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Danielsen MB, Wengel J. Cationic oligonucleotide derivatives and conjugates: A favorable approach for enhanced DNA and RNA targeting oligonucleotides. Beilstein J Org Chem 2021; 17:1828-1848. [PMID: 34386102 PMCID: PMC8329367 DOI: 10.3762/bjoc.17.125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/14/2021] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) have the ability of binding to endogenous nucleic acid targets, thereby inhibiting the gene expression. Although ASOs have great potential in the treatment of many diseases, the search for favorable toxicity profiles and distribution has been challenging and consequently impeded the widespread use of ASOs as conventional medicine. One strategy that has been employed to optimize the delivery profile of ASOs, is the functionalization of ASOs with cationic amine groups, either by direct conjugation onto the sugar, nucleobase or internucleotide linkage. The introduction of these positively charged groups has improved properties like nuclease resistance, increased binding to the nucleic acid target and improved cell uptake for oligonucleotides (ONs) and ASOs. The modifications highlighted in this review are some of the most prevalent cationic amine groups which have been attached as single modifications onto ONs/ASOs. The review has been separated into three sections, nucleobase, sugar and backbone modifications, highlighting what impact the cationic amine groups have on the ONs/ASOs physiochemical and biological properties. Finally, a concluding section has been added, summarizing the important knowledge from the three chapters, and examining the future design for ASOs.
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Affiliation(s)
- Mathias B Danielsen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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2
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Yanachkov I, Zavizion B, Metelev V, Stevens LJ, Tabatadze Y, Yanachkova M, Wright G, Krichevsky AM, Tabatadze DR. Self-neutralizing oligonucleotides with enhanced cellular uptake. Org Biomol Chem 2018; 15:1363-1380. [PMID: 28074950 DOI: 10.1039/c6ob02576e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is tremendous potential for oligonucleotide (ON) therapeutics, but low cellular penetration due to their polyanionic nature is a major obstacle. We addressed this problem by developing a new approach for ON charge neutralization in which multiple branched charge-neutralizing sleeves (BCNSs) are attached to the internucleoside phosphates of ON by phosphotriester bonds. The BCNSs are terminated with positively charged amino groups, and are optimized to form ion pairs with the neighboring phosphate groups. The new modified ONs can be prepared by standard automated phosphoramidite chemistry in good yield and purity. They possess good solubility and hybridization properties, are not involved in non-standard intramolecular aggregation, have low cytotoxicity, adequate chemical stability, improved serum stability, and above all, display significantly enhanced cellular uptake. Thus, the new ON derivatives exhibit properties that make them promising candidates for the development of novel therapeutics or research tools for modulation of the expression of target genes.
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Affiliation(s)
- Ivan Yanachkov
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Boris Zavizion
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | - Valeri Metelev
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and Department of Chemistry, Moscow State University, Leninskye gory1/40, Moscow 119991, Russian Federation
| | - Laura J Stevens
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
| | | | - Milka Yanachkova
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA. and GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - George Wright
- GLSynthesis, Inc., One Innovation Drive, Worcester, MA 01605, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd., Boston, MA 02115, USA
| | - David R Tabatadze
- ZATA Pharmaceuticals, Inc., 60 Prescott St., Worcester, MA 01605, USA.
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3
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Polyamine-oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics. Future Med Chem 2015; 7:1733-49. [PMID: 26424049 DOI: 10.4155/fmc.15.90] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chemical modification and/or the conjugation of small functional molecules to oligonucleotides have significantly improved their biological and biophysical properties, addressing issues such as poor cell penetration, stability to nucleases and low affinity for their targets. Here, the authors review the literature reporting on the biophysical, biochemical and biological properties of one particular class of modification - polyamine-oligonucleotide conjugates. Naturally derived and synthetic polyamines have been grafted onto a variety of oligonucleotide formats, including antisense oligonucleotides and siRNAs. In many cases this has had beneficial effects on their properties such as target hybridization, nuclease resistance, cellular uptake and activity. Polyamine-oligonucleotide conjugation, therefore, represents a promising direction for the further development of oligonucleotide-based therapeutics and tools.
