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1.  Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. 
Nucleic Acids Research  1997;25(14):2792-2799.
Arrays of up to some 1000 PNA oligomers of individual sequence were synthesised on polymer membranes using a robotic device originally designed for peptide synthesis. At approximately 96%, the stepwise synthesis efficiency was comparable to standard PNA synthesis procedures. Optionally, the individual, fully deprotected PNA oligomers could be removed from the support for further use, because an enzymatically cleavable but otherwise stable linker was used. Since PNA arrays could form powerful tools for hybridisation based DNA screening assays due to some favourable features of the PNA molecules, the hybridisation behaviour of DNA probes to PNA arrays was investigated for a precise understanding of PNA-DNA interactions on solid support. Hybridisation followed the Watson-Crick base pairing rules with higher duplex stabilities than on corresponding DNA oligonucleotide sensors. Both the affinity and specificity of DNA hybridisation to the PNA oligomers depended on the hybridisation conditions more than expected. Successful discrimination between hybridisation to full complementary PNA sequences and truncated or mismatched versions was possible at salt concentrations down to 10 mM Na+and below, although an increasing tendency to unspecific DNA binding and few strong mismatch hybridisation events were observed.
PMCID: PMC146815  PMID: 9207026
2.  Synthesis and evaluation of some properties of chimeric oligomers containing PNA and phosphono-PNA residues. 
Nucleic Acids Research  1998;26(2):566-575.
In an attempt to improve physico-chemical and biological properties of peptide nucleic acids (PNAs), particularly water solubility and cellular uptake, the synthesis of chimeric oligomers consisted of PNA and phosphono-PNA analogues (pPNAs) bearing the four natural nucleobases has been accomplished. To produce these chimeras, pPNA monomers of two types containing N-(2-hydroxyethyl)phosphonoglycine, or N-(2-aminoethyl)phosphonoglycine backbone, were used in conjunction with PNA monomers representing derivatives of N-(2-aminoethyl)glycine, or N-(2-hydroxyethyl)glycine. The oligomers obtained were composed of either PNA and pPNA stretches or alternating PNA and pPNA monomers. The examination of hybridization properties of PNA-pPNA chimeras to DNA and RNA complementary strands in comparison with pure PNAs, and pPNAs as well as DNA-pPNA hybrids and DNA fragments confirmed that these chimeras form stable complexes with complementary DNA and RNA fragments. They were found to be resistant to degradation by nucleases. All these properties together with good solubility in water make PNA-pPNA hybrids promising for further evaluation as potential therapeutic agents.
PMCID: PMC147292  PMID: 9421517
3.  Quantification of plasma HIV RNA using chemically-engineered peptide nucleic acids 
Nature communications  2014;5:5079.
The remarkable stability of peptide nucleic acids (PNAs) toward enzymatic degradation makes this class of molecules ideal to develop as part of a diagnostic device. Here we report the development of chemically-engineered PNAs for the quantitative detection of HIV RNA at clinically relevant levels that are competitive with current PCR-based assays. Using a sandwich hybridization approach, chemical groups were systematically introduced into a surface PNA probe and a reporter PNA probe to achieve quantitative detection for HIV RNA as low as 20 copies per milliliter of plasma. For the surface PNA probe, four cyclopentane groups were incorporated to promote stronger binding to the target HIV RNA compared to PNA without the cyclopentanes. For the reporter PNA probe, 25 biotin groups were attached to promote strong signal amplification after binding to the target HIV RNA. These general approaches to engineer PNA probes may be used to detect other RNA target sequences.
PMCID: PMC4187110  PMID: 25283173
4.  Subnanomolar antisense activity of phosphonate-peptide nucleic acid (PNA) conjugates delivered by cationic lipids to HeLa cells 
Nucleic Acids Research  2008;36(13):4424-4432.
In the search of facile and efficient methods for cellular delivery of peptide nucleic acids (PNA), we have synthesized PNAs conjugated to oligophosphonates via phosphonate glutamine and bis-phosphonate lysine amino acid derivatives thereby introducing up to twelve phosphonate moieties into a PNA oligomer. This modification of the PNA does not interfere with the nucleic acid target binding affinity based on thermal stability of the PNA/RNA duplexes. When delivered to cultured HeLa pLuc705 cells by Lipofectamine, the PNAs showed dose-dependent nuclear antisense activity in the nanomolar range as inferred from induced luciferase activity as a consequence of pre-mRNA splicing correction by the antisense-PNA. Antisense activity depended on the number of phosphonate moieties and the most potent hexa-bis-phosphonate-PNA showed at least 20-fold higher activity than that of an optimized PNA/DNA hetero-duplex. These results indicate that conjugation of phosphonate moieties to the PNA can dramatically improve cellular delivery mediated by cationic lipids without affecting on the binding affinity and sequence discrimination ability, exhibiting EC50 values down to one nanomolar. Thus the intracellular efficacy of PNA oligomers rival that of siRNA and the results therefore emphasize that provided sufficient in vivo bioavailability of PNA can be achieved these molecules may be developed into potent gene therapeutic drugs.
