Pyrrolidinyl PNA with α/β-Dipeptide Backbone: From Development to Applications

Strategies for the optimisation of troublesome peptide nucleic acid (PNA) sequences

Through the use of a pseudo-peptidic backbone, peptide nucleic acids (PNA) mimic the functionality of native nucleic acids while enjoying improved binding affinity and metabolic stability. However, many aspects of the application of PNA to biological and medicinal settings still requires sequence specific optimisation. This review highlights key areas for refinement, including synthesis, tuning of physical properties, cell permeability and analysis, including common strategies for the pracitioner to apply in each area.

Peptide nucleic acid-immobilised paper combined with multiplex recombinase polymerase amplification for the ultrasensitive and rapid detection of rifampicin-resistant tuberculosis

Rifampicin-resistant tuberculosis (RR-TB) is a critical issue with significant implications for patient care, public health, and TB control efforts that necessitate comprehensive strategies for detection. This study presents a novel point-of-care diagnostic tool for RR-TB detection employing a peptide nucleic acid (PNA)-paper-based sensor combined with isothermal recombinase polymerase amplification (RPA). The sensor targets mutations in codons 516, 526, and 531 of the rpoB gene, the top three common mutations associated with rifampicin-resistant strains. PNA probes specifically recognised wild-type sequences, generating a visual signal through a reverse hybridisation assay. The absence of a signal was observed when the mutant strains were detected because of the inability to bind the mutant sequence. Our proof-of-concept assay displayed high accuracy (100% for detecting mutations at codons 516, 526, and 531), a short turnaround time (110 min), no cross-reactivity with other bacterial pathogens, and ultrasensitivity. This PNA-paper-based sensor model can be a valuable diagnostic tool for RR-TB detection, providing an accessible diagnostic platform that can be advantageous in resource-limited settings where sophisticated laboratory infrastructure may be lacking.

Peptide nucleic acid probe-assisted paper-based electrochemical biosensor for multiplexed detection of respiratory viruses

The similar transmission patterns and early symptoms of respiratory viral infections, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza (H1N1), and respiratory syncytial virus (RSV), pose substantial challenges in the diagnosis, therapeutic management, and handling of these infectious diseases. Multiplexed point-of-care testing for detection is urgently needed for prompt and efficient disease management. Here, we introduce an electrochemical paper-based analytical device (ePAD) platform for multiplexed and label-free detection of SARS-CoV-2, H1N1, and RSV infection using immobilized pyrrolidinyl peptide nucleic acid probes. Hybridization between the probes and viral nucleic acid targets causes changes in the electrochemical response. The resulting sensor offers high sensitivity and low detection limits of 0.12, 0.35, and 0.36 pM for SARS-CoV-2 (N gene), H1N1, and RSV, respectively, without showing any cross-reactivities. The amplification-free detection of extracted RNA from 42 nasopharyngeal swab samples was successfully demonstrated and validated against reverse-transcription polymerase chain reaction (range of cycle threshold values: 17.43-25.89). The proposed platform showed excellent clinical sensitivity (100 %) and specificity (≥97 %) to achieve excellent agreement (κ ≥ 0.914) with the standard assay, thereby demonstrating its applicability for the screening and diagnosis of these respiratory diseases.

Chemically Modified Platforms for Better RNA Therapeutics

RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.

Sequential Flow Controllable Microfluidic Device for G-Quadruplex DNAzyme-Based Electrochemical Detection of SARS-CoV-2 Using a Pyrrolidinyl Peptide Nucleic Acid

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant health issue globally. Point-of-care (POC) testing that can offer a rapid and accurate diagnosis of SARS-CoV-2 at the early stage of infection is highly desirable to constrain this outbreak, especially in resource-limited settings. Herein, we present a G-quadruplex DNAzyme-based electrochemical assay that is integrated with a sequential flow controllable microfluidic device for the detection of SARS-CoV-2 cDNA. According to the detection principle, a pyrrolidinyl peptide nucleic acid probe is immobilized on a screen-printed graphene electrode for capturing SARS-CoV-2 DNA. The captured DNA subsequently hybridizes with another DNA probe that carries a G-quadruplex DNAzyme as the signaling unit. The G-quadruplex DNAzyme catalyzes the H2O2-mediated oxidation of hydroquinone to benzoquinone that can be detected using square-wave voltammetry to give a signal that corresponds to the target DNA concentration. The assay exhibited high selectivity for SARS-CoV-2 DNA and showed a good experimental detection limit at 30 pM. To enable automation, the DNAzyme-based assay was combined with a capillary-driven microfluidic device featuring a burst valve technology to allow sequential sample and reagent delivery as well as the DNA target hybridization and enzymatic reaction to be operated in a precisely controlled fashion. The developed microfluidic device was successfully applied for the detection of SARS-CoV-2 from nasopharyngeal swab samples. The results were in good agreement with the standard RT-PCR method and could be performed within 20 min. Thus, this platform offers desirable characteristics that make it an alternative POC tool for COVID-19 diagnosis.

