Magnetically induced self-assembly electrochemical biosensor with ultra-low detection limit and extended measuring range for sensitive detection of HER2 protein

An innovative electrochemical biosensor was fabricated for sensitive detection of human epidermal growth factor receptor 2 (HER2) protein, which was considered as an essential tumor marker for diagnosis and treatment evaluation of breast cancer. The sensor was constructed using Apt and PNA as recognition probes incorporated with magnetic Fe3O4/α-Fe2O3@Au nanocomposites. The sensing strategy was designed to lower the detection limit of HER2, and avoid the large steric interference caused by macromolecular HER2 on the electrode surface. Rigid structure dsDNA (Apt/ssDNA) was designed to improve the sensitivity of the sensor. Apt captured the macromolecular HER2 protein, and ssDNA chains were simultaneously released, causing a sensitive change in the electrochemical signal. PNA captured the released ssDNA chains, which converted the electrochemical signal changes caused by HER2 to those caused by the number of short strand ssDNA, so the detection range was extended. Under optimized conditions, this sensing strategy realized an ultra-low detection LOD of HER2 (4.1 fg·mL-1), and the detection range was 10 fg·mL-1-5 × 106 fg·mL-1. The experimental results confirmed that the electrochemical biosensor had excellent selectivity, reproducibility, and storage stability. Analysis of spiked serum samples exhibited a recovery rate of 95.9-115.7 %, which indicated great promise for HER2 detection in serum samples.

Targeted Delivery of Peptide Nucleic Acid by Biomimetic Nanoparticles Based on Extracellular Vesicle-coated Mesoporous Silica Nanoparticles

BACKGROUND

Peptide nucleic acid (PNA) plays an important role in antimicrobial activity, but its cellular permeability is poor. To overcome this limitation, we constructed biomimetic nanoparticles by using extracellular vesicle (EV)-coated mesoporous silicon nanoparticles (MSNs) to deliver PNA to Staphylococcus aureus (S. aureus) and improve its antisense therapeutic effect.

METHOD

MSN was prepared by the sol-gel method, and EV was extracted by affinity resin chromatography. EV was coated on MSN by simple sonication (50 W, 3 min) to prepare biomimetic nanoparticles with PNA-loaded MSN as the core and EV isolated from S. aureus as the shell.

RESULTS

The MSN prepared by the sol-gel method had a uniform particle size (100 nm) and well-defined pore size for loading PNA with good encapsulation efficiency (62.92%) and drug loading (7.74%). The concentration of EV extracted by affinity resin chromatography was about 1.74 mg/mL. EV could be well coated on MSN through simple ultrasonic treatment (50 W, 3 min), and the stability and blood compatibility of MSN@ EV were good. Internalization experiments showed that EV could selectively enhance the uptake of biomimetic nanoparticles by S. aureus. Preliminary in vitro antibacterial tests revealed that PNA@MSN@EV exhibited enhanced antibacterial activity against S. aureus and had stronger bactericidal activity than free PNA and PNA@MSN at equivalent PNA concentrations (8 μM).

CONCLUSION

Biomimetic nanoparticles based on EV-coated MSN offer a new strategy to improve the efficacy of PNA for the treatment of bacterial infections, and the technology holds promise for extension to the delivery of antibiotics that are traditionally minimally effective or prone to resistance.

Surface immobilization strategies for the development of electrochemical nucleic acid sensors

Following the recent pandemic and with the emergence of cell-free nucleic acids in liquid biopsies as promising biomarkers for a broad range of pathologies, there is an increasing demand for a new generation of nucleic acid tests, with a particular focus on cost-effective, highly sensitive and specific biosensors. Easily miniaturized electrochemical sensors show the greatest promise and most typically rely on the chemical functionalization of conductive materials or electrodes with sequence-specific hybridization probes made of standard oligonucleotides (DNA or RNA) or synthetic analogues (e.g. Peptide Nucleic Acids or PNAs). The robustness of such sensors is mostly influenced by the ability to control the density and orientation of the probe at the surface of the electrode, making the chemistry used for this immobilization a key parameter. This exhaustive review will cover the various strategies to immobilize nucleic acid probes onto different solid electrode materials. Both physical and chemical immobilization techniques will be presented. Their applicability to specific electrode materials and surfaces will also be discussed as well as strategies for passivation of the electrode surface as a way of preventing electrode fouling and reducing nonspecific binding.

Synthesis and properties of PNA containing a dicationic nucleobase based on N4-benzoylated cytosine

We report the synthesis of a peptide nucleic acid (PNA) monomer containing N⁴-bis(aminomethyl)benzoylated cytosine (^BzC²⁺ base). The ^BzC²⁺ monomer was incorporated into PNA oligomers using Fmoc-based solid-phase synthesis. The ^BzC²⁺ base in PNA had two positive charges and exhibited greater affinity for DNA G base than the natural C base. The ^BzC²⁺ base stabilized PNA-DNA heteroduplexes through electrostatic attractions, even in high salt conditions. The two positive charges on the ^BzC²⁺ residue did not compromise the sequence specificity of PNA oligomers. These insights will aid the future design of cationic nucleobases.

Peptide nucleic acid and antifouling peptide based biosensor for the non-fouling detection of COVID-19 nucleic acid in saliva

The electrochemical biosensor with outstanding sensitivity and low cost is regarded as a viable alternative to current clinical diagnostic techniques for various disease biomarkers. However, their actual analytical use in complex biological samples is severely hampered due to the biofouling, as they are also highly sensitive to nonspecific adsorption on the sensing interfaces. Herein, we have constructed a non-fouling electrochemical biosensor based on antifouling peptides and the electroneutral peptide nucleic acid (PNA), which was used as the recognizing probe for the specific binding of the viral RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Different from the negatively charged DNA probes that will normally weaken the biosensors' antifouling capabilities owing to the charge attraction of positively charged biomolecules, the neutral PNA probe will generate no side-effects on the biosensor. The biosensor demonstrated remarkable sensitivity in detecting SARS-CoV-2 viral RNA, possessing a broad linear range (1.0 fM - 1.0 nM) and a detection limit down to 0.38 fM. Furthermore, the sensing performance of the constructed electrochemical biosensor in human saliva was nearly similar to that in pure buffer, indicating satisfying antifouling capability. The combination of PNA probes with antifouling peptides offered a new strategy for the development of non-fouling sensing systems capable of assaying trace disease biomarkers in complicated biological media.