PMCID: PMC2490735  PMID: 18596083
5.  Use of Electrochemical DNA Biosensors for Rapid Molecular Identification of Uropathogens in Clinical Urine Specimens 
Journal of Clinical Microbiology  2006;44(2):561-570.
We describe the first species-specific detection of bacterial pathogens in human clinical fluid samples using a microfabricated electrochemical sensor array. Each of the 16 sensors in the array consisted of three single-layer gold electrodes—working, reference, and auxiliary. Each of the working electrodes contained one representative from a library of capture probes, each specific for a clinically relevant bacterial urinary pathogen. The library included probes for Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Enterocococcus spp., and the Klebsiella-Enterobacter group. A bacterial 16S rRNA target derived from single-step bacterial lysis was hybridized both to the biotin-modified capture probe on the sensor surface and to a second, fluorescein-modified detector probe. Detection of the target-probe hybrids was achieved through binding of a horseradish peroxidase (HRP)-conjugated anti-fluorescein antibody to the detector probe. Amperometric measurement of the catalyzed HRP reaction was obtained at a fixed potential of −200 mV between the working and reference electrodes. Species-specific detection of as few as 2,600 uropathogenic bacteria in culture, inoculated urine, and clinical urine samples was achieved within 45 min from the beginning of sample processing. In a feasibility study of this amperometric detection system using blinded clinical urine specimens, the sensor array had 100% sensitivity for direct detection of gram-negative bacteria without nucleic acid purification or amplification. Identification was demonstrated for 98% of gram-negative bacteria for which species-specific probes were available. When combined with a microfluidics-based sample preparation module, the integrated system could serve as a point-of-care device for rapid diagnosis of urinary tract infections.
PMCID: PMC1392664  PMID: 16455913
6.  Current Trends in Nanomaterial-Based Amperometric Biosensors 
Sensors (Basel, Switzerland)  2014;14(12):23439-23461.
The last decade has witnessed an intensive research effort in the field of electrochemical sensors, with a particular focus on the design of amperometric biosensors for diverse analytical applications. In this context, nanomaterial integration in the construction of amperometric biosensors may constitute one of the most exciting approaches. The attractive properties of nanomaterials have paved the way for the design of a wide variety of biosensors based on various electrochemical detection methods to enhance the analytical characteristics. However, most of these nanostructured materials are not explored in the design of amperometric biosensors. This review aims to provide insight into the diverse properties of nanomaterials that can be possibly explored in the construction of amperometric biosensors.
PMCID: PMC4299072  PMID: 25494347
electrochemical sensing; amperometric biosensors; nanomaterials; sensing design; analytical applications
7.  Dual Peptide Nucleic Acid- and Peptide-functionalized Shell Crosslinked Nanoparticles Designed to Target mRNA toward the Diagnosis and Treatment of Acute Lung Injury 
Bioconjugate Chemistry  2012;23(3):574-585.
In this work, multi-functional bio-synthetic hybrid nanostructures were prepared and studied for their potential utility in the recognition and inhibition of mRNA sequences for inducible nitric oxide synthase (iNOS), which are overexpressed at sites of inflammation, such as in cases of acute lung injury. Shell crosslinked knedel-like polymer nanoparticles (SCKs) that present peptide nucleic acids, for binding to complementary mRNAs, and cell penetrating peptides (CPPs), to gain cell entry, along with fluorescent labels and sites for radiolabeling, were prepared by a series of robust, efficient and versatile synthetic steps that proceeded from monomers to polymers to functional nanoparticles. Amphiphilic block graft copolymers having combinations of methoxy- and thioacetyl-terminated poly(ethylene glycol) (PEG) and DOTA-lysine units grafted from the backbone of poly(acrylic acid) (PAA) and extending with a backbone segment of poly(octadecyl acrylate-co-decyl acrylate) (P(ODA-co-DA)) were prepared by a combination of reversible addition-fragmentation chain transfer (RAFT) polymerization and chemical modification reactions, which were then used as the building blocks for the formation of well-defined SCKs decorated with reactive thiols accessible to the surface. Fluorescent labeling with Alexa Fluor 633 hydrazide was then accomplished by amidation with residual acrylic acid residues within the SCK shells. Finally, the PNAs and CPP units were covalently conjugated to the SCKs via Michael addition of thiols on the SCKs to maleimide units on the termini of PNAs and CPPs. Confirmation of the ability of the PNAs to bind selectively to the target iNOS mRNAs when tethered to the SCK nanoparticles was determined by in vitro competition experiments. When attached to the SCKs having a hydrodynamic diameter of 60 ± 16 nm, the Kd values of the PNAs were ca. an order of magnitude greater than the free PNAs, while the mismatched PNA showed no significant binding.
