1
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Zharkov TD, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Influence of Combinations of Lipophilic and Phosphate Backbone Modifications on Cellular Uptake of Modified Oligonucleotides. Molecules 2024; 29:452. [PMID: 38257365 PMCID: PMC10818405 DOI: 10.3390/molecules29020452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Numerous types of oligonucleotide modifications have been developed since automated synthesis of DNA/RNA became a common instrument in the creation of synthetic oligonucleotides. Despite the growing number of types of oligonucleotide modifications under development, only a few of them and, moreover, their combinations have been studied widely enough in terms of their influence on the properties of corresponding NA constructions. In the present study, a number of oligonucleotides with combinations of 3'-end lipophilic (a single cholesteryl or a pair of dodecyl residues) and phosphate backbone modifications were synthesized. The influence of the combination of used lipophilic groups with phosphate modifications of various natures and different positions on the efficiency of cell penetration was evaluated. The obtained results indicate that even a couple of phosphate modifications are able to affect a set of oligonucleotide properties in a complex manner and can remarkably change cellular uptake. These data clearly show that the strategy of using different patterns of modification combinations has great potential for the rational design of oligonucleotide structures with desired predefined properties.
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Affiliation(s)
| | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (O.V.M.); (S.A.Z.); (S.N.K.)
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2
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Bauer I, Ilina E, Zharkov T, Grigorieva E, Chinak O, Kupryushkin M, Golyshev V, Mitin D, Chubarov A, Khodyreva S, Dmitrienko E. Self-Penetrating Oligonucleotide Derivatives: Features of Self-Assembly and Interactions with Serum and Intracellular Proteins. Pharmaceutics 2023; 15:2779. [PMID: 38140119 PMCID: PMC10747088 DOI: 10.3390/pharmaceutics15122779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Lipophilic oligonucleotide derivatives are a potent approach to the intracellular delivery of nucleic acids. The binding of these derivatives to serum albumin is a determinant of their fate in the body, as its structure contains several sites of high affinity for hydrophobic compounds. This study focuses on the features of self-association and non-covalent interactions with human serum albumin of novel self-penetrating oligonucleotide derivatives. The study revealed that the introduction of a triazinyl phosphoramidate modification bearing two dodecyl groups at the 3' end region of the oligonucleotide sequence has a negligible effect on its affinity for the complementary sequence. Dynamic light scattering verified that the amphiphilic oligonucleotides under study can self-assemble into micelle-like particles ranging from 8 to 15 nm in size. The oligonucleotides with dodecyl groups form stable complexes with human serum albumin with a dissociation constant of approximately 10-6 M. The oligonucleotide micelles are simultaneously destroyed upon binding to albumin. Using an electrophoretic mobility shift assay and affinity modification, we examined the ability of DNA duplexes containing triazinyl phosphoramidate oligonucleotides to interact with Ku antigen and PARP1, as well as the mutual influence of PARP1 and albumin or Ku antigen and albumin upon interaction with DNA duplexes. These findings, together with the capability of dodecyl-containing derivatives to effectively penetrate different cells, such as HEK293 and T98G, indicate that the oligonucleotides under study can be considered as a platform for the development of therapeutic preparations with a target effect.