Hydrogel-based thermosensor using peptide nucleic acid and PEGylated graphene oxide

Developing a ready-to-use miniaturized thermosensor is a great challenge due to its individual use on a large scale for daily business such as food industry and healthcare. Herein, a polyethylene glycol (PEG)-modified graphene oxide (GO)-based hydrogel thermosensor was established with a fluorescent dye-labeled peptide nucleic acid (F-PNA). The size-tunable hydrogel with high water content and sufficient solidity allowed free movement of the oligonucleotides through the pores and improved usability for handling the sensor. In the PEG-GO hydrogel, the DNA/F-PNA duplex could be denatured by increasing the temperature, followed by selective PNA capture on the PEG-GO. Using this principle, the PEG-GO hydrogel exhibited a change in the fluorescence signal of F-PNA in a temperature-dependent manner, allowing real-time visualization of temperature on a large scale. The temperature detection range of this system can be adjusted by designing the PNA strands based on the melting temperature of the DNAzyme/PNA duplex. Its sensing specificity and detection range could be increased and broadened by observing multi-color detection using PNA probes labeled with different fluorescent dyes of different lengths in a single hydrogel. In addition, the hydrogel platform is easy to store for long time periods via dehydration and can be restored with the addition of water, allowing easy transport, storage, and use of the thermosensor in everyday life.

Fluorescence ratiometric DNA detection by peptide nucleic acid-pyrene binary probes

We developed a method for detecting DNA by excimer fluorescence from two peptide nucleic acids (PNAs) modified with a pyrene (Pyr). The two PNA-Pyr probes were prepared by solid-phase peptide synthesis, and we assessed fluorescence from the mixture of probes with DNA. From the results, excimer fluorescence derived from the two PNA-Pyr probes forming hybrids with the complementary DNA was observed, and the two probes showed the maximum excimer/monomer ratio when the probes and DNA were hybridized at a 1:1:1 ratio, indicating that the PNA-Pyr probes can detect target DNA. Furthermore, we adjusted the spatial arrangement between the two PNA-Pyr hybrids formed on the DNA to promote optimal excimer formation. As a result, optimal excimer formation was achieved by spacing the two nucleobases between the formed two hybrids and further inserting a hexamethylene linker (C6) between the PNA and Pyr of the PNA-Pyr probe on one side.

Cyclopentane peptide nucleic acid: Gold nanoparticle conjugates for the detection of nucleic acids in a microfluidic format

Routine patient testing for viral infections is critical to identify infected individuals for treatment and to prevent spreading of infections to others. Developing robust and reliable diagnostic tools to detect nucleic acids of viruses at the point-of-care could greatly assist the clinical management of viral infections. The remarkable stability and high binding affinity of peptide nucleic acids (PNAs) to target nucleic acids could make PNA-based biosensors an excellent starting point to develop new nucleic acid detection technologies. We report the application of cyclopentane-modified PNAs to capture target nucleic acids in a microfluidic channel, and the use of bioorthogonal PNAs conjugated to gold nanoparticles as probes to semi-quantitatively signal the presence of a target nucleic acid derived from HIV-1. The basic results presented could be used to develop more advanced devices to detect nucleic acids from viruses such as HIV, SARS-CoV-2, and a wide range of other human diseases.

Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing

This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.

An origami paper-based peptide nucleic acid device coupled with label-free DNAzyme probe hybridization chain reaction for prostate cancer molecular screening test

Prostate cancer associated 3 (PCA3) assay has been used to improve prostate cancer diagnosis and reduce unnecessary biopsies. In this work, we successfully developed a new PCA3 assay on an origami paper-based peptide nucleic acid device (oPAD). The PCA3 oPAD comprises an acrylic cassette and shutter slides to facilitate the molecular reaction and liquid control occurring on the paper surface. To quantify PCA3, a pyrrolidinyl peptide nucleic acid (acpcPNA) was immobilized onto the aldehyde-modified oPAD surface as a selective capture probe. A G-quadruplex (GQD) DNAzyme reporter probe was designed so that the PCA3 gene target binding triggered the hybridization chain reaction of the reporter probe, resulting in the accumulation of the GQD on the oPAD. The peroxidase activity of the GQD-hemin generated a deep green color of the oxidized ABTS substrate. Image analyses were performed in Adobe Photoshop CS6. The proposed oPAD was successfully applied in PCA3 detection ranges of 1-5 μM (r² = 0.982) with a limit of detection of 0.5 μM. Our proposed oPAD was demonstrated to measure PCA3 samples in both urine matrix and human cancer cell lines. The results reveal the great potential of our origami paper-based platform to be an alternative approach for facile, rapid, and low-cost detection of PCA3 in real samples.

Fluorophore-PNA-Quencher/Quencher-DNA probe for miRNA detection

Micro RNAs (miRNAs) are involved in a variety of biological functions and are attracting attention as diagnostic and prognostic markers for various diseases. Highly sensitive RNA detection methods are required to determine miRNA expression levels and intracellular localization. In this study, we designed new double-stranded peptide nucleic acid (PNA)/DNA probes consisting of a fluorophore-PNA-quencher (fPq) and a quencher-DNA (qD) for miR-221 detection. We optimized the fPq structure, PNA-DNA hybrid length, and hybrid position. The resultant fPq-2/qD-6b probe was a 6-bp hybrid probe with a 10-base fPq and a 6-base qD. The signal-to-background ratios of the probes showed that fPq-2/qD-6b had a higher target sensitivity than fPq (PNA beacon)-type and fP/qD-type probes. The results of the detection limit and target specificity indicate that the fPq/qD probe is promising for RNA detection in both cells and cell extracts as well as for miRNA diagnosis.

Paper-based sensor from pyrrolidinyl peptide nucleic acid for the efficient detection of Bacillus cereus

Bacillus cereus is one of the most common foodborne pathogens found in various kinds of staple foods such as rice and wheat. A rapid and accurate detection method for this pathogen is highly desirable for the sustainable production of relevant food products. While several classical and molecular-based detection methods are available for the identification of B. cereus, they suffered one or more limitations such as the requirement for a tedious and time-consuming process, less than ideal specificity, and the lack of portability. Herein, we developed the first paper-based sensing device that exhibits high species specificity with sufficiently low limit of detection for the visual detection of specific DNA sequences of B. cereus. The success is attributed to the strategic planning of fabrication in various dimensions including thorough bioinformatics search for highly specific genes, the use of the pyrrolidinyl peptide nucleic acid (PNA) probe whose selectivity advantage is well documented, and an effective PNA immobilization and DNA-binding visualization method with an internal cross-checking system for validating the results. Testing in rice matrices indicates that the sensor is capable of detecting and distinguishing B. cereus from other bacterial species. Hence, this paper-based sensor has potential to be adopted as a practical means to detect B. cereus in food industries.