Development of peptide nucleic acid-based bead array technology for Bacillus cereus detection

Numerous novel methods to detect foodborne pathogens have been extensively developed to ensure food safety. Among the important foodborne bacteria, Bacillus cereus was identified as a pathogen of concern that causes various food illnesses, leading to interest in developing effective detection methods for this pathogen. Although a standard method based on culturing and biochemical confirmative test is available, it is time- and labor-intensive. Alternative PCR-based methods have been developed but lack high-throughput capacity and ease of use. This study, therefore, attempts to develop a robust method for B. cereus detection by leveraging the highly specific pyrrolidinyl peptide nucleic acids (PNAs) as probes for a bead array method with multiplex and high-throughput capacity. In this study, PNAs bearing prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbone with groEL, motB, and 16S rRNA sequences were covalently coupled with three sets of fluorescently barcoded beads to detect the three B. cereus genes. The developed acpcPNA-based bead array exhibited good selectivity where only signals were detectable in the presence of B. cereus, but not for other species. The sensitivity of this acpcPNA-based bead assay in detecting genomic DNA was found to be 0.038, 0.183 and 0.179 ng for groEL, motB and 16S rRNA, respectively. This performance was clearly superior to its DNA counterpart, hence confirming much stronger binding strength of acpcPNA over DNA. The robustness of the developed method was further demonstrated by testing artificially spiked milk and pickled mustard greens with minimal interference from food metrices. Hence, this proof-of-concept acpcPNA-based bead array method has been proven to serve as an effective alternative nucleic acid-based method for foodborne pathogens.

Electrochemical capillary-driven microfluidic DNA sensor for HIV-1 and HCV coinfection analysis

Electrochemical DNA sensors can be operated in either static or flow-based detection schemes. In static schemes, manual washing steps are still necessary, resulting in a tedious and time-consuming process. In contrast, in flow-based electrochemical sensors, the current response is collected when the solution flows through the electrode continuously. However, the drawback of such a flow system is the low sensitivity due to the limited time for the interaction between the capturing element and the target. Herein, we propose a novel electrochemical capillary-driven microfluidic DNA sensor to combine the advantages of static and flow-based electrochemical detection systems into a single device by incorporating burst valve technology. The microfluidic device with a two-electrode configuration was applied for the simultaneous detection of two different DNA markers, human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) cDNA, via the specific interaction between pyrrolidinyl peptide nucleic acids (PNA) probes and the DNA target. The integrated system, while requiring a small sample volume (7 μL for each sample loading port) and less analysis time, achieved good performance in terms of the limits of detection (LOD) (3SD_blank/slope) and quantification (LOQ) (10SD_blank/slope) at 1.45 nM and 4.79 nM for HIV and 1.20 nM and 3.96 nM for HCV, respectively. The simultaneous detection of HIV-1 and HCV cDNA prepared from human blood samples showed results that are in complete agreement with the RT‒PCR assay. The results qualify this platform as a promising alternative for the analysis of either HIV-1/HCV or coinfection that can be easily adapted for other clinically important nucleic acid-based markers.

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.

Label free electrochemical DNA biosensor for COVID-19 diagnosis

The COVID-19 pandemic has significantly increased the development of the development of point-of-care (POC) diagnostic tools because they can serve as useful tools for detecting and controlling spread of the disease. Most current methods require sophisticated laboratory instruments and specialists to provide reliable, cost-effective, specific, and sensitive POC testing for COVID-19 diagnosis. Here, a smartphone-assisted Sensit Smart potentiostat (PalmSens) was integrated with a paper-based electrochemical sensor to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A disposable paper-based device was fabricated, and the working electrode directly modified with a pyrrolidinyl peptide nucleic acid (acpcPNA) as the biological recognition element to capture the target complementary DNA (cDNA). In the presence of the target cDNA, hybridization with acpcPNA probe blocks the redox conversion of a redox reporter, leading to a decrease in electrochemical response correlating to SARS-CoV-2 concentration. Under optimal conditions, a linear range from 0.1 to 200 nM and a detection limit of 1.0 pM were obtained. The PNA-based electrochemical paper-based analytical device (PNA-based ePAD) offers high specificity toward SARS-CoV-2 N gene because of the highly selective PNA-DNA binding. The developed sensor was used for amplification-free SARS-CoV-2 detection in 10 nasopharyngeal swab samples (7 SARS-CoV-2 positive and 3 SARS-CoV-2 negative), giving a 100% agreement result with RT-PCR.

