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Del Bene A, D'Aniello A, Tomassi S, Merlino F, Mazzarella V, Russo R, Chambery A, Cosconati S, Di Maro S, Messere A. Ultrasound-assisted Peptide Nucleic Acids synthesis (US-PNAS). ULTRASONICS SONOCHEMISTRY 2023; 95:106360. [PMID: 36913782 PMCID: PMC10024050 DOI: 10.1016/j.ultsonch.2023.106360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Herein, we developed an innovative and easily accessible solid-phase synthetic protocol for Peptide Nucleic Acid (PNA) oligomers by systematically investigating the ultrasonication effects in all steps of the PNA synthesis (US-PNAS). When compared with standard protocols, the application of the so-obtained US-PNAS approach succeeded in improving the crude product purities and the isolated yields of different PNA, including small or medium-sized oligomers (5-mer and 9-mer), complex purine-rich sequences (like a 5-mer Guanine homoligomer and the telomeric sequence TEL-13) and longer oligomers (such as the 18-mer anti-IVS2-654 PNA and the 23-mer anti-mRNA 155 PNA). Noteworthy, our ultrasound-assisted strategy is compatible with the commercially available PNA monomers and well-established coupling reagents and only requires the use of an ultrasonic bath, which is a simple equipment generally available in most synthetic laboratories.
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Affiliation(s)
- Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Francesco Merlino
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Sandro Cosconati
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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2
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Kovács L. From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives. CHEM REC 2023; 23:e202200203. [PMID: 36251934 DOI: 10.1002/tcr.202200203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/20/2022] [Indexed: 01/24/2023]
Abstract
Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using 13 C, 15 N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.
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Affiliation(s)
- Lajos Kovács
- University of Szeged, Albert Szent-Györgyi Medical School, Department of Medicinal Chemistry, H-6720, Szeged, Dóm tér 8, Hungary
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Moretta R, Terracciano M, Borbone N, Oliviero G, Schiattarella C, Piccialli G, Falanga AP, Marzano M, Dardano P, De Stefano L, Rea I. PNA-Based Graphene Oxide/Porous Silicon Hybrid Biosensor: Towards a Label-Free Optical Assay for Brugada Syndrome. NANOMATERIALS 2020; 10:nano10112233. [PMID: 33182823 PMCID: PMC7697640 DOI: 10.3390/nano10112233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA mimic that outperforms the properties of traditional oligonucleotides (ONs). On account of its outstanding features, such as remarkable binding affinity towards complementary DNA or RNA as well as high thermal and chemical stability, PNA has been proposed as a valuable alternative to the ON probe in gene-sensor design. In this study, a hybrid transducer made-up of graphene oxide (GO) nano-sheets covalently grafted onto a porous silicon (PSi) matrix has been investigated for the early detection of a genetic cardiac disorder, the Brugada syndrome (BS). A functionalization strategy towards the realization of a potential PNA-based device is described. A PNA, able to detect the SCN5A gene associated with the BS, has been properly synthesized and used as a bioprobe for the realization of a proof-of-concept label-free optical PNA-biosensor. PSi reflectance and GO photoluminescence signals were simultaneously exploited for the monitoring of the device functionalization and response.
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Affiliation(s)
- Rosalba Moretta
- Institute of Applied Sciences and Intelligent Systems, National Research Council, 80131 Naples, Italy; (R.M.); (P.D.); (I.R.)
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (N.B.); (G.P.)
- Correspondence: (M.T.); (L.D.S.); Tel.: +39-081-678521 (M.T.); +39-081-6132594 (L.D.S.)
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (N.B.); (G.P.)
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy; (G.O.); (A.P.F.)
| | - Chiara Schiattarella
- Department of Physics “E. Pancini”, University of Naples Federico II, 80126 Naples, Italy;
| | - Gennaro Piccialli
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy; (N.B.); (G.P.)
| | - Andrea Patrizia Falanga
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy; (G.O.); (A.P.F.)
| | - Maria Marzano
- Institute of Crystallography, National Research Council, 70126 Bari, Italy;
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems, National Research Council, 80131 Naples, Italy; (R.M.); (P.D.); (I.R.)
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems, National Research Council, 80131 Naples, Italy; (R.M.); (P.D.); (I.R.)
- Correspondence: (M.T.); (L.D.S.); Tel.: +39-081-678521 (M.T.); +39-081-6132594 (L.D.S.)
| | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems, National Research Council, 80131 Naples, Italy; (R.M.); (P.D.); (I.R.)