Novel peptide (RATH) mediated delivery of peptide nucleic acids for antiviral interventions

The peptide nucleic acid (PNA) is a chimeric molecule with the nucleobases connected by peptide bonds. This chimeric nature gives the PNA certain therapeutic advantages over natural antisense nucleic acid molecules. The PNA probes are known for its better and stronger complementation with target nucleic acids. However, cellular delivery of PNA is a major hurdle due to the charge-neutral nature of the PNA. For cellular delivery of PNA, peptide-PNA conjugates are used. This approach may face some practical limitation in terms of PNA antisense activity. In this study, we propose a novel RATH-2 peptide-based non-covalent PNA delivery mechanism. We observed RATH-2 shows a favorable molecular interaction with PNA at 16:1 (peptide:PNA) molar ratio resulting in co-centric nanoparticle formation. With this combination, we could achieve as high as 93% cellular delivery of the PNA. The proposed non-covalent RATH:PNA delivery model showed endocytic entrapment free delivery of PNA. The study further demonstrated the therapeutic application of PNA with in vitro antiviral intervention model. Using RATH-2 non-covalent PNA delivery system, we could inhibit 69.5% viral load. The present study demonstrates a cell-penetrating peptide:PNA interaction can lead to nanoparticle formations that facilitated cellular delivery of PNA.Key points• A novel cell-penetrating peptide (RATH-2) was identified for non-covalent delivery of PNA.• RATH-2 and PNA formed co-centric nanoparticles at appropriate molar combination.• PNA delivered through the RATH-2 inhibited the viral gene expression and reduced the viral load.

Novel method of real-time PCR-based screening for common fetal trisomies

BACKGROUND

The non-invasive prenatal test (NIPT) is based on next generation sequencing (NGS) and is used for screening for fetal trisomy. However, it is time-consuming and technically difficult. Recently, peptide nucleic acid (PNA) probe-based real-time polymerase chain reaction (RT-PCR) was developed. This study aimed to examine the performance of the RT-PCR-based NIPT for screening of common fetal trisomies METHODS: From stored maternal plasma, RT-PCR was performed using Patio™ NIPT Detection Kit. In melting curve analysis, the height of melting peaks of target chromosome and reference chromosome was calculated as a peak ratio. The adjusted peak ratio of 8 markers with correction factors in each target chromosome was summated and calculated to z-score. The cut-off value for each target chromosome was established for classification (low risk vs. high risk for trisomy) whose performance was obtained in the validation phase.

RESULTS

330 plasma samples from pregnant women with normal fetus and 22 trisomy cell-line samples were used to establish the optimal cut-off values for z-score of each target chromosome. In the validation phase, 1023 samples from pregnant women including 22 cases with fetal trisomy and 1001 cases of normal control were used. The RT-PCR-based NIPT showed 95.45% sensitivity [95% confidence interval (CI) 77.16-99.88%], 98.60% specificity (95% CI 97.66-99.23%), and 98.53% accuracy (95% CI 97.59-99.18%) for the identification of trisomy 21, 18, or 13. Of 1023 samples, fifteen cases were mismatched for classification [one case as a false negative (false negative rate: 4.5%) and 14 cases as false positives (false positive rate: 1.4%)].

CONCLUSION

The RT-PCR-based NIPT showed high sensitivity and specificity for the detection of common fetal trisomies and it could be a feasible alternative to NGS-based NIPT.

Therapeutic effects, immunogenicity and cytotoxicity of a cell penetrating peptide-peptide nucleic acid conjugate against cagA of Helicobacter pylori in cell culture and animal model

BACKGROUND AND OBJECTIVES

Helicobacter pylori causes several gastrointestinal diseases, including asymptomatic gastritis, chronic peptic ulcer, duodenal ulcer, lymphoma of the mucosa-associated lymphoid tissue (MALT), and gastric adenocarcinoma. In recent years, failure to eradicate H. pylori infections has become an alarming problem for physicians. It is now clear that the current treatment strategies may become ineffective, necessitating the development of innovative antimicrobial compounds as alternative treatments.

MATERIALS AND METHODS

In this experimental study, a cell-penetrating peptide-conjugated peptide nucleic acid (CPP-PNA) was used to target the cagA expression. cagA expression was evaluated using RT-qPCR assay after treatment by the CPPPNA in cell culture and animal model. Additionally, immunogenicity and toxicity of the CPP-PNA were assessed in both cell culture and animal models.

RESULTS

Our analysis showed that cagA mRNA levels reduced in H. pylori-infected HT29 cells after treatment with CPPPNA in a dose-dependent manner. Also, cagA expression in bacterial RNA extracted from stomach tissue of mice treated with PNA was reduced compared to that of untreated mice. The expression of inflammatory cytokines also decreased in cells and tissue of H. pylori-infected mice after PNA treatment. The tested CPP-PNA showed no significant adverse effects on cell proliferation of cultured cells and no detectable toxicity and immunogenicity were observed in mice.

CONCLUSION

These results suggest the effectiveness of CPP-PNA in targeting CagA for various research and therapeutic purposes, offering a potential antisense therapy against H. pylori infections.

Synthesis and characterization of PNA oligomers containing preQ1 as a positively charged guanine analogue

We report the synthesis of a peptide nucleic acid (PNA) monomer containing preQ₁, a positively charged guanine analogue. The new monomer was incorporated into PNA oligomers using standard Fmoc-chemistry-based solid-phase synthesis. The preQ₁ unit-containing PNA oligomers exhibited improved affinity for their complementary DNA through electrostatic attraction, and their sequence specificity was not compromised. It could be beneficial to incorporate preQ₁ into PNA oligomers instead of guanine when creating antisense/antigene agents or research tools.

Flow-FISH Using Nucleic Acid Mimic Probes for the Detection of Bacteria

Flow-Fluorescence in situ hybridization (Flow-FISH) enables multiparametric high-throughput detection of target nucleic acid sequences at the single cell-level, allowing an accurate quantification of different cell populations by using a combination of flow cytometry and fluorescent in situ hybridization (FISH). In this chapter, a flow-FISH protocol is described with labeled nucleic acid mimics (NAMs) (e.g. LNA/2'OMe and PNA) acting as the reporter molecules. This protocol allows for the specific detection of bacterial cells. Hence, this protocol can be carried out with minor adjustments, in order to simultaneously detect different species of bacteria in different types of clinical, food, or environmental samples.

Inchworm-type PNA-PEG conjugate regulates gene expression based on single nucleotide recognition

In order to detect single nucleotide mutations and suppress gene expression, we synthesized an artificial nucleic acid, an inchworm-type PNA-PEG conjugate (i-PPc), that possessed a chemical structure in which 8 residues of peptide nucleic acid (PNA) were linked to both ends of a polyethylene glycol molecule. I-PPc_T7_FM, which forms a complementary strand with the T7 promoter region of luciferase-expressing mRNA, failed to suppress the amount of luciferase produced via gene expression. However, 10 μM of i-PPc_ATG_FM, targeting the start codon of luciferase (Luc⁺), suppressed approximately 85% of Luc⁺ production compared to that of the control in the cell-free protein synthesis system. Moreover, i-PPc_ATG_MM (i-PPc_ATG_FM with a single base mutation) only suppressed the amount of luciferase produced by approximately 15%, and such suppression of luciferase expression has not been achieved with block-type PPc or PNA oligos. The thermodynamic parameters suggested that the difference in stability of each PNA segment of the i-PPc contributed to single nucleotide recognition. These results indicate that the i-PPc could be used in antisense therapy to target single nucleotide polymorphisms (SNP).