Artificial genetic polymers against human pathologies

Originally discovered by Nielsen in 1991, peptide nucleic acids and other artificial genetic polymers have gained a lot of interest from the scientific community. Due to their unique biophysical features these artificial hybrid polymers are now being employed in various areas of theranostics (therapy and diagnostics). The current review provides an overview of their structure, principles of rational design, and biophysical features as well as highlights the areas of their successful implementation in biology and biomedicine. Finally, the review discusses the areas of improvement that would allow their use as a new class of therapeutics in the future.

Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens

Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.

Aza-PNA: Engineering E-Rotamer Selectivity Directed by Intramolecular H-bonding

The replacement of α(CH₂) by NH in monomers of standard aeg PNA and its homologue β-ala PNA leads to respective aza-PNA monomers (1 and 2) in which the N_αH can form either an 8-membered H-bonded ring with folding of the backbone (DMSO and water) or a 5-membered N_αH─αCO (water) to stabilize E-type rotamers. Such aza-PNA oligomers with exclusive E rotamers and intraresidue backbone H-bonding can modulate its DNA/RNA binding and assembling properties.

Perspectives on conformationally constrained peptide nucleic acid (PNA): insights into the structural design, properties and applications

Peptide nucleic acid or PNA is a synthetic DNA mimic that contains a sequence of nucleobases attached to a peptide-like backbone derived from N-2-aminoethylglycine. The semi-rigid PNA backbone acts as a scaffold that arranges the nucleobases in a proper orientation and spacing so that they can pair with their complementary bases on another DNA, RNA, or even PNA strand perfectly well through the standard Watson-Crick base-pairing. The electrostatically neutral backbone of PNA contributes to its many unique properties that make PNA an outstanding member of the xeno-nucleic acid family. Not only PNA can recognize its complementary nucleic acid strand with high affinity, but it does so with excellent specificity that surpasses the specificity of natural nucleic acids and their analogs. Nevertheless, there is still room for further improvements of the original PNA in terms of stability and specificity of base-pairing, direction of binding, and selectivity for different types of nucleic acids, among others. This review focuses on attempts towards the rational design of new generation PNAs with superior performance by introducing conformational constraints such as a ring or a chiral substituent in the PNA backbone. A large collection of conformationally rigid PNAs developed during the past three decades are analyzed and compared in terms of molecular design and properties in relation to structural data if available. Applications of selected modified PNA in various areas such as targeting of structured nucleic acid targets, supramolecular scaffold, biosensing and bioimaging, and gene regulation will be highlighted to demonstrate how the conformation constraint can improve the performance of the PNA. Challenges and future of the research in the area of constrained PNA will also be discussed.

Synthesis of Bifacial Peptide Nucleic Acids with Diketopiperazine Backbones

We report a synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases, as well as native bases. To examine the structure-function scope of DKP bPNAs, we synthesized a set of bPNAs by using diaminopropionic acid, diaminobutyric acid, ornithine, and lysine derivatives to display the base-tripling motifs, which result in one, two, three, or four carbons linking the alpha carbon to the side-chain amine. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal side-chain linkage was four carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per side-chain were prepared through double reductive alkylation of the ε-amine of Fmoc-lysine with acetaldehyde derivatives of adenine, cytidine, uridine, and melamine. With these building blocks in hand, DKP bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine- and melamine-displaying bPNAs to T-rich DNAs of noncanonical structure, though full characterization of this behavior is ongoing. The convenient and potentially scalable method described enables rapid access to DNA-binding scaffolds of low (<1 kD) molecular weight and previously established cell permeability. We expect that this straightforward and efficient approach to nucleic acid binders will enable studies on noncanonical nucleic acid hybridization.

Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA

We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.

