1
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Singh G, Monga V. Peptide Nucleic Acids: Recent Developments in the Synthesis and Backbone Modifications. Bioorg Chem 2023; 141:106860. [PMID: 37748328 DOI: 10.1016/j.bioorg.2023.106860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
Nucleic acid represents the ideal drug candidate for protein targets that are hard to target or against which drug development is not easy. Peptide nucleic acids (PNAs) are synthesized by attaching modified peptide backbones generally derived from repetitive N-2-aminoethyl glycine units in place of the regular phosphodiester backbone and represent synthetic impersonator of nucleic acids that offers an exciting research field due to their fascinating spectrum of biotechnological, diagnostic and potential therapeutic applications. The semi-rigid peptide nucleic acid backbone serves as a nearly-perfect template for attaching complimentary base pairs on DNA or RNA in a sequence-dependent manner as described by Watson-Crick models. PNAs and their analogues are endowed with exceptionally high affinity and specificity for receptor sites, essentially due to their polyamide backbone's uncharged and flexible nature. The present review compiled various strategies to modify the polypeptide backbone for improving the target selectivity and stability of the PNAs in the body. The investigated biological activities carried out on PNAs have also been summarized in the present review.
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Affiliation(s)
- Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, GT Road, Ghal Kalan, Moga 142001, Punjab, India
| | - Vikramdeep Monga
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, VPO-Ghudda, Bathinda 151401, Punjab, India.
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2
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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3
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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4
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Samaan GN, Wyllie MK, Cizmic JM, Needham LM, Nobis D, Ngo K, Andersen S, Magennis SW, Lee SF, Purse BW. Single-molecule fluorescence detection of a tricyclic nucleoside analogue. Chem Sci 2020; 12:2623-2628. [PMID: 34164030 PMCID: PMC8179283 DOI: 10.1039/d0sc03903a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε442 = 20 000 M−1 cm−1 and Φem,540 = 0.39 in water, increasing to Φem = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. Fluorescent nucleoside analogue ABN is readily detected at the single-molecule level and retains a quantum yield >50% in duplex DNA oligonucleotides.![]()
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Affiliation(s)
- George N Samaan
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Mckenzie K Wyllie
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Julian M Cizmic
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Lisa-Maria Needham
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - David Nobis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Katrina Ngo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Susan Andersen
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Steven W Magennis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Steven F Lee
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
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5
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Antibacterial Peptide Nucleic Acids-Facts and Perspectives. Molecules 2020; 25:molecules25030559. [PMID: 32012929 PMCID: PMC7038079 DOI: 10.3390/molecules25030559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is an escalating, worldwide problem. Due to excessive use of antibiotics, multidrug-resistant bacteria have become a serious threat and a major global healthcare problem of the 21st century. This fact creates an urgent need for new and effective antimicrobials. The common strategies for antibiotic discovery are based on either modifying existing antibiotics or screening compound libraries, but these strategies have not been successful in recent decades. An alternative approach could be to use gene-specific oligonucleotides, such as peptide nucleic acid (PNA) oligomers, that can specifically target any single pathogen. This approach broadens the range of potential targets to any gene with a known sequence in any bacterium, and could significantly reduce the time required to discover new antimicrobials or their redesign, if resistance arises. We review the potential of PNA as an antibacterial molecule. First, we describe the physicochemical properties of PNA and modifications of the PNA backbone and nucleobases. Second, we review the carriers used to transport PNA to bacterial cells. Furthermore, we discuss the PNA targets in antibacterial studies focusing on antisense PNA targeting bacterial mRNA and rRNA.
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Lawson CP, Füchtbauer AF, Wranne MS, Giraud T, Floyd T, Dumat B, Andersen NK, H El-Sagheer A, Brown T, Gradén H, Wilhelmsson LM, Grøtli M. Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue. Sci Rep 2018; 8:13970. [PMID: 30228309 PMCID: PMC6143597 DOI: 10.1038/s41598-018-31897-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022] Open
Abstract
Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1 in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Tristan Giraud
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Thomas Floyd
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Nicolai K Andersen
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Henrik Gradén
- Cardiovascular, Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, Molndal, SE-431 83, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden.