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Affiliation(s)
- Irina Bauer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ekaterina Ilina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Timofey Zharkov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Evgeniya Grigorieva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Olga Chinak
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Maxim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Victor Golyshev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Dmitry Mitin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alexey Chubarov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Svetlana Khodyreva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
| | - Elena Dmitrienko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia; (I.B.); (T.Z.); (O.C.); (M.K.); (V.G.); (D.M.); (S.K.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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3
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Takahashi Y, Kakuta K, Namioka Y, Igarashi A, Sakamoto T, Iwata Hara R, Sato K, Wada T. Synthesis of P-Modified DNA from Boranophosphate DNA as a Precursor via Acyl Phosphite Intermediates. J Org Chem 2023; 88:10617-10631. [PMID: 37462534 PMCID: PMC10407935 DOI: 10.1021/acs.joc.3c00659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 08/05/2023]
Abstract
In this study, we successfully synthesized several kinds of P-modified nucleic acids from boranophosphate DNAs via an acyl phosphite intermediate in solution and on a solid support. In the solution-phase synthesis, phosphorothioate diester, phosphotriester, and phosphoramidate diester were synthesized in a one-pot reaction from boranophosphodiester via the conversion of an acyl phosphite as a key intermediate. In addition, doubly P-modified nucleic acid derivatives which were difficult to synthesize by the phosphoramidite and H-phosphonate methods were also obtained by the conversion reaction. In the solid-phase synthesis, a boranophosphate derivative was synthesized on a solid support using the H-boranophosphonate method. Then, an acyl phosphite intermediate was formed by treatment with pivaloyl chloride in pyridine, followed by appropriate transformations to obtain the P-modified derivatives such as phosphotriester and phosphorothioate diester. Notably, it was suggested that the conversion reaction of a boranophosphate to a phosphorothioate diester proceeded with retention of the stereochemistry of the phosphorous center. In addition, a phosphorothioate/phosphate chimeric dodecamer was successfully synthesized from a boranophosphate/phosphate chimeric dodecamer using the same strategy. Therefore, boranophosphate derivatives are versatile precursors for the synthesis of P-modified DNA, including chimeric derivatives.
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Affiliation(s)
- Yuhei Takahashi
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kiyoshi Kakuta
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yukichi Namioka
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayumi Igarashi
- Department
of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Taiichi Sakamoto
- Department
of Life Science, Chiba Institute of Technology, Graduate School of Advanced Engineering, Chiba 275-0016, Japan
| | - Rintaro Iwata Hara
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department
of Neurology and Neurological Science, Graduate School of Medicinal
and Dental Sciences, Tokyo Medical and Dental
University, Tokyo 113-8519, Japan
| | - Kazuki Sato
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takeshi Wada
- Department
of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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4
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Paul S, Caruthers MH. Synthesis of Backbone-Modified Morpholino Oligonucleotides Using Phosphoramidite Chemistry. Molecules 2023; 28:5380. [PMID: 37513252 PMCID: PMC10384400 DOI: 10.3390/molecules28145380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Phosphorodiamidate morpholinos (PMOs) are known as premier gene knockdown tools in developmental biology. PMOs are usually 25 nucleo-base-long morpholino subunits with a neutral phosphorodiamidate linkage. PMOs work via a steric blocking mechanism and are stable towards nucleases' inside cells. PMOs are usually synthesized using phosphoramidate P(V) chemistry. In this review, we will discuss the synthesis of PMOs, phosphoroamidate morpholinos (MO), and thiophosphoramidate morpholinos (TMO).
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Affiliation(s)
- Sibasish Paul
- Nucleic Acid Solutions Division, Agilent Technologies, Boulder, CO 80301, USA
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
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5
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Gołębiewska J, Stawinski J. Boranephosphonates. Unraveling chemistry of the P-BH 3 functional group. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2021.1990922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Justyna Gołębiewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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6
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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7
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Chen X, Luo W, Wang Y, Li Z, Ma X, Peng AY. Efficient Synthesis of Phosphonamidates through One-Pot Sequential Reactions of Phosphonites with Iodine and Amines. Chemistry 2020; 26:14474-14480. [PMID: 32776399 DOI: 10.1002/chem.202002934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 11/10/2022]
Abstract
A one-pot sequential strategy to construct phosphonamidates has been developed by generating phosphonites in situ from arylmagnesium bromides and triethyl phosphite followed by treatment with iodine and amines. A variety of phosphonamidates were obtained with good to excellent yields at room temperature from easily available materials.
