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Debacker AJ, Sharma VK, Meda Krishnamurthy P, O'Reilly D, Greenhill R, Watts JK. Next-Generation Peptide Nucleic Acid Chimeras Exhibit High Affinity and Potent Gene Silencing. Biochemistry 2018; 58:582-589. [PMID: 30520300 DOI: 10.1021/acs.biochem.8b00827] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We present a new design of mixed-backbone antisense oligonucleotides (ASOs) containing both DNA and peptide nucleic acid (PNA). Previous generations of PNA-DNA chimeras showed low binding affinity, reducing their potential as therapeutics. The addition of a 5'-wing of locked nucleic acid as well as the combination of a modified nucleotide and a PNA monomer at the junction between PNA and DNA yielded high-affinity chimeras. The resulting ASOs demonstrated high serum stability and elicited robust RNase H-mediated cleavage of complementary RNA. These properties allowed the chimeric ASOs to demonstrate high gene silencing efficacy and potency in cells, comparable with those of LNA gapmer ASOs, via both lipid transfection and gymnosis.
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Affiliation(s)
- Alexandre J Debacker
- RNA Therapeutics Institute , UMass Medical School , Worcester , Massachusetts 01605 , United States.,Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Vivek K Sharma
- RNA Therapeutics Institute , UMass Medical School , Worcester , Massachusetts 01605 , United States
| | | | - Daniel O'Reilly
- Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Rachel Greenhill
- Department of Chemistry , University of Southampton , Southampton SO17 1BJ , U.K
| | - Jonathan K Watts
- RNA Therapeutics Institute , UMass Medical School , Worcester , Massachusetts 01605 , United States.,Department of Biochemistry and Molecular Pharmacology , UMass Medical School , Worcester , Massachusetts 01605 , United States
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2
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Głowacka IE, Piotrowska DG, Andrei G, Schols D, Snoeck R, Wróblewski AE. Acyclic nucleoside phosphonates containing the amide bond. MONATSHEFTE FUR CHEMIE 2016; 147:2163-2177. [PMID: 27881885 PMCID: PMC5101293 DOI: 10.1007/s00706-016-1848-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/04/2016] [Indexed: 12/11/2022]
Abstract
Abstract To study the influence of a linker rigidity and donor–acceptor properties, the P–CH2–O–CHR– fragment in acyclic nucleoside phosphonates (e.g., acyclovir, tenofovir) was replaced by the P–CH2–HN–C(O)– residue. The respective phosphonates were synthesized in good yields by coupling the straight chain of ω-aminophosphonates and nucleobase-derived acetic acids with EDC. Based on the 1H and 13C NMR data, the unrestricted rotation within the methylene and 1,2-ethylidene linkers in phosphonates from series a and b was confirmed. For phosphonates containing 1,3-propylidene (series c) fragments, antiperiplanar disposition of the bulky O,O-diethylphosphonate and substituted amidomethyl groups was established. The synthesized ANPs P–X–HNC(O)–CH2B (X = CH2, CH2CH2, CH2CH2CH2, CH2OCH2CH2) appeared inactive in antiviral assays against a wide variety of DNA and RNA viruses at concentrations up to 100 μM while marginal antiproliferative activity (L1210 cells, IC50 = 89 ± 16 μM and HeLa cells, IC50 = 194 ± 19 μM) was noticed for the analog derived from (5-fluorouracyl-1-yl)acetic acid and O,O-diethyl (2-aminoethoxy)methylphosphonate. Graphical abstract ![]()
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Affiliation(s)
- Iwona E Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| | - Dorota G Piotrowska
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Dominique Schols
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Louvain, Belgium
| | - Andrzej E Wróblewski
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
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Porcheddu A, Giacomelli G, Piredda I, Carta M, Nieddu G. A Practical and Efficient Approach to PNA Monomers Compatible with Fmoc-Mediated Solid-Phase Synthesis Protocols. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800891] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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4
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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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Pâtureau BM, Hudson RHE, Damha MJ. Induction of RNase H activity by Arabinose-peptide nucleic acid chimeras. Bioconjug Chem 2007; 18:421-30. [PMID: 17373768 DOI: 10.1021/bc060300r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the syntheses of chimeras of peptide nucleic acid (PNA) with DNA and 2'-deoxy 2'-fluoroarabinonucleic acid (2'-FANA). Chimeric oligomers possessing a single central PNA insert were capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers. We subsequently determined the ability of the DNA and 2'-FANA oligomers of mixed-base composition to elicit human RNase H1 degradation of complementary RNA that was either unstructured or as a hairpin. In the case of the more rigid FANA strand, a PNA insert led to a higher ability of the chimera to direct the degradation of both types of RNA targets. Generally, the enhancement observed was greater for a butanediol linker than for a more rigid PNA linker. Along with previous work, these studies suggest that the general flexibility associated with an acyclic insert (e.g., butyl vs PNA)--and not necessarily the presence of local structural imperfections in the heteroduplex--is beneficial for RNase H1 activity. As well, there are implications to the charge nature of non-nucleotide inserts (neutral vs negative) and their ability to maintain RNase H activity that may serve to direct further design considerations. Together, these studies support the notion that flexibility of antisense oligonucleotide (AON)/RNA hybrids is essential for high RNase H catalysis, in which an enzyme-induced altered trajectory of the bound AON/RNA substrate could facilitate optimal interaction with the catalytic site of RNase H.