PMCID: PMC3321742  PMID: 22372643
8.  Enhancing the Sensitivity of Needle-Implantable Electrochemical Glucose Sensors via Surface Rebuilding 
Needle-implantable sensors have shown to provide reliable continuous glucose monitoring for diabetes management. In order to reduce tissue injury during sensor implantation, there is a constant need for device size reduction, which imposes challenges in terms of sensitivity and reliability, as part of decreasing signal-to-noise and increasing layer complexity. Herein, we report sensitivity enhancement via electrochemical surface rebuilding of the working electrode (WE), which creates a three-dimensional nanoporous configuration with increased surface area.
The gold WE was electrochemically rebuilt to render its surface nanoporous followed by decoration with platinum nanoparticles. The efficacy of such process was studied using sensor sensitivity against hydrogen peroxide (H2O2). For glucose detection, the WE was further coated with five layers, namely, (1) polyphenol, (2) glucose oxidase, (3) polyurethane, (4) catalase, and (5) dexamethasone-releasing poly(vinyl alcohol)/poly(lactic-co-glycolic acid) composite. The amperometric response of the glucose sensor was noted in vitro and in vivo.
Scanning electron microscopy revealed that electrochemical rebuilding of the WE produced a nanoporous morphology that resulted in a 20-fold enhancement in H2O2 sensitivity, while retaining >98% selectivity. This afforded a 4–5-fold increase in overall glucose response of the glucose sensor when compared with a control sensor with no surface rebuilding and fittable only within an 18 G needle. The sensor was able to reproducibly track in vivo glycemic events, despite the large background currents typically encountered during animal testing.
Enhanced sensor performance in terms of sensitivity and large signal-to-noise ratio has been attained via electrochemical rebuilding of the WE. This approach also bypasses the need for conventional and nanostructured mediators currently employed to enhance sensor performance.
PMCID: PMC3737646  PMID: 23567003
electrochemical; implantable glucose sensor; membranes; needle-implantable; sensitivity; surface etching
9.  Structural diversity of target-specific homopyrimidine peptide nucleic acid–dsDNA complexes 
Nucleic Acids Research  2006;34(20):5790-5799.
Sequence-selective recognition of double-stranded (ds) DNA by homopyrimidine peptide nucleic acid (PNA) oligomers can occur by major groove triplex binding or by helix invasion via triplex P-loop formation. We have compared the binding of a decamer, a dodecamer and a pentadecamer thymine–cytosine homopyrimidine PNA oligomer to a sequence complementary homopurine target in duplex DNA using gel-shift and chemical probing analyses. We find that all three PNAs form stable triplex invasion complexes, and also conventional triplexes with the dsDNA target. Triplexes form with much faster kinetics than invasion complexes and prevail at lower PNA concentrations and at shorter incubation times. Furthermore, increasing the ionic strength strongly favour triplex formation over invasion as the latter is severely inhibited by cations. Whereas a single triplex invasion complex is formed with the decameric PNA, two structurally different target-specific invasion complexes were characterized for the dodecameric PNA and more than five for the pentadecameric PNA. Finally, it is shown that isolated triplex complexes can be converted to specific invasion complexes without dissociation of the Hoogsteen base-paired triplex PNA. These result demonstrate a clear example of a ‘triplex first’ mechanism for PNA helix invasion.
PMCID: PMC1635314  PMID: 17053099
10.  Mixed Monolayers of Ferrocenylalkanethiol and Encapsulated Horseradish Peroxidase for Sensitive and Durable Electrochemical Detection of Hydrogen Peroxide 
Analytical chemistry  2009;81(24):9985-9992.
This paper describes the construction of a mixed monolayer of ferrocenylalkanethiol and encapsulated horseradish peroxidase (HRP) at a gold electrode for amperometric detection of H2O2 at trace levels. By tuning the alkanethiol chain lengths that tether the HRP enzyme and the ferrocenylalkanethiol (FcC11SH) mediator, facile electron transfer between FcC11SH and HRP can be achieved. Unlike most HRP-based electrochemical sensors, which rely on HRP-facilitated H2O2 reduction (to H2O), the electrocatalytic current is resulted from an HRP-catalyzed oxidation reaction of H2O2 (to O2). Upon optimizing other experimental conditions (surface coverage ratio, pH, and flow rate), the electrocatalytic reaction proceeding at the electrode was used to attain a low amperometric detection level (0.64 nM) and a dynamic range spanning over three orders of magnitude. Not only does the thin hydrophilic porous HRP capsule allow facile electron transfer, it also enables H2O2 to permeate. More significantly, the enzymatic activity of the encapsulated HRP is retained for a considerably longer period (> three weeks) than naked HRP molecules attached to an electrode or those wired to a redox polymer thin film. By comparing to electrodes modified with denatured HRP that are subsequently encapsulated or embedded in a poly-L-lysine matrix, it is concluded that the encapsulation has significantly preserved the native structure of HRP and therefore its enzymatic activity. The electrode covered with FcC11SH and encapsulated HRP is shown to be capable of rapidly and reproducibly detecting H2O2 present in complex sample media.
