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Special Issue "Molecular Properties and the Applications of Peptide Nucleic Acids"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (15 November 2017)

Special Issue Editor

Guest Editor
Prof. Dr. Roberto Corradini

Dipartimento di Chimica, Università di Parma, Parma, Italy
Website | E-Mail
Interests: bioorganic chemistry; nucleic acid recognition; peptide nucleic acids; chirality; stereochemistry; supramolecular chemistry; anti-miR; anti-gene; biosensing technologies

Special Issue Information

Dear Colleagues,

After 25 years since their discovery, peptide nucleic acids (PNAs) are still a source of intense inspiration for scientists. Their properties and applications are actively being studied in different fields, from fundamental Chemistry to Biology, Medicine and Material Chemistry, with more than 100 papers published on this topic and more than 5000 citations every year.

As biomolecular tools, PNAs have intriguing properties, with exceptional affinities and sequence selectivities, high biological and chemical stability, and thus high persistence in biological fluids. Due to the relatively scarce structural data, the nature of PNA:DNA and PNA:RNA interactions, and the effect of chemical variation on PNA properties is still an open field of research. The quest for even better binding affinity and sequence selectivity is not over yet, and both modelling techniques and modern synthetic procedures can be fruitfully applied to the design and synthesis of new molecules based on the PNA scaffold. Using a ‘biomolecular engineering’ approach, new functions, in addition to DNA recognition, can be added to PNAs, e.g., cleaving activity, or signalling. In cellular systems, PNAs have proven to be very effective for the regulation of gene expression, especially for applications in which an appropriate cellular delivery system is used. In diagnostics, PNAs are the base of several new ultrasensitive and very specific techniques.

PNAs can also be useful in nanofabrication and in material chemistry as programmable objects that are able to self assemble with a rational scheme. Helical handedness can be controlled in these systems much more easily than in other DNA analogs.

We intend to capture a full picture of this field of research in the journal Molecules with a dedicated Special Issue to be published in 2017. We invite contributions from scientists in all of these areas of research.

Prof. Dr. Roberto Corradini
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • PNA
  • modified PNA
  • DNA and RNA recognition
  • delivery systems
  • antisense
  • antigene
  • anti-miR
  • artificial nucleases
  • molecular  modelling
  • molecular dynamics
  • solid-phase synthesis
  • genosensing
  • ultrasensitive techniques

Published Papers (8 papers)

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Research

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Open AccessArticle DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity
Molecules 2017, 22(11), 1991; doi:10.3390/molecules22111991
Received: 29 September 2017 / Revised: 27 October 2017 / Accepted: 3 November 2017 / Published: 16 November 2017
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Abstract
The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence
[...] Read more.
The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA–PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca2+, and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessArticle Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region
Molecules 2017, 22(11), 1922; doi:10.3390/molecules22111922
Received: 26 September 2017 / Revised: 3 November 2017 / Accepted: 3 November 2017 / Published: 7 November 2017
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Abstract
Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen
[...] Read more.
Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia-derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessArticle Detection of Rare Somatic GNAS Mutation in McCune-Albright Syndrome Using a Novel Peptide Nucleic Acid Probe in a Single Tube
Molecules 2017, 22(11), 1874; doi:10.3390/molecules22111874
Received: 29 August 2017 / Revised: 23 October 2017 / Accepted: 30 October 2017 / Published: 1 November 2017
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Abstract
McCune-Albright syndrome (MAS) is characterized by the triad of precocious puberty, café au lait pigmentation, and polyostotic fibrous dysplasia (FD) of bone, and is caused by post-zygotic somatic mutations—R201H or R201C—in the guanine nucleotide binding protein, alpha stimulating (GNAS) gene. In the present
[...] Read more.
McCune-Albright syndrome (MAS) is characterized by the triad of precocious puberty, café au lait pigmentation, and polyostotic fibrous dysplasia (FD) of bone, and is caused by post-zygotic somatic mutations—R201H or R201C—in the guanine nucleotide binding protein, alpha stimulating (GNAS) gene. In the present study, a novel peptide nucleic acid (PNA) probe with fluorescent labeling was designed to detect trace amounts of somatic mutant GNAS in a single tube reaction. The method was applied to screen GNAS mutations in six patients with MAS/FD. The results showed that the PNA probe assay could detect low abundant mutants in 200-fold excess of wild-type alleles. The GNAS mutation was found in three patients with severe disease (MAS) by using the assay. The other three patients with mild disease (having only FD) showed a wild-type result. This study has provided a simple method to detect trace amounts of GNAS mutants with high sensitivity in large amounts of wild-type DNA. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessFeature PaperArticle Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA—Bulge Size and Sequence Dependence
Molecules 2017, 22(11), 1856; doi:10.3390/molecules22111856
Received: 5 October 2017 / Revised: 25 October 2017 / Accepted: 27 October 2017 / Published: 29 October 2017
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Abstract
In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the
[...] Read more.
In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the bulge formed upon binding to the PNAzyme. PNAzyme-promoted cleavage of the target RNAs was observed and variation of the substrate showed a clear dependence on the sequence and size of the bulge. For targets that form 4-nt bulges, we identified systems with an improved efficacy (an estimated half-life of ca 7–8 h as compared to 11–12 h for sequences studied earlier) as well as systems with an improved site selectivity (up to over 70% cleavage at a single site as compared to 50–60% with previous targets sequences). For targets forming 3-nt bulges, the enhancement compared to previous systems was even more pronounced. Compared to a starting point of targets forming 3-nt AAA bulges (half-lives of ca 21–24 h), we could identify target sequences that were cleaved with half-lives three times lower (ca 7–8 h), i.e., at rates similar to those found for the fastest 4-nt bulge system. In addition, with the 3-nt bulge RNA target site selectivity was improved even further to reach well over 80% cleavage at a specific site. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessArticle Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA
Molecules 2017, 22(11), 1840; doi:10.3390/molecules22111840
Received: 12 September 2017 / Revised: 18 October 2017 / Accepted: 21 October 2017 / Published: 27 October 2017
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Abstract
DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages
[...] Read more.
DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated azobenzene linker gave a stable 1:1 TC-PNA/ssDNA complex and exhibited good mismatch recognition. Our design for TC-PNA-AZO can be utilized for detecting homopurine sequences in various genes. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessArticle Peptide Nucleic Acids as miRNA Target Protectors for the Treatment of Cystic Fibrosis
Molecules 2017, 22(7), 1144; doi:10.3390/molecules22071144
Received: 31 May 2017 / Revised: 3 July 2017 / Accepted: 4 July 2017 / Published: 8 July 2017
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Abstract
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR,
[...] Read more.
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs. Herein, for the first time, is proposed the use of peptide nucleic acids (PNAs) to protect specific sequences in the 3’UTR (untranslated region) of the CFTR messenger RNA (mRNA) by action of miRNAs. Two PNAs (7 and 13 bases long) carrying the tetrapeptide Gly-SerP-SerP-Gly at their C-end, fully complementary to the 3’UTR sequence recognized by miR-509-3p, have been synthesized and the structural features of target PNA/RNA heteroduplexes have been investigated by spectroscopic and molecular dynamics studies. The co-transfection of the pLuc-CFTR-3´UTR vector with different combinations of PNAs, miR-509-3p, and controls in A549 cells demonstrated the ability of the longer PNA to rescue the luciferase activity by up to 70% of the control, thus supporting the use of suitable PNAs to counteract the reduction in the CFTR expression. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Review