Sequence-Specific Recognition of Double-Stranded DNA by Peptide Nucleic Acid Forming Double-Duplex Invasion Complex

Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids via Watson–Crick base pairing since there is no electrostatic repulsion between PNA and DNA·RNA. With this high nucleic acid affinity, PNAs have been used in a wide range of fields, from biological applications such as gene targeting, to engineering applications such as probe and sensor developments. In addition to single-stranded DNA, PNA can also recognize double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is hard to achieve with other artificial nucleic acids and is expected to be a promising method to recognize dsDNA in cellula or in vivo since the invasion does not require the prior denaturation of dsDNA. In this paper, we provide basic knowledge of PNA and mainly focus on the research of PNA invasion.

Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.

Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs

General design principles for recognition at noncanonical interfaces of DNA and RNA remain elusive. Triplex hybridization of bifacial peptide nucleic acids (bPNAs) with oligo-T/U DNAs and RNAs is a robust recognition platform that can be used to define structure-function relationships in synthetic triplex formation. To this end, a set of minimal (mw < 1 kD) bPNA variants was synthesized to probe the impact of amino acid secondary structural propensity, stereochemistry, and backbone cyclization on hybridization with short, unstructured T-rich DNA and U-rich RNAs. Thermodynamic parameters extracted from optical melting analyses of bPNA variant hybrids indicated that there are two bPNA backbone modifications that significantly improve hybridization: alternating (d, l) configuration in open-chain dipeptides and homochiral dipeptide cyclization to diketopiperazine. Further, binding to DNA is preferred over RNA for all bPNA variants. Thymine-uracil substitutions in DNA substrates revealed that the methyl group of thymine accounts for 71% of ΔΔGDNA-RNA for open-chain bPNAs but only 40% of ΔΔGDNA-RNA for diketopiperazine bPNA, suggesting a greater sensitivity to RNA conformation and more optimized stacking in the cyclic bPNA. Together, these data reveal pressure points for tuning triplex hybridization at the chiral centers of bPNA, backbone conformation, stacking effects at the base triple, and the nucleic acid substrate itself. A structural blueprint for enhancing bPNA targeting of both DNA and RNA substrates includes syndiotactic base presentation (as found in homochiral diketopiperazines and d, l peptides), expansion of base stacking, and further investigation of bPNA backbone preorganization.

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.

An alternative label-free DNA sensor based on the alternating-current electroluminescent device for simultaneous detection of human immunodeficiency virus and hepatitis C co-infection

Coinfection of HIV/HCV is a significant public health issue globally, as it increases the risk of liver cancer in co-infected individuals. The point-of-care testing (POCT) device for HIV/HCV DNA detection is promptly needed for diagnosis and monitoring of the disease progression. Here, the alternating-current electroluminescence (ACEL) technique is proposed as a sensitive POCT sensing platform for HIV/HCV cDNA detection. A conductance-based light emission modulated by the hybridization between a pyrrolidinyl PNA probe and the DNA target enabled the DNA detection in a label-free format. Enhanced electroluminescence was observed in the presence of the target DNA due to the increased proton conductivity. Under the optimal conditions, the linearity range from 1 nM to 1 μM was achieved for HIV and HCV cDNA with LODs of 1.86 pM (HIV cDNA) and 1.96 pM (HCV cDNA). The spiked HIV/HCV cDNA in healthy human serum was successfully detected, demonstrating the feasibility of the developed device for the detection of cDNA in real biological samples. Additionally, simultaneous HIV/HCV cDNA detection on a single ACEL device employing a 2x2-array detection zone design. The cross-reactivity with other viral DNA was shown to be minimal due to the high specificity of the PNA probes used. Finally, the negative and positive samples from the patient's serum were tested and the results were in 100% agreement with the commercial kit based-on real-time PCR method, thus illustrating the high sensitivity and specificity of the developed sensor.

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.

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.

Emerging self-assembling peptide nanomaterial for anti-cancer therapy

Recently it is mainly focused on anti-tumor comprehensive treatments like finding target tumor cells or activating immune cells to inhibit tumor recurrence and metastasis. At present, chemotherapy and molecular-targeted drugs can inhibit tumor cell growth to a certain extent. However, multi-drug resistance and immune escape often make it difficult for new drugs to achieve expected effects. Peptide hydrogel nanoparticles is a new type of biological material with functional peptide chains as the core and self-assembling peptide (SAP) as the framework. It has a variety of significant biological functions, including effective local inflammation suppression and non-drug-resistant cell killing. Besides, it can induce immune activation more persistently in an adjuvant independent manner when compared with simple peptides. Thus, SAP nanomaterial has great potential in regulating cell physiological functions, drug delivery and sensitization, vaccine design and immunotherapy. Not only that, it is also a potential way to focus on some specific proteins and cells through peptides, which has already been examined in previous research. A full understanding of the function and application of SAP nanoparticles can provide a simple and practical strategy for the development of anti-tumor drugs and vaccine design, which contributes to the historical transition of peptide nanohydrogels from bench to bedside and brings as much survival benefits as possible to cancer patients.