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7
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Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
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8
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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9
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Wu JC, Meng QC, Ren HM, Wang HT, Wu J, Wang Q. Recent advances in peptide nucleic acid for cancer bionanotechnology. Acta Pharmacol Sin 2017; 38:798-805. [PMID: 28414202 DOI: 10.1038/aps.2017.33] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/04/2017] [Indexed: 02/07/2023] Open
Abstract
Peptide nucleic acid (PNA) is an oligomer, in which the phosphate backbone has been replaced by a pseudopeptide backbone that is meant to mimic DNA. Peptide nucleic acids are of the utmost importance in the biomedical field because of their ability to hybridize with neutral nucleic acids and their special chemical and biological properties. In recent years, PNAs have emerged in nanobiotechnology for cancer diagnosis and therapy due to their high affinity and sequence selectivity toward corresponding DNA and RNA. In this review, we summarize the recent progresses that have been made in cancer detection and therapy with PNA biotechnology. In addition, we emphasize nanoparticle PNA-based strategies for the efficient delivery of drugs in anticancer therapies.
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10
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Schade A, Schreiter K, Rüffer T, Lang H, Spange S. Interactions of Enolizable Barbiturate Dyes. Chemistry 2016; 22:5734-48. [DOI: 10.1002/chem.201504932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander Schade
- Technische Universität Chemnitz; Department of Polymer Chemistry; 09107 Chemnitz Germany), Fax: (+49) 371-531-21239
| | - Katja Schreiter
- Technische Universität Chemnitz; Department of Polymer Chemistry; 09107 Chemnitz Germany), Fax: (+49) 371-531-21239
| | - Tobias Rüffer
- Technische Universität Chemnitz; Department of Inorganic Chemistry; 09107 Chemnitz Germany
| | - Heinrich Lang
- Technische Universität Chemnitz; Department of Inorganic Chemistry; 09107 Chemnitz Germany
| | - Stefan Spange
- Technische Universität Chemnitz; Department of Polymer Chemistry; 09107 Chemnitz Germany), Fax: (+49) 371-531-21239
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11
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Kiliszek A, Banaszak K, Dauter Z, Rypniewski W. The first crystal structures of RNA-PNA duplexes and a PNA-PNA duplex containing mismatches--toward anti-sense therapy against TREDs. Nucleic Acids Res 2015; 44:1937-43. [PMID: 26717983 PMCID: PMC4770230 DOI: 10.1093/nar/gkv1513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA–PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-glutamine diseases. We also report the first PNA–PNA duplex containing mismatches. A comparison of the PNA homoduplex and the PNA–RNA heteroduplexes reveals PNA's intrinsic structural properties, shedding light on its reported sequence selectivity or intolerance of mismatches when it interacts with nucleic acids. PNA has a much lower helical twist than RNA and the resulting duplex has an intermediate conformation. PNA retains its overall conformation while locally there is much disorder, especially peptide bond flipping. In addition to the Watson–Crick pairing, the structures contain interesting interactions between the RNA's phosphate groups and the Π electrons of the peptide bonds in PNA.
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Affiliation(s)
- Agnieszka Kiliszek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Banaszak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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12
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Autiero I, Saviano M, Langella E. Molecular dynamics simulations of PNA-PNA and PNA-DNA duplexes by the use of new parameters implemented in the GROMACS package: a conformational and dynamics study. Phys Chem Chem Phys 2014; 16:1868-74. [PMID: 24327011 DOI: 10.1039/c3cp54284j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Peptide Nucleic Acids (PNAs) still represent a growing research area thanks to their potential applications in many fields of science from chemistry and biology to medicine. In these years, structural investigations by means of either experimental or computational techniques have proved to be very useful for the understanding of the structural organization and the binding properties of PNA. In this context, we here report an all-atoms Molecular Dynamics (MD) study of a PNA-PNA duplex and a PNA-DNA hetero-duplex with the well known GROMACS simulation package, by using new force field parameters properly derived for PNA molecules. The good agreement of our results with the crystallographic and NMR data, available for both the systems under investigation, confirms the validity of our approach. Moreover, our simulations reveal new interesting features related to the conformational-dynamic behavior of the studied systems, thus demonstrating the ability of MD simulations to gain insights into the dynamic properties of biologically relevant systems. This force field parametrization represents a good starting point for the implementation of a computational platform, based on the GROMACS package, useful for the rational design of modified PNA molecules with improved conformational features for selective binding toward DNA or RNA.