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Open AccessReview Peptide Nucleic Acid-Based Biosensors for Cancer Diagnosis
Molecules 2017, 22(11), 1951; doi:10.3390/molecules22111951
Received: 18 October 2017 / Revised: 6 November 2017 / Accepted: 9 November 2017 / Published: 11 November 2017
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Abstract
The monitoring of DNA and RNA biomarkers freely circulating in the blood constitutes the basis of innovative cancer detection methods based on liquid biopsy. Such methods are expected to provide new opportunities for a better understanding of cancer disease at the molecular level,
[...] Read more.
The monitoring of DNA and RNA biomarkers freely circulating in the blood constitutes the basis of innovative cancer detection methods based on liquid biopsy. Such methods are expected to provide new opportunities for a better understanding of cancer disease at the molecular level, thus contributing to improved patient outcomes. Advanced biosensors can advance possibilities for cancer-related nucleic acid biomarkers detection. In this context, peptide nucleic acids (PNAs) play an important role in the fabrication of highly sensitive biosensors. This review provides an overview of recently described PNA-based biosensors for cancer biomarker detection. One of the most striking features of the described detection approaches is represented by the possibility to detect target nucleic acids at the ultra-low concentration with the capability to identify single-base mutations. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Open AccessFeature PaperReview Applications of PNA-Based Artificial Restriction DNA Cutters
Molecules 2017, 22(10), 1586; doi:10.3390/molecules22101586
Received: 2 September 2017 / Revised: 16 September 2017 / Accepted: 18 September 2017 / Published: 21 September 2017
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Abstract
More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In
[...] Read more.
More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In this article, recent progress of these man-made tools have been reviewed. By cutting the human genome site-selectively, desired fragments can be clipped from either the termini of chromosomes (telomeres) or from the middle of genome. These fragments should provide important information on the biological functions of complicated genome system. DNA/RNA hybrid duplexes, which are formed in living cells, are also site-selectively hydrolyzed by these cutters. In order to further facilitate the applications of the artificial DNA cutters, various chemical modifications have been attempted. One of the most important successes is preparation of PNA derivatives which can form double-duplex invasion complex even under high salt conditions. This is important for in vivo applications, since the inside of living cells is abundant of metal ions. Furthermore, site-selective DNA cutters which require only one PNA strand, in place of a pair of pcPNA strands, are developed. This progress has opened a way to new fields of PNA-based biochemistry and biotechnology. Full article
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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