Pyrrolidinyl peptide nucleic acids bearing hydroxy-modified cyclobutane building blocks: Synthesis and binding properties

The conformationally constrained pyrrolidinyl PNA with a dipeptide consisting of an alternating nucleobase-modified D-proline and a cyclic β-amino acid "spacer" exhibited improved nucleic acid binding properties compared to the original PNA. The pyrrolidinyl PNA with the four-membered ring spacer (1S,2S)-2-aminocyclobutanecarboxylic acid (acbcPNA) are among the best performed members of the pyrrolidinyl PNA family. However, these PNA suffer some limitations such as aqueous solubility and non-specific interactions due to their extreme hydrophobicity. In the present work, a hydroxy group is introduced onto the cyclobutane ring spacer of the acbcPNA with the aim of decreasing its hydrophobicity. To this end, a Fmoc/tBu ether-protected 4-hydroxy-2-aminocyclobutanecarboxylic acid building block was synthesized and resolved by chiral HPLC. Each enantiomer was used to synthesize the hydroxy-modified acbcPNA employing Fmoc solid-phase peptide synthesis. DNA/RNA binding studies indicated that the introduction of the hydroxy group to the acbcPNA decreases the binding affinity toward complementary DNA and RNA while maintaining the sequence and directional specificity of unmodified acbcPNA. The hydrophobicity of the hydroxy-modified acbcPNA decreased with the number of hydroxy groups added as indicated by the decrease in the logP values. Only two modifications were sufficient to decrease the logP by an order of magnitude without excessively lowering the binding affinity nor the specificity. This work thus demonstrated that the specific structural modifications for this type of PNA model can be performed in a modular fashion, which paves the way toward the future realization of improving hydrophilicity and nucleic acid binding affinity as well as specificity.

Fluorescent paper-based DNA sensor using pyrrolidinyl peptide nucleic acids for hepatitis C virus detection

A novel fluorescent paper-based DNA sensor employing a highly specific pyrrolidinyl peptide nucleic acid (acpcPNA) probe was developed for the sensitive and selective detection of hepatitis C virus (HCV). The acpcPNA was covalently immobilized onto partially oxidized cellulose paper via reductive alkylation between the amine and the aldehyde groups. The fluorescence-based detection was performed by monitoring the fluorescence signal response of a fluorescent dye that selectively binds to the single-strand region of the DNA target over the PNA probe employing a custom-made portable fluorescent camera gadget in combination with a smartphone camera. Under the optimal conditions, a linear relationship between the fluorescence change in the green channel and the amount of HCV DNA from 5 to 100 pmol with a correlation coefficient of 0.9956, and the limit of detection of 5 pmol were obtained for short synthetic oligonucleotides. The acpcPNA probe exhibited very high selectivity for the complementary oligonucleotides over the single-base-mismatched, two-base-mismatched, and non-complementary DNA targets. Benefitting from the signal amplification achieved through the numerous binding sites for the dye provided by the overhanging tail of long ssDNA target sequences, this system was successfully applied to detect the HCV complementary DNA (cDNA) obtained from clinical samples with satisfactory results. The proposed fluorescent paper-based sensor demonstrated a great potential to be used as a low-cost, simple, label-free, sensitive, and selective DNA sensor for point-of-care applications.

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.

Isothermal Detection of Canine Blood Parasite (Ehrlichia canis) Utilizing Recombinase Polymerase Amplification Coupled with Graphene Oxide Quenching-Based Pyrrolidinyl Peptide Nucleic Acid

Canine monocytic ehrlichiosis (CME), caused by transmitted Ehrlichia canis infection, is a major disease in dogs with worldwide distribution. Herein, a nucleic acid assay was established for the identification of E. canis infection employing a fluorescently labeled conformationally constrained pyrrolidinyl PNA probe (Flu-acpcPNA) designed to sequence-specifically target the 16S rRNA gene. The sensing principle is based on the excellent quenching ability of graphene oxide (GO) of the free PNA probe, that was diminished upon binding to the DNA target. The addition of DNase I improved the performance of the detection system by eliminating the nonspecific quenching capability of long-chain dsDNA and thus enhancing the fluorescence signaling. The assay was coupled with a recombinase polymerase amplification (RPA) technique, which could be performed under isothermal conditions (37 °C) without DNA denaturation and purification steps. The established method is simple to set up and execute, proving a rapid, specific, and sensitive detection of 16S rRNA gene of E. canis with a limit of detection at least 11.1 pM. This technique shows good potential for the visual detection of double-stranded DNA targets without the need for PCR or complicated instruments, which shows great promise for practical usage in resource limited areas.

