruplex DNA with mechanically controllable break junction electrodes

Ag+-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.

Polymorphism of G-quadruplexes formed by short oligonucleotides containing a 3'-3' inversion of polarity: From G:C:G:C tetrads to π-π stacked G-wires

G-wires are supramolecular DNA structures based on the G-quadruplex (G4) structural motif obtained by the self-assembly of interlocked slipped G-rich oligonucleotide (ON) strands, or by end-to-end stacking of G4 units. Despite the increasing interest towards G-wires due to their potential applications in DNA nanotechnologies, the self-assembly process to obtain G-wires having a predefined length and stability is still neither completely understood nor controlled. In our previous studies, we demonstrated that the d(5'CG2-3'-3'-G2C5') ON, characterized by the presence of a 3'-3'-inversion of polarity site self-assembles into a G-wire structure when annealed in the presence of K+ ions. Herein, by using CD, PAGE, HPLC size exclusion chromatography, and NMR investigations we studied the propensity of shorter analogues having sequences 5'CGn-3'-3'-GmC5' (with n = 1 and 1 ≤ m ≤ 3) to form the corresponding G-quadruplexes and stacked G-wires. The results revealed that the formation of G-wires starting from d(5'CGn-3'-3'-GmC5') ONs is possible only for the sequences having n and m > 1 in which both guanosines flanking the 5'-ending cytosines are not involved into the 3'-3' phosphodiester bond.

Single-molecular protein-based bioelectronics via electronic transport: fundamentals, devices and applications

Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.

Towards atom manufacturing with framework nucleic acids

Atom manufacturing has become a blooming frontier direction in the field of material and chemical science in recent years, focusing on the fabrication of functional materials and devices with individual atoms or with atomic precision. Framework nucleic acids (FNAs) refer to nanoscale nucleic acid framework structures with novel properties distinct from those of conventional nucleic acids. Due to their ability to be precisely positioned and assembled at the nanometer or even atomic scale, FNAs are ideal materials for atom manufacturing. They hold great promise for the bottom-up construction of electronic devices by precisely arranging and integrating building blocks with atomic or near-atomic precision. In this review, we summarize the progress of atom manufacturing based on FNAs. We begin by introducing the atomic-precision construction of FNAs and the intrinsic electrical properties of DNA molecules. Then, we describe various approaches for the fabrication of FNAs templated materials and devices, which are classified as conducting, insulating, or semiconducting based on their electrical properties. We highlight the role of FNAs in the fabrication of functional electronic devices with atomic precision, as well as the challenges and opportunities for atom manufacturing with FNAs.

G-wire-based self-quenched fluorescence probe combining with target-activated isothermal cascade amplification for ultrasensitive microRNA detection

Herein, we reported the G-wire-based self-quenched fluorescence probe and its application in ultrasensitive microRNA (miRNA) detection by combining with target-activated isothermal cascade amplification. The terminal-single-fluorescein (FAM)-labeled G-rich oligonucletides self-assembled into G-wire nanostructures (G-wires) with K⁺ and Mg²⁺. Thereafter, the G-wires brought terminal-labeled FAM into close proximity, as a result, the self-quenched signal probe formed. Besides, when there was the target miRNA, target-activated isothermal cascade amplification converted miRNA into the copious trigger DNA. After hybridization between trigger DNA and the self-quenched probe, the G-wires were splited and forced the apart of proximate FAM, and then the self-quenched probe displayed an "on" mechanism. Therefore, the approach gave a limit of detection (LOM) of 0.82 aM to miRNA-21 and could be implemented within a wide linear range of 2 aM to 2 nM. This approach was able to distinguish the single-mismatched miRNA-21, which was selective and sensitive in detecting human spiked serum samples.