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Affiliation(s)
- Ida Autiero
- National Research Council, Institute of Biostructures and Bioimaging, 80138 Naples, Italy.
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13
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Poomsuk N, Siriwong K. Structural properties and stability of PNA with (2′R,4′R)- and (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone binding to DNA: A molecular dynamics simulation study. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Gupta SK, Sur S, Prasad Ojha R, Tandon V. Influence of PNA containing 8-aza-7-deazaadenine on structure stability and binding affinity of PNA·DNA duplex: insights from thermodynamics, counter ion, hydration and molecular dynamics analysis. MOLECULAR BIOSYSTEMS 2013; 9:1958-71. [PMID: 23636232 DOI: 10.1039/c3mb25561a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This paper describes the synthesis of a novel 8-aza-7-deazapurin-2,6-diamine (DPP)-containing peptide nucleic acid (PNA) monomer and Boc protecting group-based oligomerization of PNA, replacing adenine (A) with DPP monomers in the PNA strand. The PNA oligomers were synthesized against the biologically relevant SV40 promoter region (2494-AATTTTTTTTATTTA-2508) of pEGFP-N3 plasmid. The DPP-PNA·DNA duplex showed enhanced stability as compared to normal duplex (A-PNA·DNA). The electronic distribution of DPP monomer suggested that DPP had better electron donor properties over 2,6-diamino purine. UV melting and thermodynamic analysis revealed that the PNA oligomer containing a diaminopyrazolo(3,4-d)pyrimidine moiety (DPP) stabilized the PNA·DNA hybrids compared to A-PNA·DNA. DPP-PNA·DNA duplex showed higher water activity (Δnw = 38.5) in comparison to A-PNA·DNA duplex (Δnw = 14.5). The 50 ns molecular dynamics simulations of PNA·DNA duplex containing DPP or unmodified nucleobase-A showed average H-bond distances in the DPP-dT base pair of 2.90 Å (OH-N bond) and 2.91 Å (NH-N bond), which were comparably shorter than in the A-dT base pair, in which the average distances were 3.18 Å (OH-N bond) and 2.97 Å (NH-N bond), and there was one additional H-bond in the DPP-dT base pair of around 2.98 Å (O2H-N2 bond), supporting the higher stability of DPP-PNA·DNA. The analysis of molecular dynamics simulation data showed that the system binding free energy increased at a rate of approximately -4.5 kcal mol(-1) per DPP base of the PNA·DNA duplex. In summary, increased thermal stability, stronger hydrogen bonding and more stable conformation in the DPP-PNA·DNA duplex make it a better candidate as antisense/antigene therapeutic agents.
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Affiliation(s)
- Sharad K Gupta
- Dr B. R. Ambedkar Center for Biomedical Research, Delhi, India.
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15
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Li L, Li J, Wang H, Zhang H, Fu W. Reactions of Naphthyridines with Aldehydes: Novel Derivatives with Red-Fluorescence Emissions and Two-Photon Absorptions. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201200175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Sahu B, Sacui I, Rapireddy S, Zanotti KJ, Bahal R, Armitage BA, Ly DH. Synthesis and characterization of conformationally preorganized, (R)-diethylene glycol-containing γ-peptide nucleic acids with superior hybridization properties and water solubility. J Org Chem 2011; 76:5614-27. [PMID: 21619025 PMCID: PMC3175361 DOI: 10.1021/jo200482d] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Developed in the early 1990s, peptide nucleic acid (PNA) has emerged as a promising class of nucleic acid mimic because of its strong binding affinity and sequence selectivity toward DNA and RNA and resistance to enzymatic degradation by proteases and nucleases; however, the main drawbacks, as compared to other classes of oligonucleotides, are water solubility and biocompatibility. Herein we show that installation of a relatively small, hydrophilic (R)-diethylene glycol ("miniPEG", R-MP) unit at the γ-backbone transforms a randomly folded PNA into a right-handed helix. Synthesis of optically pure (R-MP)γPNA monomers is described, which can be accomplished in a few simple steps from a commercially available and relatively cheap Boc-l-serine. Once synthesized, (R-MP)γPNA oligomers are preorganized into a right-handed helix, hybridize to DNA and RNA with greater affinity and sequence selectivity, and are more water soluble and less aggregating than the parental PNA oligomers. The results presented herein have important implications for the future design and application of PNA in biology, biotechnology, and medicine, as well as in other disciplines, including drug discovery and molecular engineering.