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Affiliation(s)
- Xunwei Chen
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Wenjun Luo
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Yanlin Wang
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Zikang Li
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Xiaorui Ma
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
| | - Ai-Yun Peng
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, China
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8
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Kumar P, Caruthers MH. DNA Analogues Modified at the Nonlinking Positions of Phosphorus. Acc Chem Res 2020; 53:2152-2166. [PMID: 32885957 DOI: 10.1021/acs.accounts.0c00078] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemically modified oligonucleotides are being developed as a new class of medicines for curing conditions that previously remained untreatable. Three primary classes of therapeutic oligonucleotides are single-stranded antisense oligonucleotides (ASOs), double stranded small interfering RNAs (siRNAs), and oligonucleotides that induce exon skipping. Recently, ASOs, siRNAs, and exon skipping oligonucleotides have been approved for patients with unmet medical needs, and many other candidates are being tested in late stage clinical trials. In coming years, therapeutic oligonucleotides may match the promise of small molecules and antibodies. Interestingly, in the 1980s when we developed chemical methods for synthesizing oligonucleotides, no one would have imagined that these highly charged macromolecules could become future medicines. Indeed, the anionic nature and poor metabolic stability of the natural phosphodiester backbone provided a major challenge for the use of oligonucleotides as therapeutic drugs. Thus, chemical modifications of oligonucleotides were essential in order to improve their pharmacokinetic properties. Keeping this view in mind, my laboratory has developed a series of novel oligonucleotides where one or both nonbridging oxygens in the phosphodiester backbone are replaced with an atom or molecule that introduces molecular properties that enhance biological activity. We followed two complementary approaches. One was the use of phosphoramidites that could act directly as synthons for the solid phase synthesis of oligonucleotide analogues. This approach sometimes was not feasible due to instability of various synthons toward the reagents used during synthesis of oligonucleotides. Therefore, using a complementary approach, we developed phosphoramidite synthons that can be incorporated into oligonucleotides with minimum changes in the solid phase DNA synthesis protocols but contain a handle for generating appropriate analogues postsynthetically.This Account summarizes our efforts toward preparing these types of analogues over the past three decades and discusses synthesis and properties of backbone modified oligonucleotides that originated from the Caruthers' laboratory. For example, by replacing one of the internucleotide oxygens with an acetate group, we obtained so-called phosphonoacetate oligonucleotides that were stable to nucleases and, when delivered as esters, entered into cells unaided. Alternatively oligonucleotides bearing borane phosphonate linkages were found to be RNase H active and compatible with the endogenous RNA induced silencing complex (RISC). Oligonucleotides containing an alkyne group directly linked to phosphorus in the backbone were prepared as well and used to attach molecules such as amino acids and peptides.
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Affiliation(s)
- Pawan Kumar
- Broad Institute of Harvard and MIT, Stanley Center for Psychiatric Research, 450 Main Street, Cambridge, Massachusetts 02142, United States
| | - Marvin H. Caruthers
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, United States
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9
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Verma RS, Mishra M, Pandey CB, Kumar S, Tiwari B. Global Access to 3/4-Phosphorylated Heterocycles via a Carbene-Catalyzed Stetter Reaction of Vinylphosphonates and Aldehydes. J Org Chem 2020; 85:8166-8175. [DOI: 10.1021/acs.joc.0c00150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ram Subhawan Verma
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, India
| | - Monika Mishra
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, India
| | - Chandra Bhan Pandey
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, India
| | - Shailesh Kumar
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, India
| | - Bhoopendra Tiwari
- Division of Molecular Synthesis & Drug Discovery, Centre of Biomedical Research, SGPGIMS-Campus, Raebareli Road, Lucknow 226014, India
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10
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Gołębiewska J, Stawinski J. Reaction of Boranephosphonate Diesters with Pyridines or Tertiary Amines in the Presence of Iodine: Synthetic and Mechanistic Studies. J Org Chem 2020; 85:4312-4323. [PMID: 32073846 DOI: 10.1021/acs.joc.9b03506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Boranephosphonate diesters react with heteroaromatic and certain tertiary amines in the presence of an oxidant (I2) to afford the boron-modified phosphodiester analogues containing a P-B-N structural motif. Our multinuclear 31P and 11B NMR spectroscopy studies lend support for a two-step mechanism involving generation of a λ3-boranephosphonate intermediate that immediately coordinates an amine in the solvent cage, leading to B-pyridinium or B-ammonium boranephosphonate betaine derivatives. We found that the type of the solvent used (e.g., dichloromethane vs acetonitrile) significantly affected the course of the reaction, resulting in either formation of boron-modified derivatives or loss of the boron group with a subsequent oxidation of the phosphorus atom. In aprotic, electron-donating, polar solvents., e.g., acetonitrile (ACN) and tetrahydrofuran (THF), a λ3-boranephosphonate intermediate can also coordinate solvent molecules forming P-B-ACN or P-B-THF complexes that may influence the type of the products formed.