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Lamparska K, Clark J, Babilonia G, Bedell V, Yip W, Smith SS. 2'-Deoxyriboguanylurea, the primary breakdown product of 5-aza-2'-deoxyribocytidine, is a mutagen, an epimutagen, an inhibitor of DNA methyltransferases and an inducer of 5-azacytidine-type fragile sites. Nucleic Acids Res 2012; 40:9788-801. [PMID: 22850746 PMCID: PMC3479176 DOI: 10.1093/nar/gks706] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
5-Aza-2′-deoxycytidine (5azaC-dR) has been employed as an inhibitor of DNA methylation, a chemotherapeutic agent, a clastogen, a mutagen, an inducer of fragile sites and a carcinogen. However, its effects are difficult to quantify because it rapidly breaks down in aqueous solution to the stable compound 2′-deoxyriboguanylurea (GuaUre-dR). Here, we used a phosphoramidite that permits the introduction of GuaUre-dR at defined positions in synthetic oligodeoxynucleotides to demonstrate that it is a potent inhibitor of human DNA methyltransferase 1 (hDNMT1) and the bacterial DNA methyltransferase (M.EcoRII) and that it is a mutagen that can form productive base pairs with either Guanine or Cytosine. Pure GuaUre-dR was found to be an effective demethylating agent and was able to induce 5azaC-dR type fragile sites FRA1J and FRA9E in human cells. Moreover, we report that demethylation associated with C:G → G:C transversion and C:G → T:A transition mutations was observed in human cells exposed to pure GuaUre-dR. The data suggest that most of the effects attributed to 5azaC-dR are exhibited by its stable primary breakdown product.
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Affiliation(s)
- Katarzyna Lamparska
- Beckman Research Institute and Division of Urology and Urologic Oncology, City of Hope, 1500 E. Duarte Rd., Duarte, CA 91010-3000, USA
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5
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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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6
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Godzina P, Adrych-Rozek K, Markiewicz WT. Synthetic Oligonucleotide Combinatorial Libraries. 3. Synthesis of Polyamevonucleosides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044615] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Przemyslaw Godzina
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12, PL-61704 , Poznah , Poland
| | - Katarzyna Adrych-Rozek
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12, PL-61704 , Poznah , Poland
| | - Wojciech T. Markiewicz
- a Institute of Bioorganic Chemistry, Polish Academy of Sciences , Noskowskiego 12, PL-61704 , Poznah , Poland
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7
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Markiewicz WT, Godzina P, Markiewicz M. Synthesis of Polyaminooligonucleotides and Their Combinatorial Libraries. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044749] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Marsh AJ, Williams DM, Grasby JA. The synthesis and properties of oligoribonucleotide-spermine conjugates. Org Biomol Chem 2004; 2:2103-12. [PMID: 15254639 DOI: 10.1039/b404150j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyamines stabilise nucleic acids against chemical and enzymatic degradation, facilitate the formation of secondary and tertiary structures and enhance cellular uptake. Therefore methods for the syntheses of polyamine-nucleic acid conjugates are of interest. A route for the syntheses of RNA-spermine conjugates has been developed. The polyamine was introduced to the C-5 position of uridine via an ethyl tether and the molecule elaborated into a synthon suitable for oligoribonucleotide assembly. The resultant oligomers were components of the hairpin ribozyme. Characterisation of the spermine-conjugated catalytic RNA revealed that attachment of the polyamine was well tolerated in three of four positions, namely U41, U37 and U34, suggesting that conjugation to C-5 brings about minimal structural perturbation.
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Affiliation(s)
- Andrew J Marsh
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield, UKS3 7HF
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9
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Introduction of structural diversity into oligonucleotides containing 6-thioguanine via on-column conjugation. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00147-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Güimil García R, Brank AS, Christman JK, Marquez VE, Eritja R. Synthesis of oligonucleotide inhibitors of DNA (Cytosine-C5) methyltransferase containing 5-azacytosine residues at specific sites. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:369-78. [PMID: 11838638 DOI: 10.1089/108729001753411335] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The incorporation of 5-azacytosine residues into DNA causes potent inhibition of DNA (Cytosine-C5) methyltransferases. The synthesis of oligodeoxyribonucleotides incorporating single or multiple 5-aza-2'-deoxycytidine residues at precise sites was undertaken to generate an array of sequences containing the reactive 5-azacytosine base as specific target sites for enzymatic methylation. Preparation of these modified oligonucleotides requires the use of 2-(p-nitrophenyl)ethyloxycarbonyl (NPEOC) groups for the protection of exocyclic amino functions. These groups are removed under mild conditions, thus avoiding conventional protocols that are detrimental to the integrity of the 5-azacytosine ring.