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Affiliation(s)
- Bichismita Sahu
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Iulia Sacui
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Kimberly J. Zanotti
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213
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Rapireddy S, Bahal R, Ly DH. Strand invasion of mixed-sequence, double-helical B-DNA by γ-peptide nucleic acids containing G-clamp nucleobases under physiological conditions. Biochemistry 2011; 50:3913-8. [PMID: 21476606 PMCID: PMC3092786 DOI: 10.1021/bi2002554] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acids (PNAs) make up the only class of nucleic acid mimics developed to date that has been shown to be capable of invading double-helical B-form DNA. Recently, we showed that sequence limitation associated with PNA recognition can be relaxed by utilizing conformationally preorganized γ-peptide nucleic acids (γPNAs). However, like all the previous studies, with the exception of triplex binding, DNA strand invasion was performed at relatively low salt concentrations. When physiological ionic strengths were used, little to no binding was observed. On the basis of this finding, it was not clear whether the lack of binding is due to the lack of base pair opening or the lack of binding free energy, either of which would result in no productive binding. In this work, we show that it is the latter. Under simulated physiological conditions, the DNA double helix is sufficiently dynamic to permit strand invasion by the designer oligonucleotide molecules provided that the required binding free energy can be met. This finding has important implications for the design oligonucleotides for recognition of B-DNA via direct Watson-Crick base pairing.
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Affiliation(s)
- Srinivas Rapireddy
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Danith H. Ly
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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18
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Yeh JI, Shivachev B, Rapireddy S, Crawford MJ, Gil RR, Du S, Madrid M, Ly DH. Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization. J Am Chem Soc 2010; 132:10717-27. [PMID: 20681704 DOI: 10.1021/ja907225d] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.
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Affiliation(s)
- Joanne I Yeh
- Department of Structural Biology, University of Pittsburgh Medical School 1036 BST3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA.
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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20
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Fu WF, Jia LF, Mu WH, Gan X, Zhang JB, Liu PH, Cao QY, Zhang GJ, Quan L, Lv XJ, Xu QQ. Synthesis, Characterization, Photoinduced Isomerization, and Spectroscopic Properties of Vinyl-1,8-naphthyridine Derivatives and Their Copper(I) Complexes. Inorg Chem 2010; 49:4524-33. [PMID: 20408579 DOI: 10.1021/ic100094y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen-Fu Fu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Lin-Fang Jia
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
| | - Wei-Hua Mu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Xin Gan
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Jia-Bing Zhang
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Ping-Hua Liu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
| | - Qian-Yong Cao
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
| | - Gui-Ju Zhang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
| | - Li Quan
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
| | - Xiao-Jun Lv
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, HKU-CAS Joint Laboratory on New Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Peking 100190, China
| | - Quan-Qing Xu
- College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650092, China
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21
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He W, Crawford MJ, Rapireddy S, Madrid M, Gil RR, Ly DH, Achim C. The structure of a gamma-modified peptide nucleic acid duplex. MOLECULAR BIOSYSTEMS 2010; 6:1619-29. [PMID: 20386807 DOI: 10.1039/c002254c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents the results of an NMR spectroscopy and distance-restrained molecular dynamics (MD) study of a gamma-methylated, palindromic, 8-base pair peptide nucleic acid (gamma-PNA) duplex. The goal of this study was to examine the impact of the gamma-backbone modification on the structure of the PNA duplex. The 2D NMR information involving the backbone methyl group, especially the NOEs between the methyl protons and those of the amide and methylene groups of the backbone, led to distance restraints useful in the elucidation of the structure of the backbone of gamma-PNA. Integration of the NOE peaks resulted in 138 inter-proton distance restraints, which were used in ten independent simulated annealing followed by 2 ns restrained MD runs. These simulations led to the conclusion that the gamma-PNA duplex adopts a general P-form helical structure similar to that observed for non-modified PNA but with a smaller base pair rise, which is an A-like helical feature, and a slight helical bending towards the major groove (PDB ID ). These properties of the gamma-PNA duplex may be induced by the gamma-methyl group. A similar effect of the methyl group was revealed by a previous NMR study of single stranded gamma-PNA [A. Dragulescu-Andrasi, S. Rapireddy, B. M. Frezza, C. Gayathri, R. R. Gil and D. H. Ly, J. Am. Chem. Soc., 2006, 128, 10258-10267]. It appears that the steric constraint exerted by the gamma-methyl on the backbone orientation is relatively independent of the base pairing and stacking and thus is likely to manifest when other substituents are introduced at the gamma-position of the PNA.