Synthesis of Pyrrolidinyl PNA and Its Site-Specific Labeling at Internal Positions by Click Chemistry

Pyrrolidinyl PNA with an α-/β-dipeptide backbone consisting of alternating nucleobase-modified D-proline and (1S,2S)-2-aminocyclopentanecarboxylic acid (also known as acpcPNA) is a class of conformationally constrained PNA that shows exceptional DNA hybridization properties including very high specificity and the inability to form self-pairing hybrids. In this chapter, details of the syntheses of acpcPNA as well as its monomers and a protocol for site-specific labeling with a fluorescent dye via click chemistry are reported.

Paper-based DNA sensor enabling colorimetric assay integrated with smartphone for human papillomavirus detection

A colorimetric paper-based DNA sensor that relies on the inhibition of PNA-induced AuNPs aggregation was combined with a simple smartphone readout for the point-of-care detection of HPV type 16 DNA.

Gem-dimethyl peptide nucleic acid (α/β/γ-gdm-PNA) monomers: synthesis and the role of gdm-substituents in preferential stabilisation of Z/E-rotamers

The flexible backbone of aminoethylglycine (aeg) PNA upon substitution becomes sterically constrained to enable conformational pre-organization for preferential binding to DNA or RNA. The bulky gem-dimethyl (gdm) substituent on carbons adjacent to the t-amide sidechain either at Cα (glycyl) or Cβ/Cγ (aminoethylene) sides may influence the Z/E rotamer ratio arising from a restricted rotation around the t-amide bond. Employing 2D NMR (NOESY), it is shown here that the Cα-gdm-PNA-T monomer exhibits exclusively the Z-rotamer, while the Cβ-gdm-PNA-T monomer shows only the E-rotamer. The unsubstituted aeg-PNA-T and Cγ-gdm-PNA-T monomers display a mixture of Z/E rotamers. The rotamers with t-amide carbonyl pointing towards the gem-dimethyl group always prevailed. The results are supported by computational studies that suggested that the preferred rotamers are the outcome of a net energetic benefit from the stabilising n-π* interactions of carbonyls (amide backbone and t-amide sidechain), and C-HO interactions and the destabilising steric clash of gem-dimethyl groups with the t-amido methylene group. The E-rotamer structure in Cγ-gdm is also characterised by X-ray crystallography. The exclusive E-rotamer for the Cβ-gdm monomer seen in solution here is the first such example among several modified PNA monomers. Since the conformation of the sidechain is important for inducing base stacking and effective base pairing, the exclusive E-rotamer in the Cβ-gdm monomer may have significance in the properties of the derived PNA : DNA/RNA duplexes with all E-rotamers.

Investigation of the Characteristics of NLS-PNA: Influence of NLS Location on Invasion Efficiency

Peptide nucleic acid can recognise sequences in double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is a promising method for the recognition of dsDNA in cellula because peptide nucleic acid (PNA) invasion does not require the prior denaturation of dsDNA. To increase its applicability, we developed PNAs modified with a nuclear localisation signal (NLS) peptide. In this study, the characteristics of NLS-modified PNAs were investigated for the future design of novel peptide-modified PNAs.

Pyrrolidinyl Peptide Nucleic Acid Probes Capable of Crosslinking with DNA: Effects of Terminal and Internal Modifications on Crosslink Efficiency

In this study, we describe a furan-modified acpcPNA as a probe that can form an interstrand crosslink (ICL) with its DNA target upon activation with N-bromosuccinimide (NBS). To overcome the problem of furan instability under acidic conditions, a simple and versatile post-synthetic methodology for the attachment of the furan group to the PNA probe was developed. Unlike in other designs, the furan was placed at the end of the PNA molecule or tethered to the PNA backbone with all the base pairs in the PNA ⋅ DNA duplexes fully preserved. Hence, the true reactivity of each nucleobase towards the crosslinking could be compared. We show that all DNA bases except T could participate in the crosslinking reaction when the furan was placed at the end of the PNA strand. The crosslinking process was sensitive to mispairing, and lower crosslinking efficiency was observed in the presence of a base-mismatch in the PNA ⋅ DNA duplex. In contrast, when the furan was placed at internal positions of the acpcPNA ⋅ DNA duplex, no ICL was observed; this was explained by the inability of a hydrogen-bonded nucleobase to participate in the crosslinking reaction. The crosslinking efficiency was considerably improved, despite lower duplex stability, when an unpaired base (in the form of C-insertion) was present in the complementary DNA strand close to the furan modification site.