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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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Slaitas A, Yeheskiely E. SYNTHESIS AND REACTIVITY OF NUCLEOSIDE SULFILIMINES. PHOSPHORUS SULFUR 2004. [DOI: 10.1080/10426500490257113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Yuan X, Ma Z, Zhou W, Niidome T, Alber S, Huang L, Watkins S, Li S. Lipid-mediated delivery of peptide nucleic acids to pulmonary endothelium. Biochem Biophys Res Commun 2003; 302:6-11. [PMID: 12593839 DOI: 10.1016/s0006-291x(03)00058-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide nucleic acid (PNA) is a DNA/RNA mimic in which the phosphodiester (PO) linkage is replaced with a peptide bond. It has a number of unique properties compared to currently used oligonucleotides including higher affinity towards RNA or DNA target, resistance to nucleases or proteases, and minimal non-specific interactions with proteins. Clinical applications of PNA, however, are limited by its inefficient intracellular delivery. In this study, we have shown that delivery of PNA to pulmonary endothelium in intact mice can be greatly improved via hybridization with a short PO oligonucleotide that serves as a carrier to form complexes with cationic liposomes. We have also shown for the first time that unlike a CpG DNA oligo that is highly proinflammatory, a CG-containing PNA is inert in triggering TNF-alpha response in cultured macrophages and in mice. Thus delivery of PNA to pulmonary endothelium may prove to be a therapeutically useful for the treatment of pulmonary vascular diseases.
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Affiliation(s)
- Xing Yuan
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, 639 Salk Hall, Pittsburgh, PA 15213, USA
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Borgatti M, Lampronti I, Romanelli A, Pedone C, Saviano M, Bianchi N, Mischiati C, Gambari R. Transcription factor decoy molecules based on a peptide nucleic acid (PNA)-DNA chimera mimicking Sp1 binding sites. J Biol Chem 2003; 278:7500-9. [PMID: 12446679 DOI: 10.1074/jbc.m206780200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide nucleic acids (PNAs) are DNA-mimicking molecules in which the sugar-phosphate backbone is replaced by a pseudopeptide backbone composed of N-(2-aminoethyl)glycine units. We determined whether double-stranded molecules based on PNAs and PNA-DNA-PNA (PDP) chimeras could be capable of stable interactions with nuclear proteins belonging to the Sp1 transcription factor family and, therefore, could act as decoy reagents able to inhibit molecular interactions between Sp1 and DNA. Since the structure of PNA/PNA hybrids is very different from that of the DNA/DNA double helix, they could theoretically alter the molecular structure of the double-stranded PNA-DNA-PNA chimeras, perturbing interactions with specific transcription factors. We found that PNA-based hybrids do not inhibit Sp1/DNA interactions. In contrast, hybrid molecules based on PNA-DNA-PNA chimeras are very effective decoy molecules, encouraging further experiments focused on the possible use of these molecules for the development of potential agents for a decoy approach in gene therapy. In this respect, the finding that PDP-based decoy molecules are more resistant than DNA/DNA hybrids to enzymatic degradation appears to be of great interest. Furthermore, their resistance can even be improved after complexation with cationic liposomes to which PDP/PDP chimeras are able to bind by virtue of their internal DNA structure.