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Affiliation(s)
- Wei He
- Department of Chemistry, Carnegie Mellon University, 4400 5th Avenue, Pittsburgh, PA 15213, USA
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22
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Preus S, Börjesson K, Kilså K, Albinsson B, Wilhelmsson LM. Characterization of nucleobase analogue FRET acceptor tCnitro. J Phys Chem B 2010; 114:1050-6. [PMID: 20039634 DOI: 10.1021/jp909471b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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23
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Totsingan F, Jain V, Bracken WC, Faccini A, Tedeschi T, Marchelli R, Corradini R, Kallenbach NR, Green MM. Conformational Heterogeneity in PNA:PNA Duplexes. Macromolecules 2010. [DOI: 10.1021/ma902797f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filbert Totsingan
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Vipul Jain
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
| | - W. Clay Bracken
- Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021
| | - Andrea Faccini
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Tullia Tedeschi
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Rosangela Marchelli
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Roberto Corradini
- Dipartimento di Chimica Organica ed Industriale, Università di Parma, Via G.P. Usberti 17/A, 43100 Parma, Italy
| | - Neville R. Kallenbach
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003
| | - Mark M. Green
- Herman F. Mark Polymer Research Institute, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, New York 11201
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24
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Mizuta M, Seio K, Ohkubo A, Sekine M. Fluorescence properties of pyrimidopyrimidoindole nucleoside dC(PPI) incorporated into oligodeoxynucleotides. J Phys Chem B 2009; 113:9562-9. [PMID: 19537698 DOI: 10.1021/jp807562c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of oligodeoxynucleotides labeled by a pyrimidopyrimidoindole deoxynucleoside (1a: dC(PPI)) and its derivatives 2a and 3a substituted with electron-donating and -withdrawing groups, respectively, were synthesized according to the phosphoramidite approach. The photophysical properties and quenching efficiencies of oligonucleotides incorporating dC(PPI) derivatives were studied in detail. The thermal denaturation experiments and molecular dynamics simulation of DNA duplexes incorporating dC(PPI) suggested that a modified base of dC(PPI) could form base pairs with guanine and adenine in canonical Watson-Crick and reverse-wobble geometries, respectively. The fluorescence of oligonucleotides incorporating dC(PPI) derivatives increased upon binding to the counter strands, except when dC(PPI) and guanine formed a base pair. It was revealed that dGMP quenched the fluorescence of the cyano derivative 3a most effectively, whereas it affected that of the methoxy derivative 2a least effectively. The involvement of the electron transfer from guanine to the dC(PPI) derivatives in the fluorescence quenching was supported by energy considerations.
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Affiliation(s)
- Masahiro Mizuta
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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25
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Osmialowski B. Systematic investigation of 2,7-dihydroxy-1,8-naphthyridine dimerization – secondary interactions and tautomeric preferences calculations. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Secondary interactions as driving force in heterocomplex formation of 2,7-disubstituted-1,8-naphthyridines: Quantum chemical, NMR and mass spectral investigations. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.05.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Peifer M, De Giacomo F, Schandl M, Vasella A. Oligonucleotide Analogues with Integrated Bases and Backbone. Part 20. Helv Chim Acta 2009. [DOI: 10.1002/hlca.200900047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Dyrager C, Börjesson K, Dinér P, Elf A, Albinsson B, Wilhelmsson LM, Grøtli M. Synthesis and Photophysical Characterisation of Fluorescent 8-(1H-1,2,3-Triazol-4-yl)adenosine Derivatives. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900018] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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29
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Siriwong K, Chuichay P, Saen-oon S, Suparpprom C, Vilaivan T, Hannongbua S. Insight into why pyrrolidinyl peptide nucleic acid binding to DNA is more stable than the DNA x DNA duplex. Biochem Biophys Res Commun 2008; 372:765-71. [PMID: 18514065 DOI: 10.1016/j.bbrc.2008.05.102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 05/20/2008] [Indexed: 11/30/2022]
Abstract
Molecular dynamics (MD) simulations and experimental measurements of the stability of a novel pyrrolidinyl PNA binding to DNA (PNA x DNA) in both parallel and antiparallel configurations were carried out. For comparison, simulations were also performed for the DNA x DNA duplex. The conformations of the three simulated systems were found to retain well-defined base pairing and base stacking as their starting B-like structure. A large gas-phase energy repulsion of the two negatively charged sugar-phosphate backbones of the DNA strands was found to reduce the stability of the DNA x DNA duplex significantly compared with that of the PNA x DNA complexes, especially in the antiparallel binding configuration. In addition, the antiparallel PNA x DNA was observed to be less solvated than that of the other two systems. The simulated binding free energies and the experimental melting temperatures for the three investigated systems are in good agreement, indicating that the antiparallel PNA x DNA is the most stable duplex.