Proton-Transfer Reactions in One-Electron-Oxidized G-Quadruplexes: A Density Functional Theory Study

Recently, G-quadruplexes (Gq) formed in B-DNA as secondary structures are found to be important therapeutic targets and material for developing nanodevices. Gq are guanine-rich and thus susceptible to oxidative damage by producing short-lived intermediate radicals via proton-transfer reactions. Understanding the mechanisms of radical formation in Gq is of fundamental interest to understand the early stages of DNA damage. Herein, we used density functional theory including aqueous phase (ωB97XD-PCM/6-31++G**) and considered single layer of Gq [G-quartets (G4): association of four guanines in a cyclic Hoogsteen hydrogen-bonded arrangement (Scheme 1)] to unravel the mechanisms of formation of intermediates by calculating the relative Gibbs free energies and spin density distributions of one-electron-oxidized G4 and its various proton-transfer states: G^•+, G(N₁-H)^•, G(N₂-H')^•, G(N₂-H″)^•, G(N₁-H)^•-(H⁺O₆)G, and G(N₂-H)^•-(H⁺N₇)G. The present calculation predicts the formation of G(N₂-H)^•-(H⁺N₇)G, which is only ca. 0.8 kcal/mol higher in energy than the initially formed G^•+. The formation of G(N₂-H)^•-(H⁺N₇)G plays a key role in explaining the formation of 8-OG along with G(N₁-H)^• formation via tautomerization from G(N₂-H)^•, as proposed recently.

Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups

The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G⁺)^● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)^● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.

Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.

Formation of Novel Octuplex DNA Molecules from Guanine Quadruplexes

Guanine quadruplex (G4)-DNA structures have sparked the interest of many scientists due to their important biological roles and their potential use in molecular nanoelectronics and nanotechnology. The high guanine content in G4-DNA endows it with mechanical stability, robustness, and improved charge transport properties-attractive attributes for a molecular nanowire. The self-driven formation of a novel G4-DNA-based nanostructure, coined guanine octuplex (G8)-DNA, is reported herein. Atomic force microscopy and scanning tunneling microscopy characterization of this molecule reveal its organized coiled-coil structure, which is found to be stable under different temperatures and surrounding conditions. G8-DNA exhibits enhanced stiffness, mechanical and thermodynamic stability when compared to its parent G4-DNA. These, along with its high guanine content, make G8-DNA a compelling new molecule, and a highly prospective candidate for molecular nanoelectronics.

Moving Electrons Purposefully through Single Molecules and Nanostructures: A Tribute to the Science of Professor Nongjian Tao (1963-2020)

Electrochemistry intersected nanoscience 25 years ago when it became possible to control the flow of electrons through single molecules and nanostructures. Many surprises and a wealth of understanding were generated by these experiments. Professor Nongjian Tao was among the pioneering scientists who created the methods and technologies for advancing this new frontier. Achieving a deeper understanding of charge transport in molecules and low-dimensional materials was the first priority of his experiments, but he also succeeded in discovering applications in chemical sensing and biosensing for these novel nanoscopic systems. In parallel with this work, the investigation of a range of phenomena using novel optical microscopic methods was a passion of his and his students. This article is a review and an appreciation of some of his many contributions with a view to the future.

GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly

GCn and GCnCG, where n = (G2AG4AG2), fold into well-defined, dimeric G-quadruplexes with unprecedented folding topologies in the presence of Na+ ions as revealed by nuclear magnetic resonance spectroscopy. Both G-quadruplexes exhibit unique combination of structural elements among which are two G-quartets, A(GGGG)A hexad and GCGC-quartet. Detailed structural characterization uncovered the crucial role of 5'-GC ends in formation of GCn and GCnCG G-quadruplexes. Folding in the presence of 15NH4+ and K+ ions leads to 3'-3' stacking of terminal G-quartets of GCn G-quadruplexes, while 3'-GC overhangs in GCnCG prevent dimerization. Results of the present study expand repertoire of possible G-quadruplex structures. This knowledge will be useful in DNA sequence design for nanotechnological applications that may require specific folding topology and multimerization properties.

π–π stacked DNA G-wire nanostructures formed by a short G-rich oligonucleotide containing a 3′–3′ inversion of polarity site

Rod-shaped G-wire assemblies potentially useful to obtain new hybrid and conducting materials were obtained by annealing short G-rich oligonucleotides incorporating a 3′–3′ inversion of polarity site in the presence of potassium or ammonium ions.