Nucleic acid sensing via electrochemical oligonucleotide-templated reactions

Short single-stranded nucleic acids as found in a variety of bodily fluids have recently emerged as minimally invasive biomarkers for a broad range of pathologies, most notably cancer. Because of their small size, low natural abundance and high sequence homology between family members they are challenging to detect using standard technologies suitable for use at the point-of-care. Herein we report the design, engineering and testing of a novel sensing strategy: electrochemically active molecular probes based on peptide nucleic acid (PNA) scaffolds for the detection of single-stranded oligonucleotides, in particular microRNAs (or miRs). As a proof-of-principle, a wide range of probes were designed and tested to detect miR-141, a known diagnostic biomarker for prostate cancer. Optimal quantitative sensing of miR-141 was achieved via the first example of an electrochemical oligonucleotide-templated reaction (EOTR), whereby two PNA probes - functionalized with an aniline and a 1,4-catechol respectively - preferentially react with each other upon simultaneous hybridization to the same RNA target strand, serving here as a template. Quantitative, electrochemical detection of the product of this bio-orthogonal reaction showed direct correlation between adduct formation and miR-141 concentration. Coupling the specificity of OTR with the speed and sensitivity of electrochemical sensing delivers EOTRs as a promising new technique for fast, low-cost, quantitative and sequence-specific detection of short nucleic acids from liquid biopsies.

Ultrasensitive label-free detection for lung cancer CYFRA 21-1 DNA based on ring-opening polymerization

Cytokeratin fragment antigen 21-1 (CYFRA 21-1) DNA is perceived as sensitive tumor marker for the diagnosis of non-small cell lung cancer and other tumor. Herein, linear chain poly(ε-caprolactone) (PCL) synthesized by ring-opening polymerization is applied to ultrasensitive label-free electrochemical impedance detection system for CYFRA 21-1 DNA. First, thiolated peptide nucleic acid (PNA) is self-assembled into the Au electrode surface through the formation of Au-S bonds, allowing the PNA to act as biomolecular probe and form PNA/DNA heteroduplex with the target DNA via specific hybridization. Then, PCL is conjugated to the immobilized DNA on the electrode via "carboxylate-Zr⁴⁺-phosphate" bridges. Finally, the electrochemical response of modified PNA/DNA/Zr⁴⁺/PCL electrode is determined by electrochemical impedance method to quantify of CYFRA 21-1 DNA. Under optimal conditions, this method exhibits highly sensitivity with a broad linear range (0.1 fM - 1 nM) (R² = 0.995) and the limit of detection (LOD) is as low as 10.73 aM, which is equivalent to just 64 molecules in a 10 μL sample. What's more, the high selectivity, good anti-interference, label-free operation, and real-time monitoring in complex samples of the proposed strategy demonstrate its broad application for the early diagnosis and clinical monitoring.

Facile Preparation of PNA-Peptide Conjugates with a Polar Maleimide-Thioether Linkage

Conjugation of a delivery peptide containing a thiol functionality (e.g., a cysteine residue) with a PNA oligomer displaying a single unprotected aliphatic primary amine (e.g., the N-terminus or a C-terminal lysine residue) can be achieved via a one-pot modification with a bisfunctional maleimide linker also displaying a reactive N-hydroxysuccinimidyl ester group (e.g., Mal-PEG2-OSu). Here, an optimized protocol with respect to ratios between the reactants as well as recommended reaction times is presented. Formation and conversion of the maleimide-PNA intermediate was followed by analytical HPLC as exemplified by its conjugation to (KFF)₃K-Cys-NH₂. In addition, the reaction time required for direct conversion of a preformed Mal-(CH₂)₂-(C=O)-PNA oligomer in the presence of a slight excess of thiol-modified peptide (with a varying degree of sterical hindrance: HS-(CH₂)₂-CONH-(KFF)₃K-NH₂, (KFF)₃K-hCys-NH₂ and (KFF)₃K-Cys-NH₂) is provided.

Reactive Quantum Dot-Based FRET Systems for Target-Catalyzed Detection of RNA

Oligonucleotide-templated reactions (OTRs) between two reactive hybridization probes allow for the detection of a DNA or RNA of interest by exploiting the target molecule as a catalyst of chemical reactions. The product of such a reaction commonly exhibits distinct fluorescence properties and can be detected by the means of fluorescence spectroscopy. The vast majority of OTR systems utilize organic dyes as fluorescent reporters. However, the use of brighter emitters, such as semiconductor quantum dots (QDs), has potential to improve the sensitivity of detection by providing brighter signals and permitting the use of probes at very low concentrations. Here we report an RNA-templated reaction between two fluorescently labeled peptide nucleic acid (PNA)-based probes, which proceeds on the surface of a QD. The QD-bound PNA probe bears a cysteine functionality, while the other PNA is functionalized with an organic dye as a thioester. OTR between these probes proceeds through a transfer of the organic dye to the QD and can be conveniently monitored via fluorescence resonance energy transfer (FRET) from the QD to the Cy5. The reaction was performed in a conventional fluorescence microplate reader and permits the detection of RNA in the picomolar range.

Fmoc-Based Assembly of PNA Oligomers: Manual and Microwave-Assisted Automated Synthesis

Exploration of PNA-peptide conjugates as potential antisense antibiotics necessitates a fast and efficient synthesis protocols for amounts that facilitate determination of structure-activity relationships and in vivo studies in animal infection models. Fmoc/Boc-protected PNA monomers are here used for assembly of oligomers by optimized protocols involving either a manual synthesis method at room temperature or automated microwave-assisted coupling of monomers on a peptide synthesizer.

Peptide Nucleic Acid (PNA) Clamps to Reduce Co-amplification of Plant DNA During PCR Amplification of 16S rRNA Genes from Endophytic Bacteria

High-throughput sequencing of universal bacterial 16S rRNA gene (16S rDNA) amplicons is a routine method for characterizing bacterial diversity in a range of environments. For eukaryotic host-associated communities, however, plastid and mitochondrial genes are often co-amplified with, and greatly outnumber, bacterial 16S rDNA. This makes it difficult to obtain sufficient numbers of target 16S rDNA sequences to characterize the diversity of endophytic bacterial communities. This chapter describes a method that improves the amplification of bacterial 16S rDNA from plant tissues by using a peptide nucleic acid (PNA) PCR clamp. The PNA clamp selectively binds to a targeted region of the plant genome and inhibits its amplification during PCR. PNA clamps are especially useful for characterizing bacterial communities on plant tissues with lower levels of microbial colonization such as the root tips and leaves.