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Affiliation(s)
- Khatcharin Siriwong
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
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30
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Pensato S, Saviano M, Romanelli A. New peptide nucleic acid analogues: synthesis and applications. Expert Opin Biol Ther 2007; 7:1219-32. [PMID: 17696820 DOI: 10.1517/14712598.7.8.1219] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Peptide nucleic acids are oligonucleotide mimics characterised by high chemical and enzymatic stability, high specificity and affinity toward complementary DNA/RNA. The lack of charge and polar groups in the backbone decrease their solubility in aqueous environment and their ability to cross cell membranes, reducing their performance in in vivo applications. To improve solubility, increase affinity and specificity of binding and to control recognition between nucleic acids, several analogues bearing modifications on the nucleobase, nucleobase-backbone linker and on the backbone were synthesised. This paper describes the synthesis and applications of Peptide nucleic acid analogues and discusses the potential of analogues for which no application is reported.
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Affiliation(s)
- Soccorsa Pensato
- Università degli Studi di Napoli Federico II, Dipartimento delle Scienze Biologiche, Facoltà di Scienze Biotecnologiche, Napoli, Italy
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31
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Zhao X, Chen Y, Fu W, Zhang J. Synthesis of Novel Pyrrolo[1′,5′‐a]‐1,8‐naphthyridine Derivatives through a Facile One‐Pot Process. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910701392574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Xi‐Juan Zhao
- a Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing, China
- b Graduate University of Chinese Academy of Sciences , Beijing, China
| | - Yong Chen
- a Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing, China
- b Graduate University of Chinese Academy of Sciences , Beijing, China
| | - Wen‐Fu Fu
- a Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Beijing, China
- b Graduate University of Chinese Academy of Sciences , Beijing, China
- c College of Chemistry and Engineering, Yunnan Normal University , Kunming, China
| | - Jia‐Bing Zhang
- c College of Chemistry and Engineering, Yunnan Normal University , Kunming, China
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32
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Sen A, Nielsen PE. On the stability of peptide nucleic acid duplexes in the presence of organic solvents. Nucleic Acids Res 2007; 35:3367-74. [PMID: 17478520 PMCID: PMC1904262 DOI: 10.1093/nar/gkm210] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the medium decreases. Study of nucleobase paired duplexes in the absence of water and ultimately in pure aprotic, non-polar organic solvents is not possible with natural phosphodiester nucleic acids due to the ionic phosphate groups and the associated cations, but could be possible with non-ionic nucleic acid analogues or mimics such as peptide nucleic acids. We now report that peptide nucleic acid (PNA) (in contrast to DNA) duplexes show almost unaffected stability in up to 70% dimethylformamide (DMF) or dioxane, and extrapolation of the data to conditions of 100% organic solvents indicates only minor (or no) destabilization of the PNA duplexes. Our data indicate that stacking forces contribute little if at all to the duplex stability under these conditions. The differences in behaviour between the PNA and the DNA duplexes are attributed to the differences in hydration and counter ion release rather than to the differences in nucleobase interaction. These results support the possibility of having stable nucleobase paired double helices in organic solvents.