An ultrasensitive guanine wire-based resonance light scattering method using G-quadruplex self-assembly for determination of microRNA-122

An enzyme-free resonance light scattering (RLS) method is described for the determination of microRNA-122. A guanine nanowire (G-wire) is used that consists of a predesigned DNA1 and a G-quadruplex sequence DNA2. These hybridize with microRNA-122 and partially hybridize with DNA2. After formation of stable double strands with DNA1, DNA2 is released. On addition of K⁺ and Mg²⁺ ions, the G-quadruplex sequences undergo self-assembly to form long filamentous G-wires. This increases the intensity of RLS. A 6.1 pM detection limit was obtained, and the linear response covers the 50 pM to 300 nM microRNA concentration range. The method was successfully applied to the quantitation of microRNA-122 in hepatocellular carcinoma cell lysates. Conceivably, this assay can be extended to other RLS methods for biomarker detection by simply changing the sequence of DNA1. Graphical abstract The G-quadruplex sequences of DNA2 were locked with DNA1. The G-quadruplex fragments of DNA2 were released after the hybridization of microRNA-122 with DNA1. These liberated G-quadruplex sequences were self-assembled into long filamentous guanine nanowires (G-wires) which increased resonance light intensity in the presence of Mg²⁺.

New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes

G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG₄T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG₄T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC⁻size-exclusion chromatography (HPLC⁻SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG₄T)₄. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.

A Minimal Sequence for Left-Handed G-Quadruplex Formation

Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.

Voltammetry and molecular assembly of G-quadruplex DNAzyme on single-crystal Au(111)-electrode surfaces - hemin as an electrochemical intercalator

DNA quadruplexes (qs) are a class of "non-canonical" oligonucleotides (OGNs) composed of stacked guanine (G) quartets stabilized by specific cations. Metal porphyrins selectively bind to G-qs complexes to form what is known as DNAzyme, which can exhibit peroxidase and other catalytic activity similar to heme group metalloenzymes. In the present study we investigate the electrochemical properties and the structure of DNAzyme monolayers on single-crystal Au(111)-electrode surfaces using cyclic voltammetry and scanning tunnelling microscopy under electrochemical potential control (in situ STM). The target DNAzyme is formed from a single-strand OGN with 12 guanines and iron(iii) porphyrin IX (hemin), and assembles on Au(111) through a mercapto alkyl linker. The DNAzyme monolayers exhibit a strong pair of redox peaks at 0.0 V (NHE) at pH 7 in acetate buffer, shifted positively by about 50 mV compared to free hemin weakly physisorbed on the Au(111)-electrode surface. The voltammetric hemin signal of DNAzyme is enhanced 15 times compared with that of hemin adsorbed directly on the Au(111)-electrode surface. This is indicative of both the formation of a close to dense DNAzyme monolayer and that hemin is strongly bound to the immobilized 12G-qs in well-defined orientation favorable for interfacial ET with a rate constant of 6.0 ± 0.4 s^-1. This is supported by in situ STM which discloses single-molecule G-quartet structures with a size of 1.6 ± 0.2 nm.

Electrostatic Force Triggering Elastic Condensation of Double-Stranded DNA for High-Performance One-Step Immunoassay

Current strategies for high-performance immunoassay generally require a sandwich structure for signal amplification. This strategy is limited to multivalent antigens and complicates the detection scheme. Herein we demonstrate a class of simple one-step ultrasensitive immunoassay with the adoption of double-stranded DNA (dsDNA) as "conductive spring" to bridge the electrode and redox-reporter/antibody-receptor comodified gold nanoparticles (AbFc@AuNPs). Upon biorecognition between antigen and antibody, the charge of the AuNPs changes, enhancing the electrostatic interaction between the AuNPs and Au electrode surface, and condensing the dsDNA chain. For the first time, the sensitive response of the electrochemical redox current to the DNA chain length is utilized to achieve an ultrahigh sensitivity down to fM level. Only the primary antibody needed in the recognition interface ensures the one-step immunoreaction works well with monovalent antigens, which ensure this method as a promising general alternative means for fast, high-throughput or point-of-care clinical applications even for very challenging clinically relevant samples.

High-resolution AFM structure of DNA G-wires in aqueous solution

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G₄T₂G₄] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

DNA and RNA G-quadruplexes can stack to form higher-order structures called G-wires. Here the authors report high-resolution AFM images of higher-order DNA G-quadruplexes in aqueous solution that could impact the design of G-wire based nanodevices and the understanding of G-wires in biology.