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Affiliation(s)
- Monica Borgatti
- Department of Biochemistry and Molecular Biology, Ferrara University, Via L.Borsari n.46, 44100 Ferrara, Italy
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Slaitas A, Yeheskiely E. Fast and efficient peptide bond formation using bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur. Part I. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2002; 60:283-91. [PMID: 12383118 DOI: 10.1034/j.1399-3011.2002.21015.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study towards the development of sulfurane-based coupling agents shows that bis-[alpha,alpha-bis(trifluoromethyl)-benzyloxy]diphenylsulfur (BTBDS) can facilitate rapid amide bond formation between Nalpha-urethane-protected l-amino acids and l-phenylalanine ethyl ester in the absence of an external base. The corresponding dipeptide esters were obtained in excellent yields and with no detectable racemization, as judged by analysis of the formed dipeptides by chiral-phase HPLC. In addition, BTBDS-mediated condensation of benzoyl-l-phenylalanine with l-phenylalanine ethyl ester was also investigated. The results indicate that sulfuranes can be useful for application in racemization-sensitive systems, such as segment condensation.
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Affiliation(s)
- A Slaitas
- Division of Organic and Bioorganic Chemistry, MBB, Scheele Laboratory, Karolinska Institute, Stockholm, Sweden
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11
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Piva R, Gambari R. Transcription factor decoy (TFD) in breast cancer research and treatment. Technol Cancer Res Treat 2002; 1:405-16. [PMID: 12625767 DOI: 10.1177/153303460200100512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Synthetic oligonucleotides have recently been the object of many investigations aimed to develop sequence-selective compounds able to modulate, either positively or negatively, transcription of eukaryotic and viral genes. Alteration of transcription could be obtained by using synthetic oligonucleotides mimicking target sites of transcription factors (the transcription factor decoy -TFD- approach). This could lead to either inhibition or activation of gene expression, depending on the biological functions of the target transcription factors. Since several transcription factors are involved in tumor onset and progression, this issue is of great interest in order to design anti-tumor compounds. In addition to oligonucleotides, peptide nucleic acids (PNA) can be proposed for the modulation of gene expression. In this respect, double-stranded PNA-DNA chimeras have been shown to be capable to exhibit strong decoy activity. In the case of treatment of breast cancer cells, decoy oligonucleotides mimicking CRE binding sites, promoter region of estrogen receptor alpha gene, NF-kB binding sites have been used with promising results. Therefore, the transcription factor decoy approach could be object of further studies to develop protocols for the treatment of breast cancer. In the future, transcription factors regulating cell cycle, hormone-dependent differentiation, tumor invasion and metastasis are expected to be suitable targets for transcription factor decoy.
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Affiliation(s)
- Roberta Piva
- Department of Biochemistry and Molecular Biology, Ferrara University, Via Luigi Borsari, 46, 44100 Ferrara, Italy
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12
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Capasso D, De Napoli L, Di Fabio G, Messere A, Montesarchio D, Pedone C, Piccialli G, Saviano M. Solid phase synthesis of DNA-3′-PNA chimeras by using Bhoc/Fmoc PNA monomers. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00944-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mokhir AA, Connors WH, Richert C. Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine-homopyrimidine DNA triple helices. Nucleic Acids Res 2001; 29:3674-84. [PMID: 11522839 PMCID: PMC55894 DOI: 10.1093/nar/29.17.3674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A total of 16 oligodeoxyribonucleotides of general sequence 5'-TCTTCTZTCTTTCT-3', where Z denotes an N-acyl-N-(2-hydroxyethyl)glycine residue, were prepared via solid phase synthesis. The ability of these oligonucleotides to form triplexes with the duplex 5'-AGAAGATAGAAAGA-HEG-TCTTTCTATCTTCT-3', where HEG is a hexaethylene glycol linker, was tested. In these triplexes, an 'interrupting' T:A base pair faces the Z residue in the third strand. Among the acyl moieties of Z tested, an anthraquinone carboxylic acid residue linked via a glycinyl group gave the most stable triplex, whose UV melting point was 8.4 degrees C higher than that of the triplex with 5'-TCTTCTGTCTTTCT-3' as the third strand. The results from exploratory nuclease selection experiments suggest that a combinatorial search for strands capable of recognizing mixed sequences by triple helix formation is feasible.