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Inagaki M, Uematsu R, Mizutani T, Unabara D, Araki Y, Sakamoto S, Kashida H, Nishijima M, Asanuma H, Inoue Y, Wada T. N-Benzoyl-protected Peptide Nucleic Acid (PNA) Monomers Expand the Range of Nucleobases Available for PNA-DNA Chimera. CHEM LETT 2019. [DOI: 10.1246/cl.181048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Masahito Inagaki
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Ryohei Uematsu
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tatsuya Mizutani
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Daisuke Unabara
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Seiji Sakamoto
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Masaki Nishijima
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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Synthesis and gene silencing properties of siRNAs containing terminal amide linkages. BIOMED RESEARCH INTERNATIONAL 2014; 2014:901617. [PMID: 24791003 PMCID: PMC3984766 DOI: 10.1155/2014/901617] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/23/2014] [Indexed: 01/04/2023]
Abstract
The active components of the RNAi are 21 nucleotides long dsRNAs containing a 2 nucleotide overhang at the 3′ end, carrying 5′-phosphate and 3′-hydroxyl groups (siRNAs). Structural analysis revealed that the siRNA is functionally bound at both ends to RISC. Terminal modifications are considered with interest as the introduction of chemical moieties interferes with the 3′ overhang recognition by the PAZ domain and the 5′-phosphate recognition by the MID and PIWI domains of RISC. Herein, we report the synthesis of modified siRNAs containing terminal amide linkages by introducing hydroxyethylglycine PNA (hegPNA) moieties at 5′, and at 3′ positions and on both terminals. Results of gene silencing studies highlight that some of these modifications are compatible with the RNAi machinery and markedly increase the resistance to serum-derived nucleases even after 24 h of incubation. Molecular docking simulations were attained to give at atomistic level a clearer picture of the effect of the most performing modifications on the interactions with the human Argonaute 2 PAZ, MID, and PIWI domains. This study adds another piece to the puzzle of the heterogeneous chemical modifications that can be attained to enhance the silencing efficiency of siRNAs.
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Amato J, Stellato MI, Pizzo E, Petraccone L, Oliviero G, Borbone N, Piccialli G, Orecchia A, Bellei B, Castiglia D, Giancola C. PNA as a potential modulator of COL7A1 gene expression in dominant dystrophic epidermolysis bullosa: a physico-chemical study. MOLECULAR BIOSYSTEMS 2013; 9:3166-74. [PMID: 24121392 DOI: 10.1039/c3mb70283a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dominant diseases are single gene disorders occurring in the heterozygous state. The mutated allele exerts a dominant effect because it produces an abnormal polypeptide that interferes with the function of the normal allele product. Peptide Nucleic Acids (PNAs) offer a route for a potential therapy for dominant diseases by selectively silencing the allele carrying the dominant mutation. Here, we have synthesized and studied the properties of a 15-mer PNA fully complementary to the site of the c.5272-38T>A sequence variation, which identifies a recurrent mutant COL7A1 allele causing dominant dystrophic epidermolysis bullosa (DDEB), a mendelian disease characterized by skin blistering. The PNA was conjugated with four lysine residues at the C-terminus and a fluorescent probe at the N-terminus. Physico-chemical results proved the formation of a stable, selective PNA/mutant-DNA heteroduplex in vitro. Intriguingly, when transfected into normal human fibroblasts, the PNA correctly localized in the cell nucleus. Our results open new therapeutic possibilities for patients with DDEB.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Naples, Italy.
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Avitabile C, Moggio L, D’Andrea LD, Pedone C, Romanelli A. Development of an efficient and low-cost protocol for the manual PNA synthesis by Fmoc chemistry. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.05.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lönnberg H. Solid-phase synthesis of oligonucleotide conjugates useful for delivery and targeting of potential nucleic acid therapeutics. Bioconjug Chem 2009; 20:1065-94. [PMID: 19175328 DOI: 10.1021/bc800406a] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Olignucleotide-based drugs show promise as a novel form of chemotherapy. Among the hurdles that have to be overcome on the way of applicable nucleic acid therapeutics, inefficient cellular uptake and subsequent release from endosomes to cytoplasm appear to be the most severe ones. Covalent conjugation of oligonucleotides to molecules that expectedly facilitate the internalization, targets the conjugate to a specific cell-type or improves the parmacokinetics offers a possible way to combat against these shortcomings. Since workable chemistry is a prerequisite for biological studies, development of efficient and reproducible methods for preparation of various types of oligonucleotide conjugates has become a subject of considerable importance. The present review summarizes the advances made in the solid-supported synthesis of oligonucleotide conjugates aimed at facilitating the delivery and targeting of nucleic acid drugs.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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9
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RNA interference in mammalia cells by RNA-3'-PNA chimeras. Int J Mol Sci 2008; 9:299-315. [PMID: 19325750 PMCID: PMC2635679 DOI: 10.3390/ijms9030299] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/29/2008] [Accepted: 02/29/2008] [Indexed: 12/12/2022] Open
Abstract
The discovery of siRNAs as the mediators of RNA interference has led to an increasing interest in their therapeutic applications. Chemical modifications are introduced into siRNAs to optimize the potency, the stability and the pharmacokinetic properties in vivo. Here, we synthesize and test the effects of RNA-3’-PNA chimeras on siRNA functioning and stability. We demonstrate that the chemical modifications are compatible with the siRNA machinery, because all the PNA-modified siRNAs can efficiently mediate specific gene silencing in mammalian cells. Furthermore, we find that the modification on the sense strand of siRNA results in an increased persistence of the activity, whereas modification on both strands results in enhanced nuclease resistance in serum.