Studying Seed Microbiomes

Recent studies indicate that seed microbiomes affect germination and plant performance. However, the interplay between seed microbiota and plant health is still poorly understood. To get a complete picture of the system, a comprehensive analysis is required, comprising culture-dependent and culture-independent techniques. In this chapter, we provide a combination of methods that are established and optimized for the analysis of the seed microbiome. These include methods to: (1) activate and cultivate dormant seed microbiota, (2) analyze microbiota in germinated seeds (with and without substrate), (3) quantify microbial DNA via real-time PCR, (4) deplete host DNA for amplicon and metagenome analysis, and (5) visualize seed endophytes in microtomed sections using fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM). A deep understanding of the seed microbiome and its functions can help in developing new seed treatments and breeding strategies for sustainable agriculture.

Analysis of Telomere Length and Aberrations by Quantitative FISH

A key component of sustained cellular proliferation is the preservation of telomere integrity. Telomeres are nucleoprotein structures that cap and protect linear chromosomes. Their linearity and repetitive sequence represent a challenge for the replication machinery and cause telomere shortening, fragility, and losses. Here we describe the common technique of quantitative fluorescent in situ hybridization that allows for the scoring of telomere aberrations and measurement of telomere length directly on metaphase chromosomes through the use of highly specific peptide nucleic acid probes.

Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates

Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5'-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5'-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5'-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5'-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.

Therapeutic efficacy of modified anti-miR21 in metastatic prostate cancer

Despite improved therapeutic efficacy of the locked nucleic acid (LNA)- and peptide nucleic acid (PNA)-modified antisense microRNAs (anti-miRs), their wider application in clinical practice is still not thoroughly investigated. This study aimed to investigate the stability and therapeutic efficacy of the modified LNA- and PNA-type anti-miRs in a murine prostate cancer model under various treatment conditions. After verifying the anti-cancer potential of anti-miR21 by targeting tumor suppressor PTEN, the potential of the modified LNA- and PNA-type anti-miR21s was compared in vitro and in vivo. We found that PNA-type anti-miR21 showed better stability and therapeutic efficacy in the xenografted mouse tumor model than the LNA-type anti-miR21. Furthermore, PNA-type anti-miR21 treatment showed reduced tumor metastasis. This study may serve as a ground for exploring diverse choices in therapeutic oligonucleotide modification techniques to improve cancer treatment.

A peptide nucleic acid-regulated fluorescence resonance energy transfer DNA assay based on the use of carbon dots and gold nanoparticles

A convenient fluorometric method was developed for specific determination of DNA based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs). In this system, CDs that display lake blue fluorescence with excitation/emission maxima at 345/445 nm were used as fluorometric reporter, while AuNPs were used as fluorescence nanoquencher. A neutral PNA probe, which is designed to recognize the target DNA, was used as a coagulant to control the dispersion and aggregation of AuNPs. Without DNA, PNA can induce immediate AuNP aggregation, thus leading to the recovery of the FRET-quenched fluorescence emission of CDs. However, the addition of the complementary target DNA can protect AuNPs from being aggregated due to the formation of DNA/PNA complexes, which subsequently produces a high fluorescence quenching efficiency of CDs by dispersed AuNPs. Under optimized conditions, quantitative evaluation of DNA was achieved in a linear range of 5-100 nM with a detection limit of 0.21 nM. This method exhibited an excellent specificity towards fully matched DNA. In addition, the application of this assay for sensitive determination of DNA in cell lysate demonstrates its potential for bioanalysis and biodetection. Graphical abstract A simple fluorometric biosensor for specific detection of DNA was developed based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs).

Visual genotyping of thalassemia by using pyrrolidinyl peptide nucleic acid probes immobilized on carboxymethylcellulose-modified paper and enzyme-induced pigmentation

A simple probe pair was designed for the detection of hemoglobin E (HbE) genotype, a single-point mutation that leads to abnormal red blood cells commonly found in South East Asia. The key to differentiation is the use of a conformationally constrained peptide nucleic acid (PNA) that was immobilized on carboxymethylcellulose-modified paper. This was then used for target DNA binding and visualization by an enzyme-catalyzed pigmentation. The biotinylated target DNA bound to the immobilized probe was visually detected via alkaline phosphatase-linked streptavidin. This enzyme conjugate catalyzed the dephosphorylation of the substrate 5-bromo-4-chloro-3-indolyl phosphate, leading to a series of reactions that generate an intense, dark blue pigment. The test was validated with 100 DNA samples, which shows good discrimination among different genotypes (normal, HbE, and heterozygous) with 100% accuracy when optimal conditions of analysis were applied. The method does not require temperature control and can be performed at ambient temperature. This is an attractive feature for diagnosis in primary care, which accounts for a large part of affected population. Graphical abstract Schematic representation of a paper-based sensor for the detection of the gene Hemoglobin E. The interaction between an immobilized peptide nucleic acid and a DNA target leads to enzymatic pigmentation, allowing simple visual readout with up to 100% accuracy.

Modulation of DNA and RNA by PNA

Peptide nucleic acid (PNA), a synthetic DNA mimic that is devoid of the (deoxy)ribose-phosphate backbone yet still perfectly retains the ability to recognize natural nucleic acids in a sequence-specific fashion, can be employed as a tool to modulate gene expressions via several different mechanisms. The unique strength of PNA compared to other oligonucleotide analogs is its ability to bind to nucleic acid targets with secondary structures such as double-stranded and quadruplex DNA as well as RNA. This digest aims to introduce general readers to the advancement in the area of modulation of DNA/RNA functions by PNA, its current status and future research opportunities, with emphasis on recent progress in new targeting modes of structured DNA/RNA by PNA and PNA-mediated gene editing.

Peptide nucleic acid based tension sensor for cellular force imaging with strong DNase resistance

DNA is a versatile biomaterial with well-defined mechanical and biochemical properties. It has been broadly adopted to synthesize tension sensors that calibrate and visualize cellular forces at the cell-matrix interface. Here we showed that DNA-based tension sensors are vulnerable to deoxyribonucleases (DNases) which cells may express on cell membrane or secret to the culture environment. These DNases can damage the sensors, lower signal-to-noise ratio or even produce false signal in cellular force imaging. To address this issue, we tested peptide nucleic acid (PNA), chemically modified RNA and their hybrids with DNA as alternative biomaterials for constructing tension sensors. Four duplexes: double-stranded DNA (dsDNA), PNA/DNA, dsRNA (modified RNA) and PNA/RNA, were tested and evaluated in terms of DNase resistance, cellular force imaging ability and material robustness. The results showed that all PNA/DNA, dsRNA and PNA/RNA exhibited strong resistance to both soluble DNase I and membrane-bound DNase on cells. However, PNA/RNA-based tension sensor had low signal-to-noise ratio in cellular force imaging, and dsRNA-based tension sensor exhibited strong non-specific signal unrelated to cellular forces. Only PNA/DNA-based tension sensor reported cellular forces with highest signal-to-noise ratio and specificity. Collectively, we confirmed that PNA/DNA hybrid is an accessible material for the synthesis of DNase-resistant tension sensor that retains the force-reporting capability and remains stable in DNase-expressing cells. This new class of tension sensors will broaden the application of tension sensors in the study of cell mechanobiology.