Electrical and SERS detection of disulfide-mediated dimerization in single-molecule benzene-1,4-dithiol junctions

Electrical and in situ SERS characterization of the benzene-1,4-dithiol (BDT) junction suggested that dimerization of BDT contributed to the low conductance.

We applied a combination of mechanically controllable break junction (MCBJ) and in situ surface enhanced Raman spectroscopy (SERS) methods to investigate the long-standing single-molecule conductance discrepancy of prototypical benzene-1,4-dithiol (BDT) junctions. Single-molecule conductance characterization, together with configuration analysis of the molecular junction, suggested that disulfide-mediated dimerization of BDT contributed to the low conductance feature, which was further verified by the detection of S–S bond formation through in situ SERS characterization. Control experiments demonstrated that the disulfide-mediated dimerization could be tuned via the chemical inhibitor. Our findings suggest that a combined electrical and SERS method is capable of probing chemical reactions at the single-molecule level.

DNA-Based Single-Molecule Electronics: From Concept to Function

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity

The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca2+, and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies.

Self-Assembly of G-Rich Oligonucleotides Incorporating a 3'-3' Inversion of Polarity Site: A New Route Towards G-Wire DNA Nanostructures

Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions. Our results expand the repertoire of synthetic methodologies to obtain new tailored DNA G-wire nanostructures.

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K⁺ and Na⁺, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the method's accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li⁺, Na⁺, K⁺, or Rb⁺) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within ΔE is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K⁺ or two Rb⁺ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.

Synthesis and biophysical properties of (L)-aTNA based G-quadruplexes

Novel G-quadruplex structures are constructed by acyclic (L)-threninol nucleic acid and their synthesis and biophysical properties are described. Pyrene excimer fluorescence and circular dichroism (CD) data revealed that four strands of aTNA are oriented in antiparallel direction.

Ultrasensitive Label-Free Resonance Rayleigh Scattering Aptasensor for Hg(2+) Using Hg(2+)-Triggered Exonuclease III-Assisted Target Recycling and Growth of G-Wires for Signal Amplification

A novel signal-on and label-free resonance Rayleigh scattering (RRS) aptasensor was constructed for detection of Hg(2+) based on Hg(2+)-triggered Exonuclease III-assisted target recycling and growth of G-quadruplex nanowires (G-wires) for signal amplification. The hairpin DNA (H-DNA) was wisely designed with thymine-rich recognition termini and a G-quadruplex sequence in the loop and employed as a signal probe for specially recognizing trace Hg(2+) by a stable T-Hg(2+)-T structure, which automatically triggered Exonuclease III (Exo-III) digestion to recycle Hg(2+) and liberate the G-quadruplex sequence. The free G-quadruplex sequences were self-assembled into guanine nanowire (G-wire) superstructure in the presence of Mg(2+) and demonstrated by gel electrophoresis. The RRS intensity was dramatically amplified by the resultant G-wires, and the maximum RRS signal at 370 nm was linear with the logarithm of Hg(2+) concentration in the range of 50.0 pM to 500.0 nM (R = 0.9957). Selectivity experiments revealed that the as-prepared RRS sensor was specific for Hg(2+), even coexisting with high concentrations of other metal ions. This optical aptasensor was successfully applied to identify Hg(2+) in laboratory tap water and river water samples. With excellent sensitivity and selectivity, the proposed RRS aptasensor was potentially suitable for not only routine detection of Hg(2+) in environmental monitoring but also various target detection just by changing the recognition sequence of the H-DNA probe.

Electronic excitations in Guanine quadruplexes

Guanine rich DNA strands, such as those encountered at the extremities of human chromosomes, have the ability to form four-stranded structures (G-quadruplexes) whose building blocks are guanine tetrads. G-quadruplex structures are intensively studied in respect of their biological role, as targets for anticancer therapy and, more recently, of their potential applications in the field of molecular electronics. Here we focus on their electronic excited states which are compared to those of non-interacting mono-nucleotides and those of single and double stranded structures. Particular emphasis is given to excited state relaxation processes studied by time-resolved fluorescence spectroscopy from femtosecond to nanosecond time scales. They include ultrafast energy transfer and trapping of ππ* excitations by charge transfer states. The effect of various structural parameters, such as the nature of the metal cations located in the central cavity of G-quadruplexes, the number of tetrads or the conformation of the constitutive single strands, are examined.