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Affiliation(s)
- Justyna Gołębiewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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11
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Kostov O, Liboska R, Páv O, Novák P, Rosenberg I. Solid-Phase Synthesis of Phosphorothioate/Phosphonothioate and Phosphoramidate/Phosphonamidate Oligonucleotides. Molecules 2019; 24:molecules24101872. [PMID: 31096640 PMCID: PMC6571627 DOI: 10.3390/molecules24101872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 11/30/2022] Open
Abstract
We have developed a robust solid-phase protocol which allowed the synthesis of chimeric oligonucleotides modified with phosphodiester and O-methylphosphonate linkages as well as their P-S and P-N variants. The novel O-methylphosphonate-derived modifications were obtained by oxidation, sulfurization, and amidation of the O-methyl-(H)-phosphinate internucleotide linkage introduced into the oligonucleotide chain by H-phosphonate chemistry using nucleoside-O-methyl-(H)-phosphinates as monomers. The H-phosphonate coupling followed by oxidation after each cycle enabled us to successfully combine H-phosphonate and phosphoramidite chemistries to synthesize diversely modified oligonucleotide strands.
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Affiliation(s)
- Ondřej Kostov
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Pavel Novák
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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12
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Chen X, Xiao Z, Chu H, Wang B, Peng AY. Reinvestigation of the iodine-mediated phosphoramidation reaction of amines and P(OR) 3 and its synthetic applications. Org Biomol Chem 2019; 16:6783-6790. [PMID: 30198043 DOI: 10.1039/c8ob01840e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on the iodine-mediated phosphoramidation reaction of amines and trialkyl phosphites was conducted, which not only disclosed the factors affecting the reaction but also revealed that it could proceed smoothly in CH2Cl2 at room temperature in open air. Using this method, various phosphoramidates with different aliphatic amines and aromatic amines were synthesized in good to excellent yields. Our present investigation shows that this underused method is actually a mild, practical and general way to synthesize phosphoramidates and will have wide applications.
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Affiliation(s)
- Xunwei Chen
- School of Chemistry, Sun Yat-sen University, 135 Xingangxi Lu, Guangzhou, 510275, China.
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13
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Su Y, Fujii H, Burakova EA, Chelobanov BP, Fujii M, Stetsenko DA, Filichev VV. Neutral and Negatively Charged Phosphate Modifications Altering Thermal Stability, Kinetics of Formation and Monovalent Ion Dependence of DNA G-Quadruplexes. Chem Asian J 2019; 14:1212-1220. [PMID: 30600926 DOI: 10.1002/asia.201801757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/22/2018] [Indexed: 12/18/2022]
Abstract
The effect of phosphate group modifications on formation and properties of G-quadruplexes (G4s) has not been investigated in detail. Here, we evaluated the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes formed by oligodeoxynucleotides d(G4 T), d(TG4 T) and d(TG5 T), in which all phosphates were replaced with N-methanesulfonyl (mesyl) phosphoramidate or phosphoryl guanidine groups resulting in either negatively charged or neutral DNA sequences, respectively. We established that all modified sequences were able to form G-quadruplexes of parallel topology; however, the presence of modifications led to a decrease in thermal stability relative to unmodified G4s. In contrast to negatively charged G4s, assembly of neutral G4 DNA species was faster in the presence of sodium ions than potassium ions, and was independent of the salt concentration used. Formation of mixed G4s composed of both native and neutral G-rich strands has been detected using native gel electrophoresis, size-exclusion chromatography and ESI-MS. In summary, our results indicate that the phosphate modifications studied are compatible with G-quadruplex formation, which could be used for the design of biologically active compounds.