Mitochondrial DNA screening by melting curve analysis using peptide nucleic acid probes

Analysis of single nucleotide polymorphisms (SNPs) in mitochondrial (mt)DNA hypervariable regions (HV) 1/2 is valuable in forensic investigations. We developed a method for mtDNA screening of the HV1 and HV2 regions by melting curve analysis, using peptide nucleic acid (PNA) probes. This method focuses on melting peak patterns obtained by thermal dissociation of PNA/DNA duplexes in amplified mtDNA products. Five PNA probe sets were designed to detect 25 SNPs in the two HV regions. We also detected non-target SNPs based on unexpected melting temperature (T_m) shifts. In fact, 62 SNPs (42 SNPs in HV1 and 20 in HV2) were identified, including the 25 target SNPs. Using this method, 46 melting peak patterns, including 8 pattern groups, were obtained in 60 unrelated individuals. The peak patterns were compared to 55 haplotypes identified by Sanger sequencing. The results obtained from analysis of target mtDNA SNPs were entirely consistent with those obtained by Sanger sequencing. Screening the HV1 and HV2 regions of mtDNA by this method may help minimize unnecessary recourse to full sequence analysis, allows to rapidly exclude samples that do not match evidence and reference samples, and may reduce turnaround times and analysis costs. Overall, this method may be effective and helpful in forensic investigations.

Antisense peptide nucleic acids againstftsZ andefaA genes inhibit growth and biofilm formation of Enterococcusfaecalis

Enterococcus faecalis is one of the important causes of nosocomial infections. Nowadays, increasing prevalence of antibiotic-resistant bacteria and slow progress in recognizing new antimicrobial agents has limited the efficiency of conventional antibiotics, which cause to find novel strategies to overcome bacteria. Therefore, in this study, we aimed to assess the role of efaA gene in the biofilm formation and the role of ftsZ gene in the controlling of bacterial growth by the anti-sense PNAs(Peptide Nucleic Acid).E. faecalis ATCC® 29212™was used for the study of PNAs designed to targeting the start codon section of the ftsZ andefaA genes. PNA attachment to RNA was confirmed by blotting. Electroporation technique was used for the intracellular transfer of anti-ftsZ PNAs. The spot-plating method was used to the assessment of alteration in bacterial growth. Biofilm formation assay and real-time PCR were used for detection of biofilm inhibitory effect of cell penetrating peptide (CPP) conjugated to anti-efaA PNAs.ByftsZ PNAs treatment, no growth was seen from the strain in agar by a spot plating method and the inhibition zone of anti-ftsZ PNAs was not seen. PNAs against the efaA gene decreased by 95% the expression of the efaA gene and biofilm formation. In addition, the(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide) MTT assay showed no toxicity on MCF7 cells for both of anti-ftsZand anti-efaA PNAs.This study used new genetic and molecular tools to inhibit pathogenicity and infection by E. faecalis. In this study, we suggested that efaA gene plays a critical role in the biofilm formation and anti-efaA PNAs could decrease the formation of biofilm, as well as, anti-ftsZ PNAs could eliminate bacterial growth.

A convenient route to synthesize N2-(isobutyryl)-9-(carboxymethyl)guanine for aeg-PNA backbone

Synthesis of exclusive N²-(isobutyryl)-9-(carboxymethyl)guanine, an important moiety for peptide nucleic acid synthesis has been reported through a high-yielding reaction scheme starting from 6-chloro-2-amino purine. Crystal structures of two intermediates confirmed the formation of N9-regioisomer. This new synthetic route can potentially replace the conventional tedious method with moderate overall yield.

Label-free peptide nucleic acid biosensor for visual detection of multiple strains of influenza A virus suitable for field applications

Accurate and rapid diagnosis of Influenza A viruses (IAVs) is challenging because of multiple strains circulating in humans and animal populations, and the emergence of new strains. In this study, we demonstrate a simple and rapid strategy for visual detection of multiple strains of IAVs (H1 to H16 subtypes) using peptide nucleic acid (PNA) as a biosensor and unmodified gold nanoparticles (AuNPs) as a reporter. The design principle of the assay is based on the color change on account of free PNA-induced aggregation of AuNPs in the presence of non-complementary viral RNA sequence and vice-versa. The assay could detect IAV RNA with a visual limit of detection of 2.3 ng. The quantification of RNA with a considerable accuracy on a simple spectrophotometer was achieved on plotting the PNA-induced colorimetric changes (absorption ratio of A₆₄₀/A₅₂₀) in the presence of a varying concentration of complementary RNA. As a proof-of-concept, the visual assay was validated on 419 avian clinical samples and receiver operating characteristic (ROC) curve analysis showed a high diagnostic specificity (96.46%, 95% CI = 93.8 to 98.2) and sensitivity (82.41%, 95% CI = 73.9 to 89.1) when RT-qPCR was used as reference test. Hence, the simplicity, rapidity, and universality of this strategy make it a potential candidate visual assay for clinical diagnosis and surveillance of IAVs, especially in the resource-limited settings. The proposed strategy establishes new avenues for developing a simple and rapid diagnostic system for viral infections and biomolecules.

Synthesis and Application of LKγT Peptide Nucleic Acids

Displaying ligands in a succinct and predictable manner is essential for elucidating multivalent molecular-level binding events. Organizing ligands with high precision and accuracy provides a distinct advantage over other ligand-display systems, such as polymers, because the number and position of the ligand(s) can be accurately and fully characterized. Here we describe the synthesis of peptide nucleic acids (PNAs), which are oligonucleotide mimics with a pseudopeptide backbone that can hybridize to oligonucleotides through Watson-Crick base pair to form highly predictable and organized scaffold for organizing a ligand. The ligand(s) are covalently attached to the PNA through a squarate coupling reaction that occurs between a free amine on the ligand and a free amine appended to the pseudopeptide backbone of the PNA. In this chapter we describe the synthesis of a ^LKγT monomer, which ultimately yields the free amine off the backbone of the PNA, incorporation of the monomer in a PNA oligomer, and the sequential squarate coupling to conjugate the ligand.

Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg²⁺ (-49.6 kcal/mol), Zn²⁺ (-45.3 kcal/mol) and Cu²⁺ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg²⁺ and Cu²⁺ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn²⁺ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu²⁺ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg²⁺ and Zn²⁺ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu²⁺ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg²⁺, Zn²⁺, and Cu²⁺ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg²⁺ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn²⁺, Cu²⁺) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu²⁺ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Peptide nucleic acid-mediated re-sensitization of colistin resistance Escherichia coli KP81 harboring mcr-1 plasmid

Escherichia coli is a gram-negative bacterium and it causes a variety of diseases in humans. It causes a wide range of clinical infections in humans; urinary tract infections is the most prevalent infection caused by uropathogenic Escherichia coli. In recent years, the observation of antibiotic-resistant genes such as resistance to colistin, makes the Escherichia coli resistant to antibiotics like colistin (polymyxin E), because of that the use of new therapies like peptide nucleic acid (PNA) has attracted the consideration of scientists. The aim of this study is the assessment of the inhibitory role of PNA against mcr-1 gene and reduction of mcr-1 gene expression and MIC in colistin resistant E. coli by PNA. NCBI database was used to design PNA. Our study was carried out on E. coli KP81 bacteria containing the mcr-1 gene. Microbroth dilution (MIC) method was used to survey phenotypic sensitivity and determine the sensitivity of the bacteria to the colistin antibiotic. E. coli KP81 isolates were further investigated by polymerase chain reaction to assess the presence of mcr-1 genes and target genes were quantified by real-time PCR assay using specific primers. The MIC result after treatment with specific PNA showed that the resistance to colistin reduced about three fold and the resistance level dropped from 32 μg/ml to 4 μg/ml. The expression analysis of mcr-1 gene in E. coli KP81 isolate indicates the PNA, 95% reduced the expression of the mcr-1 gene. Our observations showed that by inhibiting the expression of mcr-1, sensitivity to colistin can be defeated. Using higher concentrations of PNA and an in vivo study can reveal more clinical application of this method.

High selective spectroelectrochemical biosensor for HCV-RNA detection based on a specific peptide nucleic acid

Hepatitis C virus (HCV) is a blood-borne virus that causes infectious chronic hepatitis. Egypt has the largest epidemic of HCV in the world, with about 14.7% of the Egyptian population. Thus, HCV, which could cause severe risks for human health including liver failure, becomes a public health concern for Egyptians. Development of highly selective and sensitive biosensors for accurate detection of HCV levels without extensive sample preparation has received great attention. The present work reported on developing a new rapid, highly selective and highly selective HCV-based biosensor for early detection of HCV-RNA extracted from clinical samples. The HCV-based biosensor was constructed by fabrication of gold nanodots/indium tin oxide substrate and followed by immobilization of a specific peptide nucleic acid (as bio-receptors) terminated with thiol group onto gold nanodots/indium tin oxide. The principle of the developed biosensor was based on the selective hybridization between the peptide nucleic acid and the HCV-RNA at the untranslated regions (5'-UTR). Raman spectroscopy and Square wave voltammetry techniques were used to monitor the interaction between the HCV-RNA and the immobilized peptide nucleic acid. The reported HCV-biosensor demonstrated a high capability to detect HCV-RNA.

Red-emitting FIT-PNAs: "On site" detection of RNA biomarkers in fresh human cancer tissues

To date, there are limited approaches for the direct and rapid visualization (on site) of tumor tissues for pathological assessment and for aiding cytoreductive surgery. Herein, we have designed FIT-PNAs (forced-intercalation-peptide nucleic acids) to detect two RNA cancer biomarkers. Firstly, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. The latter, an mRNA termed KRT20, has been shown to be over-expressed in metastases originating from colorectal cancer (CRC). To these FIT-PNAs, we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605-610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for peritoneal metastasis of colon cancer with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. In addition, a non-targeted FIT-PNA shows no fluorescent signal after spraying this FIT-PNA on fresh tumor tissue emphasizing the specificity of these molecular sensors. This study is the first to show on-site direct and immediate visualization of an RNA cancer biomarker on fresh human cancer tissues by topical application (spraying) of a molecular sensor.

Film-Spotting chiral miniPEG-γPNA array for BRCA1 gene mutation detection

Peptide nucleic acids array technology is a method of greatly increasing the throughput of laboratory processes to efficiently perform large-scale genetic tests. Diethylene glycol-containing chiral γPNA (miniPEG-γPNA) is considered to be the best PNA derivative and one of the best candidates for gene detection, because it can hybridize DNA with greater affinity and sequence selectivity than DNA and ordinary aminoethylglycyl PNA (aegPNA). Herein, miniPEG-γPNA probes are synthesized by 9-fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS) in a mild condition, and a new biochip fabrication method "Film-Spotting" is invented, by which γPNA arrays with regular pattern, uniform luminance, and very low fluorescence background are obtained easily and cheaply. The miniPEG-γPNA array can effectively distinguish the full matched and mismatched targets in SSarc buffer, serum and urine, and the detection limit of complementary DNA is less than 5.97 nM. A miniPEG-γPNA array for BRCA1 gene mutation (3099delT) detection is also fabricated with a very good detection performance. This work provides an effective avenue for the diagnosis of breast cancer biomarker and expands the application of miniPEG-γPNA in the field of biochip.

Differential detection of porcine reproductive and respiratory syndrome virus genotypes by a fluorescence melting curve analysis using peptide nucleic acid probe-mediated one-step real-time RT-PCR

Peptide nucleic acids (PNAs), artificially synthesized DNA analogues, hybridize strongly with DNA and are useful for fluorescence melting curve analyses (FMCA) based on the thermal denaturation of the probe-target duplex. In this study, we developed a PNA-based one-step real-time RT-PCR assay for the differential and qualitative detection of the porcine reproductive and respiratory syndrome virus genotypes PRRSV1 and PRRSV2. The specificity of the assay was analyzed in silico using previously reported primers and probes and was subsequently verified using Korean PRRSV panels and clinical samples. Seven clinical samples showing low curves with high Ct values were confirmed as negative by FMCA. The sensitivities of one-step real-time PCR for PRRSV1 and PRRSV2 were 15 and 11 copies, respectively, and the results were in 100% agreement with those of conventional RT-PCR combined with nested PCR using clinical samples. Therefore, the assay is highly specific for the detection of current PRRSV1 and PRRSV2 without non-specific amplification by FMCA.