PMCID: PMC2795022  PMID: 19928778
11.  Antisense peptide nucleic acid-functionalized cationic nanocomplex for in vivo mRNA detection 
Interface Focus  2013;3(3):20120059.
Acute lung injury (ALI) is a complex syndrome with many aetiologies, resulting in the upregulation of inflammatory mediators in the host, followed by dyspnoea, hypoxemia and pulmonary oedema. A central mediator is inducible nitric oxide synthase (iNOS) that drives the production of NO and continued inflammation. Thus, it is useful to have diagnostic and therapeutic agents for targeting iNOS expression. One general approach is to target the precursor iNOS mRNA with antisense nucleic acids. Peptide nucleic acids (PNAs) have many advantages that make them an ideal platform for development of antisense theranostic agents. Their membrane impermeability, however, limits biological applications. Here, we report the preparation of an iNOS imaging probe through electrostatic complexation between a radiolabelled antisense PNA-YR9 · oligodeoxynucleotide (ODN) hybrid and a cationic shell-cross-linked knedel-like nanoparticle (cSCK). The Y (tyrosine) residue was used for 123I radiolabelling, whereas the R9 (arginine9) peptide was included to facilitate cell exit of untargeted PNA. Complete binding of the antisense PNA-YR9 · ODN hybrid to the cSCK was achieved at an 8 : 1 cSCK amine to ODN phosphate (N/P) ratio by a gel retardation assay. The antisense PNA-YR9 · ODN · cSCK nanocomplexes efficiently entered RAW264.7 cells, whereas the PNA-YR9 · ODN alone was not taken up. Low concentrations of 123I-labelled antisense PNA-YR9 · ODN complexed with cSCK showed significantly higher retention of radioactivity when iNOS was induced in lipopolysaccharide+interferon-γ-activated RAW264.7 cells when compared with a mismatched PNA. Moreover, statistically, greater retention of radioactivity from the antisense complex was also observed in vivo in an iNOS-induced mouse lung after intratracheal administration of the nanocomplexes. This study demonstrates the specificity and sensitivity by which the radiolabelled nanocomplexes can detect iNOS mRNA in vitro and in vivo and their potential for early diagnosis of ALI.
PMCID: PMC3638413  PMID: 24427537
cationic nanoparticles; acute lung injury; peptide nucleic acid; inducible nitric oxide synthase; radiolabelling; targeting
12.  Peptide Nucleic Acid-Based Array for Detecting and Genotyping Human Papillomaviruses▿  
Journal of Clinical Microbiology  2009;47(6):1785-1790.
We describe a novel array for accurate and reliable genotyping of human papillomavirus (HPV) using peptide nucleic acid (PNA) probes. In order to exploit the superior hybridization properties of PNA with target HPV DNAs, we developed a novel PNA array (PANArray HPV). PANArray HPV enables the detection and genotyping of HPVs using 32 type-specific PNA capture probes for medically important HPVs. All tested HPV types showed highly unique hybridization patterns with type-specific PNA probes. PNA array results showed stable specificities and sensitivities after up to 13 months of storage at room temperature. Also, we demonstrated the superior specificity, sensitivity, and stability of PNA arrays for HPV genotyping. We compared the genotyping results of the PNA array to sequencing with MY09/11 PCR products derived from 72 clinical samples. The results showed excellent agreement between the PNA array and sequencing, except for samples reflecting multiple infections. The results from the PNA array were compared with those of type-specific PCR when discrepant results occurred owing to multiple infections. The results for the PNA array matched those of type-specific PCR in all cases. Newly developed PNA arrays show excellent specificity and sensitivity and long shelf life. Our results suggest that the PNA array represents a reliable alternative to conventional DNA arrays for HPV genotyping, as well as for diagnostics.
PMCID: PMC2691110  PMID: 19369432
13.  Inhibiting Gene Expression with Peptide Nucleic Acid (PNA)–Peptide Conjugates that Target Chromosomal DNA 
Biochemistry  2007;46(25):7581-7589.