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Affiliation(s)
- Yongdong Su
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Hirofumi Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Ekaterina A Burakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Boris P Chelobanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Masayuki Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
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14
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Abstract
Borane phosphonate DNA is a promising molecule for biological applications as well as post-synthesis DNA modification, including DNA functionalization.
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Affiliation(s)
- Rajen Kundu
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder
- USA
- CSIR – Central Mechanical Engineering Research Institute
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15
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Gołębiewska J, Rachwalak M, Jakubowski T, Romanowska J, Stawinski J. Reaction of Boranephosphonate Diesters with Amines in the Presence of Iodine: The Case for the Intermediacy of H-Phosphonate Derivatives. J Org Chem 2018; 83:5496-5505. [DOI: 10.1021/acs.joc.8b00419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justyna Gołębiewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Marta Rachwalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Tomasz Jakubowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Joanna Romanowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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16
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Roy S, Paul S, Roy M, Kundu R, Monfregola L, Caruthers MH. Pyridinium Boranephosphonate Modified DNA Oligonucleotides. J Org Chem 2017; 82:1420-1427. [PMID: 28099007 DOI: 10.1021/acs.joc.6b02599] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of previously unknown derivatives of boranephosphonate that contain amine substitutions at boron and the incorporation of these derivatives into the backbone of DNA oligonucleotides is described. These derivatives result from iodine-mediated replacement of one BH3 hydride of a boranephosphonate linkage by pyridine, various substituted pyridines, other aromatic amines, and certain unsaturated amines. Oligonucleotides containing these backbone modifications show enhanced uptake, relative to unmodified DNA, in mammalian cells. The redox behavior of the boranephosphonate and pyridinium boranephosphonate conjugated linkages has also been studied.
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Affiliation(s)
- Subhadeep Roy
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
| | - Sibasish Paul
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
| | - Mithun Roy
- Department of Basic Sciences and Humanities, National Institute of Technology, Manipur , Langol, Imphal, 795004 Manipur, India
| | - Rajen Kundu
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
| | - Luca Monfregola
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
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17
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Feng M, Ruan Z, Shang J, Xiao L, Tong A, Xiang Y. Photocaged G-Quadruplex DNAzyme and Aptamer by Post-Synthetic Modification on Phosphodiester Backbone. Bioconjug Chem 2016; 28:549-555. [PMID: 27931100 DOI: 10.1021/acs.bioconjchem.6b00646] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile post-synthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phosphodiester without any artificial scar. Similarly, the caged G-quadruplex thrombin-binding aptamer also showed light-induced activation of thrombin inhibition activity. This method could serve as a general strategy to prepare photocaged G-quadruplex DNA with other activities for noninvasive control of their functions.