Graphene-DNAzyme Junctions: A Platform for Direct Metal Ion Detection with Ultrahigh Sensitivity

Many metal ions are present in biology and in the human body in trace amounts. Despite numerous efforts, metal sensors with ultrahigh sensitivity (< a few picomolar) are rarely achieved. Here, we describe a platform method that integrates a Cu2+-dependent DNAzyme into graphene-molecule junctions and its application for direct detection of paramagnetic Cu2+ with femtomolar sensitivity and high selectivity. Since DNAzymes specific for other metal ions can be obtained through in vitro selection, the method demonstrated here can be applied to the detection of a broad range of other metal ions.

On the use of metal purine derivatives (M=Ir, Rh) for the selective labeling of nucleosides and nucleotides

The reactions of neutral or cationic IrIII and RhIII derivatives of phenyl purine nucleobases with unsymmetrical alkynes produce new metallacycles in a predictable manner, which allows for the incorporation of either photoactive (anthracene or pyrene) or electroactive (ferrocene) labels in the nucleotide or nucleoside moiety. The reported methodology (metalation of the purine derivative and subsequent marker insertion) could be used for the postfunctionalization and unambiguous labeling of oligonucleotides.

Revealing the direct effect of individual intercalations on DNA conductance toward single-molecule electrical biodetection

The effect of individual intercalations on DNA conductance is revealed electrically at the single-molecule level by using DNA-functionalized molecular junctions.

Direct observation of guanine radical cation deprotonation in G-quadruplex DNA

Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G(+•)) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2-H instead of imino proton N1-H) and slower (1-2 orders of magnitude) deprotonation rate of G(+•) within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, mechanistic insights have been further achieved, showing that it should be the non-hydrogen-bonded free proton to be released during deprotonation in G-quadruplexes, which is the N2-H exposed to solvent for G bases in G-quartets or the free N1-H for G base in the loop. The slower N2-H deprotonation rate can thus ensure less interruption of the hole transfer. The unique deprotonation features observed here for G-quadruplexes open possibilities for their interesting applications as molecular electronic devices, while the elucidated mechanisms can provide illuminations for the rational design of G-quadruplex structures toward such applications and enrich the fundamental understandings of DNA radical chemistry.

Long-range charge transport in single G-quadruplex DNA molecules

DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set-ups, and transporting significant current through individual DNA-based molecules remains a considerable challenge. Here, we report reproducible charge transport in guanine-quadruplex (G4) DNA molecules adsorbed on a mica substrate. Currents ranging from tens of picoamperes to more than 100 pA were measured in the G4-DNA over distances ranging from tens of nanometres to more than 100 nm. Our experimental results, combined with theoretical modelling, suggest that transport occurs via a thermally activated long-range hopping between multi-tetrad segments of DNA. These results could re-ignite interest in DNA-based wires and devices, and in the use of such systems in the development of programmable circuits.

Origin of discrete current fluctuations in a single molecule junction

A series of fresh molecular junctions at a single molecule level were created and the current fluctuations were studied as electrons passed through them. Our results indicate that telegraph-like current fluctuations at room temperature neither originate from electron trapping/detrapping processes nor from molecule re-conformation. Our results will be helpful in better understanding the mechanism of current fluctuations.

More than one non-canonical phosphodiester bond in the G-tract: formation of unusual parallel G-quadruplex structures

In this article, we report an investigation, based on NMR and CD spectroscopic and electrophoretic techniques, of 5'TGGGGT3' analogues containing two or three 3'-3' or 5'-5' inversion sites in the G-run, namely 5'TG3'-3'G5'-5'GGT3' (Q350), 5'TG3'-3'GG5'-5'GT3' (Q305), 5'TGG3'-3'G5'-5'GT3' (Q035), 5'TG3'-3'G5'-5'G3'-3'GT5' (Q353) and 3'TG5'-5'G3'-3'G5'-5'GT3' (Q535). Although the sequences investigated contain either no or only one natural 3'-5' linkage in the G-tract, all modified oligodeoxyribonucleotides (ODNs) have been shown to form stable tetramolecular quadruplex structures. The ability of the 3'-3' or 5'-5' inversion sites to affect the glycosidic conformation of guanosines and, consequently, base stacking, has also been investigated. The results of this study allow us to propose some generalizations concerning strand arrangements and the glycosidic conformational preference of residues adjacent to inverted polarity sites. These rules could be of general interest in the design of modified quadruplex structures, in view of their application as G-wires and modified aptamers.