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Affiliation(s)
| | - Peter E. Nielsen
- *To whom correspondence should be addressed. Tel: +45 35 327762; Fax: +45 35 396042;
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33
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Nielsen PE. The many faces of PNA. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-4860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Rasmussen H, Liljefors T, Petersson B, Nielsen PE, Liljefors T, Kastrup JS. The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals. J Biomol Struct Dyn 2004; 21:495-502. [PMID: 14692794 DOI: 10.1080/07391102.2004.10506943] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The X-ray structure of a self-complementary PNA hexamer (H-CGTACG-L-Lys-NH(2)) has been determined to 2.35 A resolution. The introduction of an L-lysine moiety has previously been shown to induce a preferred left-handedness of the PNA double helices in aqueous solution. However, in the crystal structure an equal amount of interchanging right- and left-handed helices is observed. The lysine moieties are pointing into large solvent channels and no significant interactions between this moiety and the remaining PNA molecule are observed. In contrast, molecular mechanics calculations show a preference for the left-handed helix of this hexameric PNA in aqueous solution as expected. The calculations indicate that the difference in the free energy of solvation between the left-handed and the right-handed helix is the determining factor for the preference of the left-handed helix in aqueous solution.
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Affiliation(s)
- H Rasmussen
- Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100, Copenhagen, Denmark
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35
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Wilhelmsson LM, Sandin P, Holmén A, Albinsson B, Lincoln P, Nordén B. Photophysical Characterization of Fluorescent DNA Base Analogue, tC. J Phys Chem B 2003. [DOI: 10.1021/jp034930r] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Marcus Wilhelmsson
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Peter Sandin
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Anders Holmén
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Bo Albinsson
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Per Lincoln
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
| | - Bengt Nordén
- Physical Chemistry Section at the Department of Chemistry and Bioscience, Chalmers University of Technology, SE-41296 Gothenburg, Sweden, and Physical Chemistry, Discovery Bioanalytical Chemistry & Technologies, AstraZeneca R&D Mölndal, S-43183 Mölndal, Sweden
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36
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37
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Hollenstein M, Leumann CJ. Synthesis and incorporation into PNA of fluorinated olefinic PNA (F-OPA) monomers. Org Lett 2003; 5:1987-90. [PMID: 12762703 DOI: 10.1021/ol034579s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] A fluorinated OPA monomer containing the base thymine ((Z)-t-F-OPA) was synthesized in 12 steps, featuring a highly selective allylic over homoallylic Mitsunobu substitution for the introduction of the nucleobase. F-OPA modified PNA decamers were prepared by the MMTr/acyl protection strategy. The thermal stability of duplexes of PNA decamers containing (Z)-t-F-OPA units with antiparallel complementary DNA was measured. We found a strong dependence of stability from the sequential position of the (Z)-t-F-OPA units, ranging from DeltaT(m) of +2.4 to -8.1 degrees C/modification relative to unmodified PNA.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Ausín C, Ortega JA, Robles J, Grandas A, Pedroso E. Synthesis of amino- and guanidino-G-clamp PNA monomers. Org Lett 2002; 4:4073-5. [PMID: 12423089 DOI: 10.1021/ol026815p] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Syntheses of the protected amino- and guanidino-G-clamp PNA monomers, 9a and 9b, respectively, have been accomplished in eight steps from 5-bromouracil. Enhanced stacking interactions and additional hydrogen bonds with guanine should increase the affinity of PNAs incorporating these cytosine analogues for their complementary strands. [reaction: see text]
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Affiliation(s)
- Cristina Ausín
- Departament de Química Orgànica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
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Christensen C, Eldrup AB, Haaima G, Nielsen PE. 1,8-Naphthyridin-2,7-(1,8H)-dione is an effective mimic of protonated cytosine in peptide nucleic acid triplex recognition systems. Bioorg Med Chem Lett 2002; 12:3121-4. [PMID: 12372515 DOI: 10.1016/s0960-894x(02)00658-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel bicyclic mimic of protonated cytosine [1,8-naphthyridin-2,7-(1,8H)-dione, (K)] for Hoogsteen type triplex recognition of guanine has been designed for incorporation into peptide nucleic acids. Bis-PNA clamps with the K base incorporated in the Hoogsteen strand showed a significant stabilization of the triplexes at pH 7 as compared to similar triplexes with PNA oligomers containing either cytosine (6.7 degrees C per unit) or pseudoisocytosine (1.5 degrees C per unit). Cooperative stabilization was observed when the K units were placed in adjacent positions ( approximately 3 degrees C per unit).
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Affiliation(s)
- Caspar Christensen
- Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3, DK-2200 N, Copenhagen, Denmark
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