Peptide nucleic acids (PNAs) are a nonionic DNA/RNA mimic that can recognize complementary sequences by Watson–Crick base–pairing. The neutral PNA backbone facilitates recognition of duplex DNA by strand invasion, suggesting that antigene PNAs (agPNAs) can be important tools for exploring the structure and function of chromosomal DNA inside cells. However, before agPNAs can enter wide use it will be necessary to develop straightforward strategies for introducing them into cells. Here we demonstrate that agPNA–peptide conjugates can target promoter DNA and block progesterone receptor (PR) gene expression inside cells. Thirty–six agPNA–peptide conjugates were synthesized and tested. We observed inhibition of gene expression using cationic peptides containing either arginine or lysine residues, with eight or more cationic amino acids being preferred. Both thirteen and nineteen base agPNA-peptide conjugates were inhibitory. Inhibition was observed in human cancer cell lines expressing either high or low levels of progesterone receptor. Modification of agPNA–peptide conjugates with hydrophobic amino acids or small molecule hydrophobic moities yielded improved potency. Inhibition by agPNAs did not require cationic lipid or any other additive, but adding agents to cell growth media that promote endosomal release caused modest increases in agPNA potency. These data demonstrate that chromosomal DNA is accessible to agPNA–peptide conjugates and that chemical modifications can improve potency.
PMCID: PMC2564818  PMID: 17536840
14.  Poly(lactic acid)/Carbon Nanotube Fibers as Novel Platforms for Glucose Biosensors 
Biosensors  2012;2(1):70-82.
The focus of this paper is the development and investigation of properties of new nanostructured architecture for biosensors applications. Highly porous nanocomposite fibers were developed for use as active materials in biosensors. The nanocomposites comprised poly(lactic acid)(PLA)/multi-walled carbon nanotube (MWCNT) fibers obtained via solution-blow spinning onto indium tin oxide (ITO) electrodes. The electrocatalytic properties of nanocomposite-modified ITO electrodes were investigated toward hydrogen peroxide (H2O2) detection. We investigated the effect of carbon nanotube concentration and the time deposition of fibers on the sensors properties, viz., sensitivity and limit of detection. Cyclic voltammetry experiments revealed that the nanocomposite-modified electrodes displayed enhanced activity in the electrochemical reduction of H2O2, which offers a number of attractive features to be explored in development of an amperometric biosensor. Glucose oxidase (GOD) was further immobilized by drop coating on an optimized ITO electrode covered by poly(lactic acid)/carbon nanotube nanofibrous mats. The optimum biosensor response was linear up to 800 mM of glucose with a sensitivity of 358 nA·mM−1 and a Michaelis-Menten constant (KM) of 4.3 mM. These results demonstrate that the solution blow spun nanocomposite fibers have great potential for application as amperometric biosensors due to their high surface to volume ratio, high porosity and permeability of the substrate. The latter features may significantly enhance the field of glucose biosensors.
PMCID: PMC4263541  PMID: 25585633
nanofibers; glucose biosensor; carbon nanotube; poly(lactic acid)
15.  Stage-specific variations in lectin binding to Leishmania donovani. 
Infection and Immunity  1984;46(1):128-134.
Visceral leishmaniasis is caused by the dimorphic protozoan Leishmania donovani, which exists as an aflagellar amastigote within mammalian mononuclear phagocytes and as a flagellated extracellular promastigote in its sandfly vector. We have identified four plant lectins that bind to the L. donovani surface, and through these we have documented stage-specific differences in exposed surface carbohydrates. Concanavalin A bound to both promastigotes and amastigotes; binding was inhibited by mannose or alpha-methyl-mannoside, implying a mannose-containing residue on the surface of both parasite stages. Ricinus communis agglutinin, which binds to galactose-containing residues, also bound to both stages and was inhibited by lactose, implying a galactose-containing glycoconjugate on the parasite surface. Two other lectins, wheat germ agglutinin (WGA) and peanut agglutinin (PNA), exhibited stage specificity in their binding characteristics. Amastigotes bound WGA but not PNA. During the process of conversion from the amastigote to the promastigote stage, the WGA-binding glycoconjugate was lost, and a PNA-binding residue was newly displayed. WGA binding was inhibited by N-acetyl-D-glucosamine and was not altered by neuraminidase treatment, suggesting the presence of an exposed N-acetyl-D-glucosamine moiety on the amastigote surface. The PNA binding site is known to accommodate the oligosaccharide beta-D-galactose-(1----3)-N-acetyl-D-galactosamine; in our system, PNA may have identified an internal rather than a terminal galactose on the promastigote surface. Localized binding of WGA and PNA to the surface of intermediate phases of the parasite suggested inhomogeneous and changing surface characteristics during conversion from amastigote to promastigote stages. This evolution of L. donovani surface glycoconjugates may be important in the adaptation of the organism to its divergent mammalian host and arthropod vector environments.