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Affiliation(s)
- A A Mokhir
- Department of Chemistry, University of Constance, Fach M 709, D-78457 Konstanz, Germany
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14
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Malchère C, Verheijen J, van der Laan S, Bastide L, van Boom J, Lebleu B, Robbins I. A short phosphodiester window is sufficient to direct RNase H-dependent RNA cleavage by antisense peptide nucleic acid. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2000; 10:463-8. [PMID: 11198930 DOI: 10.1089/oli.1.2000.10.463] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The potential pharmacologic benefits of using peptide nucleic acid (PNA) as an antisense agent are tempered by its incapacity to activate RNase H. The mixed backbone oligonucleotide (ON) (or gapmer) approach, in which a short internal window of RNAse H-competent residues is embedded within an RNase H-incompetent ON has not been applied previously to PNA because PNA and DNA hybridize to RNA with very different helical structures, creating structural perturbations at the two PNA-DNA junctions. It is demonstrated here for the first time that a short internal phosphodiester window within a PNA is sufficient to evoke the RNase H-dependent cleavage of a targeted RNA and to abrogate translation elongation in a well-characterized in vitro assay.
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Affiliation(s)
- C Malchère
- Institut de Génétique Moléculaire, UMR 5535 and EP 2030, CNRS, Montpellier, France
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Mokhir AA, Richert C. Synthesis and monitored selection of 5'-nucleobase-capped oligodeoxyribonucleotides. Nucleic Acids Res 2000; 28:4254-65. [PMID: 11058125 PMCID: PMC113132 DOI: 10.1093/nar/28.21.4254] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2000] [Revised: 09/08/2000] [Accepted: 09/08/2000] [Indexed: 11/13/2022] Open
Abstract
Oligodeoxynucleotides bearing 5'-appendages consisting of a nucleobase and an amide linkage were prepared from 5'-amino-5'-deoxyoligonucleotides, amino acid building blocks and thymine or uracil derivatives. Small chemical libraries of 5'-modified oligonucleotides bearing the nucleobase moieties via five, three or two atom linkages were subjected to spectrometrically monitored nuclease selections to identify members with high affinity for target strands. The smallest of the appendages tested, a uracil acetic acid substituent, was found to convey the greatest duplex stabilizing effect on the octamer 5'-T*GGTTGAC-3', where T* denotes the 5'-amino-5'-deoxythymidine residue. Compared to 5'-TTGGTTGAC-3', the modified sequence 5'-u-T*GGTTGAC-3' gives a duplex with 5'-GTCAACCAA-3' that melts 4 degrees C higher. The duplex-stabilizing effect of this 5'-substituent does not require a specific residue at the 3'-terminus of the complement and the available data suggest that the uracil moiety is located in the major groove of the duplex.
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Affiliation(s)
- A A Mokhir
- Department of Chemistry, Tufts University, Medford, MA 02155, USA and Department of Chemistry, University of Constance, Fach M709, D-78457 Konstanz, Germany
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16
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Verheijen JC, Chen L, Bayly SF, Torrence PF, van der Marel GA, van Boom JH. Synthesis and RNAse L binding and activation of a 2-5A-(5')-DNA-(3')-PNA chimera, a novel potential antisense molecule. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1821-30. [PMID: 11200276 DOI: 10.1080/15257770008045463] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fully automated solid-phase synthesis gave access to a hybrid in which 5'-phosphorylated-2'-5'-linked oligoadenylate (2-5A) is connected to the 5'-terminus of DNA which, in turn, is linked at the 3'-end to PNA [2-5A-(5')-DNA-(3')-PNA chimera]. This novel antisense molecule retains full RNase L activation potency while suffering only a slight reduction in binding affinity.