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Petraccone L, Pagano B, Esposito V, Randazzo A, Piccialli G, Barone G, Mattia CA, Giancola C. Thermodynamics and kinetics of PNA-DNA quadruplex-forming chimeras. J Am Chem Soc 2006; 127:16215-23. [PMID: 16287312 DOI: 10.1021/ja0545923] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PNA-DNA chimeras present the interesting properties of PNA, such as the high binding affinity to complementary single-strand (DNA or RNA), and the resistance to nuclease and protease degradation. At the same time, the limitations of an oligomer containing all PNA residues, such as low water solubility, self-aggregation, and low cellular uptake, are effectively overcome. Further, PNA-DNA chimeras possess interesting biological properties as antisense agents. We have explored the ability of PNA-DNA chimeric strands to assemble in quadruplex structures. The rate constant for association of the quadruplexes and their thermodynamic properties have been determined by CD spectroscopy and differential scanning calorimetry (DSC). Thermal denaturation experiments indicated higher thermal and thermodynamic stabilities for chimeric quadruplexes in comparison with the corresponding unmodified DNA quadruplex. Singular value decomposition analysis (SVD) suggests the presence of kinetically stable intermediate species in the quadruplex formation process. The experimental results have been discussed on the basis of molecular dynamic simulations. The ability of PNA-DNA chimeras to form stable quadruplex structures expands their potential utility as therapeutic agents.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Farmaceutiche, Via Ponte Don Melillo, 84084, Fisciano (SA), Italy
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11
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Petraccone L, Erra E, Messere A, Montesarchio D, Piccialli G, De Napoli L, Barone G, Giancola C. Targeting duplex DNA with DNA-PNA chimeras? Physico-chemical characterization of a triplex DNA-PNA/DNA/DNA. Biopolymers 2004; 73:434-42. [PMID: 14991660 DOI: 10.1002/bip.10599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Targeting double-stranded DNA with homopyrimidine PNAs results in strand displacement complexes PNA/DNA/PNA rather than PNA/DNA/DNA triplex structures. Not much is known about the binding properties of DNA-PNA chimeras. A 16-mer 5'-DNA-3'-p-(N)PNA(C) has been investigated for its ability to hybridize a complementary duplex DNA by DSC, CD, and molecular modeling studies. The obtained results showed the formation of a triplex structure having similar, if not slightly higher, stability compared to the same all-DNA complex.
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Affiliation(s)
- L Petraccone
- Dipartimento di Chimica, Università "Federico II" di Napoli, Via Cintia 4, 80126-Napoli, Italy
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12
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Barone G, De Napoli L, Di Fabio G, Erra E, Giancola C, Messere A, Montesarchio D, Petraccone L, Piccialli G. Synthesis and DNA binding properties of DNA-PNA chimeras. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1089-91. [PMID: 14565351 DOI: 10.1081/ncn-120022743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A systematic study to evaluate the ability of 5'-DNA-3'-p-(N)-PNA-(C) chimeras to form triple helix structures has been undertaken. Preliminary results carried out on a 16-mer chimera with three PNA monomers at the 3'-end showed the formation of a stable DNA-PNA/DNA/DNA triplex, having similar conformational behaviour to a canonical DNA/DNA/DNA triplex.
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Affiliation(s)
- G Barone
- Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Napoli, Italy
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Esposito V, Galeone A, Mayol L, Messere A, Piccialli G, Randazzo A. PNA-DNA chimeras forming quadruplex structures. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1681-4. [PMID: 14565494 DOI: 10.1081/ncn-120023112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
1H-NMR, CD, and UV spectroscopy have been used to investigate the structure of PNA/DNA chimeras forming quadruplex structures. In particular, we synthesized 5'TGGG3'-t (1) and 5'TGG3'-gt (2), where lower and upper case letters indicate PNA and DNA residues, respectively. CD spectrum and all NMR data of (1) are typical of quadruplexes involving four parallel strands. UV melting profile of (1) indicates that its thermal stability is quite similar to that observed for the reference structure [d(TGGGT)]4. 1H-NMR spectrum for 5'TGG3'-gt (2) shows that this oligonucleotide is not able to fold into a single, well-defined species.
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Affiliation(s)
- Veronica Esposito
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Napoli, Italy
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Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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