PMCID: PMC261432  PMID: 6480103
16.  NO2 Detection Using Microcantilever Based Potentiometry 
Sensors (Basel, Switzerland)  2008;8(11):7144-7156.
A highly sensitive and novel sensor platform for gases and volatile chemicals using microcantilever based potentiometry is reported. A resonant cantilever is used to detect the changes in surface work functions of functionalized substrates caused by adsorption of target gas molecules. Surface work function (SWF) changes were measured for different functionalization layers made of transition metal oxide thin films with the flow of NO2. The rate of change in SWF for In2O3 and SnO2 were found to be ∼80 and ∼100 μV/sec, respectively, for 70 ppm NO2. A sensitivity of 64 μV/sec for SWF change was also found for 70 ppm NO2 concentration for isolated clusters of ZnO nanowires, indicating that this technique is applicable even for nano-clusters of sensing materials where amperometric detection is impossible due to material discontinuity. NO2 detection as low as 400 ppb was possible using highly insulating In2O3 and SnO2 thin films (resistivity > 1 TΩ/□. Two different forms of nano scale graphite were compared with the transition oxide based functionalization layer for sensing sub-ppm NO2 sensing. It was observed that nanostructured graphite (NG) shows much higher sensitivity and lower response time than transition metal oxides.
PMCID: PMC3787436
Microcantilever; potentiometry; surface work function; nanoscale graphite; NO2 sensor
17.  Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting. 
Nucleic Acids Research  1994;22(24):5218-5222.
Biotinylated homopyrimidine decamer peptide nucleic acids (PNAs) are shown to form sequence-specific and stable complexes with complementary oligopurine targets in linear double-stranded DNA. The noncovalent complexes are visualized by electron microscopy (EM) without chemical fixation using streptavidin as an EM marker. The triplex stoichiometry of the PNA-DNA complexes (two PNA molecules presumably binding by Watson-Crick and Hoogsteen pairing with one of the strands of the duplex DNA) is indicated by the appearance of two streptavidin 'beads' per target site in some micrographs, and is also supported by the formation of two retardation bands in a gel shift assay. Quantitative analysis of the positions of the streptavidin 'beads' revealed that under optimized conditions PNA-DNA complexes are preferably formed with the fully complementary target. An increase in either the PNA concentration or the incubation time leads to binding at sites containing one or two mismatches. Our results demonstrate that biotinylated PNAs can be used for EM mapping of short targets in duplex DNA.
PMCID: PMC332063  PMID: 7816609
18.  Detection of Single-Nucleotide Polymorphism on uidA Gene of Escherichia coli by a Multiplexed Electrochemical DNA Biosensor with Oligonucleotide-Incorporated Nonfouling Surface 
Sensors (Basel, Switzerland)  2011;11(8):8018-8027.
We report here a practical application of a multiplexed electrochemical DNA sensor for highly specific single-nucleotide polymorphism (SNP) detection. In this work, a 16-electrode array was applied with an oligonucleotide-incorporated nonfouling surfaces (ONS) on each electrode for the resistance of unspecific absorption. The fully matched target DNA templated the ligation between the capture probe assembled on gold electrodes and the tandem signal probe with a biotin moiety, which could be transduced to peroxidase-based catalyzed amperometric signals. A mutant site (T93G) in uidA gene of E. coli was analyzed in PCR amplicons. 10% percentage of single mismatched mutant gene was detected, which clearly proved the selectivity of the multiplexed electrochemical DNA biosensor when practically applied.
PMCID: PMC3231733  PMID: 22164059
electrochemical biosensor; single-nucleotide polymorphism (SNP); nonfouling electrode surface; Escherichia coli
19.  PNA microarrays for hybridisation of unlabelled DNA samples 
Nucleic Acids Research  2003;31(19):e119.
Several strategies have been developed for the production of peptide nucleic acid (PNA) microarrays by parallel probe synthesis and selective coupling of full-length molecules. Such microarrays were used for direct detection of the hybridisation of unlabelled DNA by time-of-flight secondary ion mass spectrometry. PNAs were synthesised by an automated process on filter-bottom microtitre plates. The resulting molecules were released from the solid support and attached without any purification to microarray surfaces via the terminal amino group itself or via modifications, which had been chemically introduced during synthesis. Thus, only full-length PNA oligomers were attached whereas truncated molecules, produced during synthesis because of incomplete condensation reactions, did not bind. Different surface chemistries and fitting modifications of the PNA terminus were tested. For an examination of coupling selectivity, bound PNAs were cleaved off microarray surfaces and analysed by MALDI-TOF mass spectrometry. Additionally, hybridisation experiments were performed to compare the attachment chemistries, with fully acetylated PNAs spotted as controls. Upon hybridisation of unlabelled DNA to such microarrays, binding events could be detected by visualisation of phosphates, which are an integral part of nucleic acids but missing entirely in PNA probes. Overall best results in terms of selectivity and sensitivity were obtained with thiol-modified PNAs on maleimide surfaces.