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Affiliation(s)
- J C Verheijen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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17
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Verheijen JC, Deiman BALM, Yeheskiely E, van der Marel GA, van Boom JH. Efficient Hydrolysis of RNA by a PNA – Diethylenetriamine Adduct. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/(sici)1521-3757(20000117)112:2<377::aid-ange377>3.0.co;2-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Abstract
Peptide nucleic acids (PNAs) have been around for more than seven years and it was hoped, at their introduction, that they would quickly enter the fields of antisense and antigene technology and drug development. Despite their extremely favorable hybridization and stability properties, as well as the encouraging antisense and antigene activity of PNA in cell-free systems, progress has been slow and experiments on cells in culture and in animals have been lacking. Judging from the very promising results published within the past year, however, there is every reason to believe that both PNA antisense and, possibly, PNA antigene research will strongly pick up momentum again. Specifically, it has been demonstrated that certain peptide-PNA conjugates are taken up very efficiently by, at least some, eukaryotic cells and that antisense down regulation of target genes in nerve cells in culture is attainable using such PNA conjugates. Perhaps even more exciting is that antisense-compatible effects have been reported using PNAs injected into the brain of rats. Finally, it has been shown that the bacterium Escherichia coli is susceptible to antisense gene regulation using PNA.
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Affiliation(s)
- P E Nielsen
- Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, The Panum Institute, Copenhagen, Denmark.
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19
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Lutz MJ, Will DW, Breipohl G, Benner SA, Uhlmann E. Synthesis of a monocharged peptide nucleic acid (PNA) analog and its recognition as substrate by DNA polymerases. NUCLEOSIDES & NUCLEOTIDES 1999; 18:393-401. [PMID: 10408922 DOI: 10.1080/15257779908043084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The preparation of a novel phosphoramidite monomer based on thyminyl acetic acid coupled to the secondary nitrogen of 2-(2-amino-ethylamino)ethanol is described. This monomer can be used to attach a deoxynucleotide to the carboxy terminus of a PNA oligomer by solid-phase synthesis. The resulting PNA primer is recognized as a substrate by various DNA polymerases.
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Affiliation(s)
- M J Lutz
- Swiss Federal Institute of Technology, Department of Chemistry, Zürich, Switzerland
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20
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Maison W, Schlemminger I, Westerhoff O, Martens J. Modified PNAs: a simple method for the synthesis of monomeric building blocks. Bioorg Med Chem Lett 1999; 9:581-4. [PMID: 10098668 DOI: 10.1016/s0960-894x(99)00024-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The synthesis of PNA-monomers with variations in the substitution pattern using the Ugi-Reaction is described. The one-pot procedure leads to new totally protected PNA-monomers which can be selectively cleaved to N-protected monomeric building blocks for PNA synthesis.
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Affiliation(s)
- W Maison
- Fachbereich Chemie, Universität Oldenburg, Germany
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21
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Steinbeck C, Richert C. The Role of Ionic Backbones in RNA Structure: An Unusually Stable Non-Watson−Crick Duplex of a Nonionic Analog in an Apolar Medium. J Am Chem Soc 1998. [DOI: 10.1021/ja9817951] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christoph Steinbeck
- Contribution from the Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155
| | - Clemens Richert
- Contribution from the Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155
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22
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Foiani M, Ferrari M, Liberi G, Lopes M, Lucca C, Marini F, Pellicioli A, Muzi Falconi M, Plevani P. S-phase DNA damage checkpoint in budding yeast. Biol Chem 1998; 379:1019-23. [PMID: 9792433 DOI: 10.1515/bchm.1998.379.8-9.1019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Eukaryotic cells must be able to coordinate DNA repair, replication and cell cycle progression in response to DNA damage. A failure to activate the checkpoints which delay the cell cycle in response to internal and external cues and to repair the DNA lesions results in an increase in genetic instability and cancer predisposition. The use of the yeast Saccharomyces cerevisiae has been invaluable in isolating many of the genes required for the DNA damage response, although the molecular mechanisms which couple this regulatory pathway to different DNA transactions are still largely unknown. In analogy with prokaryotes, we propose that DNA strand breaks, caused by genotoxic agents or by replication-related lesions, trigger a replication coupled repair mechanism, dependent upon recombination, which is induced by the checkpoint acting during S-phase.
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Affiliation(s)
- M Foiani
- Dipartimento di Genetica e di Biologia dei Microorganismi, Universita' degli Studi di Milano, Italy.
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