Site-specific conjugation of recognition tags to trastuzumab for peptide nucleic acid-mediated radionuclide HER2 pretargeting

Pretargeting is a promising strategy to reach high imaging contrast in a shorter time than by targeting with directly radiolabeled monoclonal antibodies (mAbs). One of problems in pretargeting is a site-specific, reproducible and uniform conjugation of recognition tags to mAbs. To solve this issue we propose a photoconjugation to covalently couple a recognition tag to a mAb via a photoactivatable Z domain. The Z-domain, a 58-amino acid protein derived from the IgG-binding B-domain of Staphylococcus aureus protein A, has a well-characterized binding site in the Fc portion of IgG. We tested the feasibility of this approach using pretargeting based on hybridization between peptide nucleic acids (PNAs). We have used photoconjugation to couple trastuzumab with the PNA-based hybridization probe, HP1. A complementary [⁵⁷Co]Co-labeled PNA hybridization probe ([⁵⁷Co]Co-HP2) was used as the secondary targeting probe. In vitro studies demonstrated that trastuzumab-ZHP1 bound specifically to human epidermal growth factor receptor 2 (HER2)-expressing cells with nanomolar affinity. The binding of the secondary [⁵⁷Co]Co-HP2 probe to trastuzumab-PNA-pretreated cells was in the picomolar affinity range. A two-fold increase in SKOV-3 tumor targeting was achieved when [⁵⁷Co]Co-HP2 (0.7 nmol) was injected 48 h after injection of trastuzumab-ZHP1 (0.5 nmol) compared with trastuzumab-ZHP1 alone (0.8 ± 0.2 vs. 0.33 ± 0.06 %ID/g). Tumor accumulation of [⁵⁷Co]Co-HP2 was significantly reduced by pre-saturation with trastuzumab or when no trastuzumab-ZHP1 was preinjected. A tumor-to-blood uptake ratio of 1.5 ± 0.3 was achieved resulting in a clear visualization of HER2-expressing xenografts as confirmed by SPECT imaging. In conclusion, the feasibility of stable site-specific coupling of a PNA-based recognition tag to trastuzumab and successful pretargeting has been demonstrated. This approach can hopefully be used for a broad range of mAbs and recognition tags.

Peptide nucleic acid and amino acid modified peptide nucleic acid analysis by capillary zone electrophoresis

A rapid, high resolution, and low sample consumption CZE method is developed for peptide nucleic acid (PNA) analysis for the first time. 30% v/v acetonitrile in PNA sample and 20% v/v acetonitrile in 50 mM borax-boric acid (pH 8.7) as BGE were employed after optimization. The calibration curves were linear for PNA concentration ranging from 1 to 50 μmol/L. LOD and LOQ of PNA were 0.2 and 1.0 μmol/L, respectively. Since the commercially available reagent gives rise to huge PNA peak and an apparent impurity peak, the purity of PNA was evaluated to be about 81.4% by CZE method, obviously lower than the supplier's purity value of 99.9% evaluated by RP-HPLC, and also lower than 94.8% determined with RP-HPLC by our research group. The CZE method takes only 5 min, needs only 90 nL PNA, much less than 20 min and 20 μL PNA in RP-HPLC method. Moreover, the CZE method is applicable for the analysis of glutamic acid modified and lysine modified PNAs, they show different migration time with their corresponding complementary PNAs. Our results show CZE provides a new choice for PNA and modified PNA analysis, also their purity or quality evaluation.

Sequence-specific recognition of structured RNA by triplex-forming peptide nucleic acids

While <2% of DNA encodes for functional proteins, >70% is transcribed into RNA. Although the function of most RNA transcripts is unknown, such non-coding RNAs are attractive targets for molecular recognition because of the potentially important roles they play in regulation of gene expression and development of disease. In this chapter, we describe peptide nucleic acids (PNAs) that form sequence-specific triple helices with double-stranded RNA (dsRNA). We provide protocols for sequence design and biophysical characterization of PNAs and discuss first examples where such PNAs have been used for functional modulation of dsRNA. The triplex-forming PNAs represent a new approach for RNA recognition that may find future applications in fundamental science, biotechnology and medicine.

Synthesis of a new disulfide Fmoc monomer for creating biologically susceptible linkages in peptide nucleic acid oligomers

Peptide nucleic acids (PNA) are one of many synthetic mimics of DNA and RNA that have found applications as biological probes, as nano-scaffold components, and in diagnostics. In an effort to use PNA as constructs for cellular delivery we investigated the possibility of installing a biologically susceptible disulfide bond in the backbone of a PNA oligomer. Here we report the synthesis of a new abasic Fmoc monomer containing a disulfide bond that can be incorporated into a PNA oligomer (DS-PNA) using standard solid phase peptide synthesis. The disulfide bond survives cleavage from the resin and DS-PNA forms duplexes with complementary PNA oligomers. Initial studies aimed at determining if the disulfide bond is cleavable to reducing agents while in a duplex are explored using UV thermal analysis and HPLC.

Selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans by antisense peptide nucleic acids

Peptide nucleic acids (PNA) are DNA/RNA analogs in which the sugar-phosphate backbone is replaced by N-2-aminoethylglycine. PNA are widely used for experimental antisense therapy due to their strong affinity to mRNA. By targeting specific genes, protein synthesis and the growth of bacteria or cancer cells can be inhibited by PNA. Here, we report the design and evaluation of antisense PNA for selective growth inhibition of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, potent pathogens associated with periodontitis. Antisense PNA against groEL and acpP were prepared with carrier peptide (KFFKFFKFFK). Anti-groEL PNA for P. gingivalis specifically inhibited growth in a dose-dependent manner, and growth was inhibited for 5 h at a concentration of 3 μM. Anti-groEL PNA for A. actinomycetemcomitans inhibited growth for 2 h at a concentration of 3 μM with reduced GroEL protein expression. Anti-acpP PNA did not show a marked growth inhibitory effect on either species. Although further studies are needed to develop more effective antisense PNA for both species, anti-groEL PNA may be potentially useful species-specific antibacterial tools against oral pathogens.

Filter paper grafted with epoxide-based copolymer brushes for activation-free peptide nucleic acid conjugation and its application for colorimetric DNA detection

Epoxide-bearing filter paper was first prepared by surface-initiated reversible addition-fragmentation chain transfer (RAFT) copolymerization of glycidyl methacrylate (GMA) and poly(ethylene glycol)methacrylate (PEGMA). Without the need for activation step, the capture peptide nucleic acid (PNA) probes carrying a C-terminal lysine modification can be directly immobilized on the surface-grafted poly[glycidyl methacrylate-ran-poly(ethylene glycol)methacrylate] (P(GMA-ran-PEGMA)) through ring-opening of epoxide groups in the GMA repeating units by amino groups in the PNA's structure. The success of P(GMA-ran-PEGMA) grafting on the filter paper and subsequent PNA immobilization was confirmed by fluorescence microscopy, Fourier transform-infrared spectroscopy and X-ray photoelectron spectroscopy. Colorimetric detection with signal amplification upon DNA hybridization relies on sandwich-hybridization assay employing another biotinylated PNA strand as a reporter probe together with streptavidin-horseradish peroxidase conjugate (SA-HRP) and o-phenylenediamine (OPD) substrate. It was found that increasing ionic strength during the DNA hybridization step by addition of NaCl can increase the signal intensity, which can be visualized by naked eye. The sensing platform showed the best performance in preventing non-specific adsorption from the non-complementary DNA and discriminating between complementary and single-mismatched targets of at least 50 fmol without the requirement for stringent hybridization or washing condition. This superior ability to suppress non-specific adsorption of non-target DNA as well as other non-DNA components may be explained as a result of hydrophilic PEGMA repeating units in the surface-grafted copolymer.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system.