PMCID: PMC206485  PMID: 14500847
20.  Synthesis of polyacrylamides N-substituted with PNA-like oligonucleotide mimics for molecular diagnostic applications. 
Nucleic Acids Research  1999;27(22):4416-4426.
Two types of oligonucleotide mimics relative to peptide nucleic acids (PNAs) were tested as probes in nucleic acid hybridisation assays based on polyacrylamide technology. One type of mimic oligomers represented a chimera constructed of PNA and phosphono-PNA (pPNA) monomers, and the other one contained pPNA residues alternating with PNA-like monomers on the base of trans -4-hydroxy-L-proline (HypNA). A chemistry providing efficient and specific covalent attachment of these DNA mimics to acrylamide polymers using a convenient approach based on the co-polymerisation of acrylamide and some reactive acrylic acid derivatives with oligomers bearing 5'- or 3'-terminal acrylamide groups has been developed. A comparative study of polyacrylamide conjugates with oligonucleotides and mimic oligomers demonstrated the suitability and high potential of PNA-pPNA and HypNA-pPNA chimeras as sequence-specific probes in capture and detection of target nucleic acid fragments to serve current forms of DNA arrays.
PMCID: PMC148725  PMID: 10536151
21.  Scalable, high performance, enzymatic cathodes based on nanoimprint lithography 
Here we detail high performance, enzymatic electrodes for oxygen bio-electroreduction, which can be easily and reproducibly fabricated with industry-scale throughput. Planar and nanostructured electrodes were built on biocompatible, flexible polymer sheets, while nanoimprint lithography was used for electrode nanostructuring. To the best of our knowledge, this is one of the first reports concerning the usage of nanoimprint lithography for amperometric bioelectronic devices. The enzyme (Myrothecium verrucaria bilirubin oxidase) was immobilised on planar (control) and artificially nanostructured, gold electrodes by direct physical adsorption. The detailed electrochemical investigation of bioelectrodes was performed and the following parameters were obtained: open circuit voltage of approximately 0.75 V, and maximum bio-electrocatalytic current densities of 18 µA/cm2 and 58 µA/cm2 in air-saturated buffers versus 48 µA/cm2 and 186 µA/cm2 in oxygen-saturated buffers for planar and nanostructured electrodes, respectively. The half-deactivation times of planar and nanostructured biocathodes were measured to be 2 h and 14 h, respectively. The comparison of standard heterogeneous and bio-electrocatalytic rate constants showed that the improved bio-electrocatalytic performance of the nanostructured biocathodes compared to planar biodevices is due to the increased surface area of the nanostructured electrodes, whereas their improved operational stability is attributed to stabilisation of the enzyme inside nanocavities.
PMCID: PMC4505184  PMID: 26199841
bilirubin oxidase; bio-electrocatalysis; direct electron transfer; nanoimprint lithography; oxygen reduction reaction
22.  Delivery of Antisense Peptide Nucleic Acids to Cells by Conjugation with Small Arginine-Rich Cell-Penetrating Peptide (R/W)9 
PLoS ONE  2014;9(8):e104999.
Peptide nucleic acids (PNAs) are very attractive antisense and antigene agents, but these molecules are not passively taken into cells. Here, using a functional cell assay and fluorescent-based methods, we investigated cell uptake and antisense activity of a tridecamer PNA that targets the HIV-1 polypurine tract sequence delivered using the arginine-rich (R/W)9 peptide (RRWWRRWRR). At micromolar concentrations, without use of any transfection agents, almost 80% inhibition of the target gene expression was obtained with the conjugate in the presence of the endosomolytic agent chloroquine. We show that chloroquine not only induced escape from endosomes but also enhanced the cellular uptake of the conjugate. Mechanistic studies revealed that (R/W)9-PNA conjugates were internalized via pinocytosis. Replacement of arginines with lysines reduced the uptake of the conjugate by six-fold, resulting in the abolition of intracellular target inhibition. Our results show that the arginines play a crucial role in the conjugate uptake and antisense activity. To determine whether specificity of the interactions of arginines with cell surface proteoglycans result in the internalization, we used flow cytometry to examine uptake of arginine- and lysine-rich conjugates in wild-type CHO-K1 and proteoglycan-deficient A745 cells. The uptake of both conjugates was decreased by four fold in CHO-745 cells; therefore proteoglycans promote internalization of cationic peptides, irrespective of the chemical nature of their positive charges. Our results show that arginine-rich cell-penetrating peptides, especially (R/W)9, are a promising tool for PNA internalization.