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11
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Harris TM, Harris CM. Synthesis of N2‐Substituted Deoxyguanosine Nucleosides from 2‐Fluoro‐6‐
O
‐(Trimethylsilylethyl)‐2′‐Deoxyinosine. ACTA ACUST UNITED AC 2001; Chapter 1:Unit 1.3. [DOI: 10.1002/0471142700.nc0103s00] [Citation(s) in RCA: 5] [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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12
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Potier PF, Behr JP. Recognition of DNA by strand invasion with oligonucleotide-spermine conjugates. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:809-13. [PMID: 11563121 DOI: 10.1081/ncn-100002435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Modified oligonucleotides bearing spermine groups (ODN-sper) with increased binding affinity to DNA have been synthesized. The ability of these ODN-sper to bind within superhelical double-stranded DNA by strand invasion has been studied. The uptake by a supercoiled plasmid was 3 fold higher for the ODN-sper than for the unmodified oligonucleotides.
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Affiliation(s)
- P F Potier
- Laboratoire de Chimie Génétique, UMR 7514, Faculté de Pharmacie de Strasbourg, BP 24, F-67401 Illkirch, France
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13
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Potier P, Abdennaji A, Behr JP. Synthesis and hybridization properties of oligonucleotides containing polyamines at the C-2 position of purines: a pre-synthetic approach for the incorporation of spermine into oligodeoxynucleotides containing 2-(4,9,13-triazatridecyl)-2'-deoxyguanosine. Chemistry 2000; 6:4188-94. [PMID: 11128283 DOI: 10.1002/1521-3765(20001117)6:22<4188::aid-chem4188>3.0.co;2-n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have developed a synthesis of spermine-containing oligonucleotides (ODN-sper) which allows incorporation of multiple polyamine residues. This approach was based on the pertrifluoroacetylated 5'DMT-dGsper phosphoramidite synthon. Its coupling yield with resin-bound ODN decreased dramatically when close to the 3'-end. Optimization of the coupling conditions allowed 22-mer ODNs containing up to six spermine residues to be synthesized. Several ODNs of different sequences with 1-4 pendent spermines could be purified and their hybridization properties were evaluated. Duplex melting temperatures increased linearly with the number of polyamine residues (deltaTm/sper = 3.0 +/- 0.2 degrees C in 100mM NaCl). This compares very favorably with values reported for duplexes of similar initial stability containing other cation-substituted bases. Moreover, the stability increase was neither sequence nor position-dependent, and even contiguous spermine residues did not cross-talk. Extrapolation based on these findings leads to the conclusion that a duplex formed with a 22-mer oligonucleotide containing seven spermine residues would be as stable as genomic DNA, which highlights its potential for DNA strand invasion.
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Affiliation(s)
- P Potier
- Laboratoire de Chimie Génétique associé CNRS, Université Louis Pasteur de Strasbourg, Illkirch, France
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14
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Markiewicz WT, Astriab A, Godzina P, Markiewicz M. Synthetic oligonucleotide combinatorial libraries and their applications. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 2000; 55:174-7. [PMID: 10919074 DOI: 10.1016/s0014-827x(00)00014-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The application of synthetic oligonucleotide combinatorial libraries is described in the studies of triplex DNA. A new method of selection of dispersed (beaded) oligonucleotide combinatorial libraries based on the use of streptavidin magnetic beads is presented. A combinatorial chemistry approach is also proposed for studies of polyaminooligonucleotides.
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Affiliation(s)
- W T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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15
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Kim HY, Nechev L, Zhou L, Tamura P, Harris CM, Harris TM. Synthesis and adduction of fully deprotected oligodeoxynucleotides containing 6-chloropurine. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01462-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Fàbrega C, Güimil García R, Díaz AR, Eritja R. Studies on the synthesis of oligonucleotides containing photoreactive nucleosides: 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine. Biol Chem 1998; 379:527-33. [PMID: 9628347 DOI: 10.1515/bchm.1998.379.4-5.527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Oligonucleotides containing the photoreactive nucleosides 2-azido-2'-deoxyinosine and 8-azido-2'-deoxyadenosine have been prepared using protected 2-fluoro-2'-deoxyinosine and 8-bromo-2'-deoxyadenosine phosphoramidites. After the assembly of the oligonucleotides, the nucleoside derivatives are converted to the corresponding azido derivatives by treatment with lithium azide in dry DMF. Deprotection of oligonucleotides carrying these azidonucleosides is performed with concentrated ammonia at room temperature.
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Affiliation(s)
- C Fàbrega
- European Molecular Biology Laboratory, Heidelberg, Germany
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