Selective enrichment of zein gene of maize from cereal products using magnetic support having pyrrolidinyl peptide nucleic acid probe

Here, we describe DNA enrichment of the zein gene from maize using pyrrolidinyl peptide nucleic acid (PNA) immobilized on a magnetic solid support as a capture element. Magnetite nanoparticles (MNP) with a capacity of 373 pmolPNA/mg and coated with poly(N-acryloylglycine) (PNAG) showed a good response to magnetic field. The PNA probe immobilized on the MNP discriminated between non-complementary and complementary DNA using fluorophore-tagged DNA as a model. We applied this system for the enrichment of the zein gene from maize in eight cereal product samples. After DNA desorption from the MNP, and its amplification via polymerase chain reaction (PCR), gel electrophoresis indicated that only cereal samples containing the zein gene from maize yielded positive results, indicating a high binding specificity between the PNA used and the complementary DNA. This PNA-functionalized MNP is potentially useful as an effective nano-solid support for DNA enrichment from other samples.

Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we present a hitherto unreported high-efficiency quenching (up to 90%) of various fluorescently labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probes by oligodeoxyguanosine (dGX). The quenching principle relies on the electrostatic interaction between the positively charged lysine-modified acpcPNA probe and the negatively charged oligodeoxyguanosine. The addition of stoichiometric quantities of a DNA target with the sequence complementary to the PNA probe restored the fluorescence to the original level. This was explained by the binding of the DNA to the PNA via a specific base pairing, which resulted in the separation of the oligodeoxyguanosine quencher from the fluorophore. Much less fluorescence restoration was observed in the DNA containing one or more mismatched bases. Applications of the oligodeoxyguanosine-quenched PNA probes for DNA sequence determination, including in multiplex formats, are demonstrated. The performance in terms of sensitivity and mismatch discrimination is comparable to classical PNA-based molecular beacons but without the need for double-labeling, which is expensive and presents solubility issues, or a dedicated quencher probe. This exemplifies a novel use of the unique electrostatic properties of PNA to develop a DNA sensing platform for DNA sequence determination.

Peptide Nucleic Acids: Applications in Biomedical Sciences

The DNA mimic, PNA (peptide nucleic acid), has been with us now for almost 3 decades [...].

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.

Clickable styryl dyes for fluorescence labeling of pyrrolidinyl PNA probes for the detection of base mutations in DNA

Fluorescent hybridization probes are important tools for rapid, specific and sensitive analysis of genetic mutations. In this work, we synthesized novel alkyne-modified styryl dyes for conjugation with pyrrolidinyl peptide nucleic acid (acpcPNA) by click chemistry for the development of hybridization responsive fluorescent PNA probes. The free styryl dyes generally exhibited weak fluorescence in aqueous media, and the fluorescence was significantly enhanced (up to 125-fold) upon binding with DNA duplexes. Selected styryl dyes that showed good responses with DNA were conjugated with PNA via sequential reductive alkylation-click chemistry. Although these probes showed little fluorescence change when hybridized to complementary DNA, significant fluorescence enhancements were observed in the presence of structural defects including mismatched, abasic and base-inserted DNA targets. The largest increase in fluorescence quantum yield (up to 14.5-fold) was achieved with DNA carrying base insertion. Although a number of probes were designed to give fluorescence response to complementary DNA targets, probes that are responsive to mutations such as single nucleotide polymorphism (SNP), base insertion/deletion and abasic site are less common. Therefore, styryl-dye-labeled acpcPNA is a unique probe that is responsive to structural defects in the duplexes that may be further applied for diagnostic purposes.