PMCID: PMC4134252  PMID: 25127364
23.  Intravascular Glucose/Lactate Sensors Prepared with Nitric Oxide Releasing Poly(lactide-co-glycolide)-Based Coatings for Enhanced Biocompatibility 
Biosensors & bioelectronics  2011;26(11):4276-4282.
Intravenous amperometric needle-type enzymatic glucose/lactate sensors intended for continuous monitoring are prepared with a novel nitric oxide (NO) releasing layer to improve device hemocompatibility. To create an underlying NO release coating, the sensors with immobilized enzymes (either glucose oxidase or lactate oxidase) are prepared with a thin layer of poly(lactide-co-glycolide) (PLGA) loaded with lipophilic diazeniumdiolate species that slowly release NO via a proton driven reaction. An outer thin layer (ca. 30 µm) of PurSil (polyurethane/dimethylsiloxane copolymer) limits the flux of glucose and lactate to the inner layer of enzyme, to provide the desired linear amperometric response. A 30 µm coating of PLGA containing 33 wt% of the appropriate NO donor (N-diazeniumdiolated dibutylhexanediamine, DBHD/N2O2) can release NO at a physiologically relevant rate > 1 × 10−10 mol min−1cm−2 for at least 7 d without influencing the analytical performance of the glucose/lactate sensors. In vitro, the sensors exhibit relatively stable amperometric response over a one-week period with high selectivity over interferences (e.g., ascorbic acid) required for blood monitoring applications. Glucose sensors implanted in the veins of rabbits for 8 h exhibit significantly enhanced hemocompatibility for the NO release sensors vs. corresponding controls (without NO release in same animals), with greatly reduced thrombus formation on their surfaces. Further, the analytical performance of the NO release glucose sensors are superior to controls placed in the veins of the same animals, with a greater accuracy in measuring blood glucose levels as evaluated using a Clark error grid type analysis.
PMCID: PMC3120931  PMID: 21592764
intravascular glucose/lactate sensor; nitric oxide release; enhanced blood-compatibility
24.  An Internalin A Probe-Based Genosensor for Listeria monocytogenes Detection and Differentiation 
BioMed Research International  2013;2013:640163.
Internalin A (InlA), a protein required for Listeria monocytogenes virulence, is encoded by the inlA gene, which is only found in pathogenic strains of this genus. One of the best ways to detect and confirm the pathogenicity of the strain is the detection of one of the virulence factors produced by the microorganism. This paper focuses on the design of an electrochemical genosensor used to detect the inlA gene in Listeria strains without labelling the target DNA. The electrochemical sensor was obtained by immobilising an inlA gene probe (single-stranded oligonucleotide) on the surfaces of screen-printed gold electrodes (Au-SPEs) by means of a mercaptan-activated self-assembled monolayer (SAM). The hybridisation reaction occurring on the electrode surface was electrochemically transduced by differential pulse voltammetry (DPV) using methylene blue (MB) as an indicator. The covalently immobilised single-stranded DNA was able to selectively hybridise to its complementary DNA sequences in solution to form double-stranded DNA on the gold surface. A significant decrease of the peak current of the voltammogram (DPV) upon hybridisation of immobilised ssDNA was recorded. Whole DNA samples of L. monocytogenes strains could be discriminated from other nonpathogenic Listeria species DNA with the inlA gene DNA probe genosensor.
PMCID: PMC3618917  PMID: 23586053
25.  A Comprehensive Review of Glucose Biosensors Based on Nanostructured Metal-Oxides 
Sensors (Basel, Switzerland)  2010;10(5):4855-4886.
Nanotechnology has opened new and exhilarating opportunities for exploring glucose biosensing applications of the newly prepared nanostructured materials. Nanostructured metal-oxides have been extensively explored to develop biosensors with high sensitivity, fast response times, and stability for the determination of glucose by electrochemical oxidation. This article concentrates mainly on the development of different nanostructured metal-oxide [such as ZnO, Cu(I)/(II) oxides, MnO2, TiO2, CeO2, SiO2, ZrO2, and other metal-oxides] based glucose biosensors. Additionally, we devote our attention to the operating principles (i.e., potentiometric, amperometric, impedimetric and conductometric) of these nanostructured metal-oxide based glucose sensors. Finally, this review concludes with a personal prospective and some challenges of these nanoscaled sensors.
PMCID: PMC3292151  PMID: 22399911
nanostructured metal-oxides; glucose biosensor; electrochemical principles; enzymatic sensor; nonenzymatic sensor

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