Mechanically controllable break junctions for molecular electronics

A mechanically controllable break junction (MCBJ) represents a fundamental technique for the investigation of molecular electronic junctions, especially for the study of the electronic properties of single molecules. With unique advantages, the MCBJ technique has provided substantial insight into charge transport processes in molecules. In this review, the techniques for sample fabrication, operation and the various applications of MCBJs are introduced and the history, challenges and future of MCBJs are discussed.

A novel equilibrium relating to the helix handedness in G-quadruplexes formed by heterochiral oligonucleotides with an inversion of polarity site

Investigations of heterochiral oligodeoxynucleotides 5'-TD1GD2GD3-3'-3'-GL3GL2TL1-5' (L33) and 3'-TD1GD2GD3-5'-5'-GL3GL2TL1-3' (L55) forming quadruplex structures are reported. Data indicate the presence of enantiomeric left- and right-handed quadruplex helices. In the case of L55, NMR experiments point to an unusual equilibrium between them.

Guided assembly of tetramolecular G-quadruplexes

Nucleic acids are finding applications in nanotechnology as nanomaterials, mechanical devices, templates, and biosensors. G-quadruplex DNA, formed by π-π stacking of guanine (G) quartets, is an attractive alternative to regular B-DNA because of the kinetic and thermodynamic stability of quadruplexes. However, they suffer from a fatal flaw: the rules of recognition, i.e., the formation of a G-quartet in which four identical bases are paired, prevent the controlled assembly between different strands, leading to complex mixtures. In this report, we present the solution to this recognition problem. The proposed design combines two DNA elements: parallel-stranded duplexes and a quadruplex core. Parallel-stranded duplexes direct controlled assembly of the quadruplex core, and their strands present convenient points of attachments for potential modifiers. The exceptional stability of the quadruplex core provides integrity to the entire structure, which could be used as a building block for nucleic acid-based nanomaterials. As a proof of principle for the design's versatility, we assembled quadruplex-based 1D structures and visualized them using atomic force and transmission electron microscopy. Our findings pave the way to broader utilization of G-quadruplex DNA in structural DNA nanomaterials.

Formation of a thymine-Hg(II)-thymine metal-mediated DNA base pair: proposal and theoretical calculation of the reaction pathway

A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg(II) ion, which results in the formation of a (T)N3-Hg(II)-N3(T) metal-mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg(II)-N3(T) bond is triggered by deprotonation of the imino N3 atom in thymine with a hydroxo ligand on the Hg(II) ion. The formation of the second Hg(II)-N3(T) bond proceeds through water-assisted tautomerization of the remaining, metal-nonbonded thymine base or through thymine deprotonation with a hydroxo ligand of the Hg(II) ion already coordinated to the thymine base. The thermodynamic parameters ΔGR =-9.5 kcal mol(-1), ΔHR =-4.7 kcal mol(-1), and ΔSR =16.0 cal mol(-1)  K(-1) calculated with the ONIOM (B3LYP:BP86) method for the reaction agreed well with the isothermal titration calorimetric (ITC) measurements by Torigoe et al. [H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010, 16, 13218-13225]. The peculiar positive reaction entropy measured previously was due to both dehydration of the metal and the change in chemical bonding. The mercury reactant in the theoretical model contained one hydroxo ligand in accord with the experimental pKa  value of 3.6 known for an aqua ligand of a Hg(II) center. The chemical modification of T:T mismatched to the T-Hg(II)-T metal-mediated base pair was modeled for the middle base pair within a trinucleotide B-DNA duplex, which ensured complete dehydration of the Hg(II) ion during the reaction.