Triplex Hybridization of siRNA with Bifacial Glycopolymer Nucleic Acid Enables Hepatocyte-Targeted Silencing

Herein, we describe a versatile non-covalent strategy for packaging nucleic acid cargo with targeting modalities, based on triplex hybridization of oligo-uridylate RNA with bifacial polymer nucleic acid (bPoNA). Polyacrylate bPoNA was prepared and side chain-functionalized with N-acetylgalactosamine (GalNAc), which is known to enable delivery to hepatocytes and liver via binding to the asialoglycoprotein receptor (ASGPR). Polymer binding resulted in successful delivery of both native and synthetically modified siRNAs to HepG2 cells in culture, yielding in low nanomolar IC50 silencing of the endogenous ApoB target, in line with observations of expected Dicer processing of the polymer-siRNA targeting complex. Indeed, in vitro Dicer treatment of the polymer complex indicated that triplex hybridization does not impede RNA processing and release from the polymer. The complex itself elicited a quiescent immunostimulation profile relative to free RNA in a cytokine screen, setting the stage for a preliminary in vivo study in a high-calorie-diet mouse model. Gratifyingly, we observed significant ApoB silencing in a preliminary animal study, validating bPoNA as an in vivo carrier platform for systemic siRNA delivery. Thus, this new siRNA carrier platform exhibits generally useful function and is accessible through scalable synthesis. In addition to its utility as a carrier, the triplex-hybridizing synthetic platform could be useful for optimization screens of siRNA sequences using the identical polymer carriers, thus alleviating the need for covalent ligand modification of each RNA substrate.

Oligonucleotide Analogs and Mimics for Sensing Macromolecular Biocompounds

Living organisms create life-sustaining macromolecular biocompounds including biopolymers. Artificial polymers can selectively recognize biocompounds and are more resistant to harsh physical, chemical, and physiological conditions than biopolymers are. Due to recognition at a molecular level, molecularly imprinted polymers (MIPs) provide powerful tools to correlate structure with biological functionality and are often used to build next-generation chemosensors. We envision an increasing emergence of nucleic acid analogs (NAAs) or biorelevant monomers built into nature-mimicking polymers. For example, if nucleobases bearing monomers arranged by a complementary template are polymerized to form NAAs, the resulting MIPs will open up novel perspectives for synthesizing NAAs. Despite their usefulness, it is still challenging to use MIPs to devise adaptive biomaterials and to implement them in point-of-care testing.

Oligonucleotide Determination via Peptide Nucleic Acid Macromolecular Imprinting in an Electropolymerized CG-Rich Artificial Oligomer Analogue

We devised and fabricated a chemosensor for determination of the genetically relevant 5'-GCGGCGGC-3' (G = guanine; C = cytosine) oligonucleotide. For that, we simultaneously electrosynthesized and electrode-immobilized a sequence-defined octakis(2,2'-bithien-5-yl) DNA hybridizing probe using both a "macromolecular imprinting in polymer strategy" and a sequence-programmable peptide nucleic acid (PNA) template. With electrochemical impedance spectroscopy (EIS) and surface plasmon resonance (SPR) transductions under stagnant-solution and flow injection analysis (FIA) conditions, respectively, we determined the above oligonucleotide with 200-pM EIS limit of detection. With its EIS-determined apparent imprinting factor of ∼4.0, the chemosensor was discriminative to both mismatched oligonucleotides and Dulbecco's modified Eagle's medium sample interferences.

Electrochemical impedance-based DNA sensor using pyrrolidinyl peptide nucleic acids for tuberculosis detection

A label-free electrochemical DNA sensor based on pyrrolidinyl peptide nucleic acid (acpcPNA)-immobilized on a paper-based analytical device (PAD) was developed. Unlike previous PNA-based electrochemical PAD (ePAD) sensors where the capture element was placed directly on the electrode, acpcPNA was covalently immobilized onto partially oxidized cellulose paper allowing regeneration by simple PAD replacement. As an example application, a sensor probe was designed for Mycobacterium tuberculosis (MTB) detection. The ePAD DNA sensor was used to determine a synthetic 15-base oligonucleotide of MTB by measuring the fractional change in the charge transfer resistance (R_ct) obtained from electrochemical impedance spectroscopy (EIS). The R_ct of [Fe(CN)₆]^3-/4- before and after hybridization with the target DNA could be clearly distinguished. Cyclic voltammetry (CV) was used to verify the EIS results, and showed an increase in peak potential splitting in a similar stepwise manner for each immobilization step. Under optimal conditions, a linear calibration curve in the range of 2-200 nM and the limit of detection 1.24 nM were measured. The acpcPNA probe exhibited very high selectivity for complementary oligonucleotides over single-base-mismatch, two-base-mismatch and non-complementary DNA targets due to the conformationally constrained structure of the acpcPNA. Moreover, the ePAD DNA sensor platform was successfully applied to detect PCR-amplified MTB DNA extracted from clinical samples. The proposed paper-based electrochemical DNA sensor has potential to be an alternative device for low-cost, simple, label-free, sensitive and selective DNA sensor.

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.