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Affiliation(s)
- Mengli Feng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Zhiyuan Ruan
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University , Beijing 100084, China
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18
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Paul S, Caruthers MH. Synthesis of Phosphorodiamidate Morpholino Oligonucleotides and Their Chimeras Using Phosphoramidite Chemistry. J Am Chem Soc 2016; 138:15663-15672. [PMID: 27934012 DOI: 10.1021/jacs.6b08854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Phosphorodiamidate morpholinos (PMOs) and PMO-DNA chimeras have been prepared on DNA synthesizers using phosphoramidite chemistry. This was possible by first generating boranephosphoroamidate morpholino internucleotide linkages followed by oxidative substitution with four different amines: N,N-dimethylamine, N-methylamine, ammonia, and morpholine. When compared to a natural DNA duplex, the amino modified PMO was found to have a higher melting temperature with either complementary DNA or RNA, whereas the remaining PMO analogues having morpholino, dimethylamino, or N-methylamino phosphorodiamidate linkages had melting temperatures that were either comparable or reduced. Additionally the N,N-dimethylamino PMO-DNA chimeras were found to stimulate RNaseH1 activity. Treatment of HeLa cells with fluorescently labeled PMO chimeras demonstrated that these analogues were efficiently taken up by cells in the presence of a lipid transfection reagent. Because of the simplistic synthesis procedures, various PMO analogues are now readily available and should therefore open new pathways for research into the antisense, diagnostic, and nanotechnology oligonucleotide fields.
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Affiliation(s)
- Sibasish Paul
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309, United States
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19
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20
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Wang X, Feng M, Xiao L, Tong A, Xiang Y. Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme. ACS Chem Biol 2016; 11:444-51. [PMID: 26669486 DOI: 10.1021/acschembio.5b00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.
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Affiliation(s)
- Xiaoyan Wang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Mengli Feng
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
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21
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Shi J, Tang XD, Wu YC, Fang JF, Cao L, Chen XY, Wang ZY. A radical coupling reaction of DMSO with sodium arylsulfinates in air : mild utilization of DMSO as C1 resource for the synthesis of arylsulfonyl dibromomethane. RSC Adv 2016. [DOI: 10.1039/c6ra01393g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A radical coupling reaction of DMSO with ArSO2Na without the needs of anaerobic atmosphere to afford ArSO2CHBr2 is described.
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Affiliation(s)
- Jie Shi
- School of Chemistry and Environment
- South China Normal University
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- Guangzhou 510006
| | - Xiao-Dong Tang
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510640
- P. R. China
| | - Yan-Cheng Wu
- School of Chemistry and Environment
- South China Normal University
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- Guangzhou 510006
| | - Jie-Fang Fang
- School of Chemistry and Environment
- South China Normal University
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- Guangzhou 510006
| | - Liang Cao
- School of Chemistry and Environment
- South China Normal University
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- Guangzhou 510006
| | - Xiao-Yun Chen
- School of Environmental and Chemical Engineering
- Jiangsu University of Science and Technology
- Zhenjiang
- P. R. China
| | - Zhao-Yang Wang
- School of Chemistry and Environment
- South China Normal University
- Key Laboratory of Theoretical Chemistry of Environment
- Ministry of Education
- Guangzhou 510006
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22
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Buck HM. Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/jbpc.2016.71003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Ziemniak M, Kowalska J, Lukaszewicz M, Zuberek J, Wnek K, Darzynkiewicz E, Jemielity J. Phosphate-modified analogues of m(7)GTP and m(7)Gppppm(7)G-Synthesis and biochemical properties. Bioorg Med Chem 2015; 23:5369-81. [PMID: 26264844 DOI: 10.1016/j.bmc.2015.07.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 01/05/2023]
Abstract
The synthesis and biochemical properties of 17 new mRNA cap analogues are reported. Six of these nucleotides are m(7)GTP derivatives, whereas 11 are 'two headed' tetraphosphate dinucleotides based on a m(7)Gppppm(7)G structure. The compounds contain either a boranophosphate or phosphorothioate moiety in the nucleoside neighbouring position(s) and some of them possess an additional methylene group between β and γ phosphorus atoms. The compounds were prepared by divalent metal chloride-mediated coupling of an appropriate m(7)GMP analogue with a given P(1),P(2)-di(1-imidazolyl) derivative. The analogues were evaluated as tools for studying cap-dependent processes in a number of biochemical assays, including determination of affinity to eukaryotic initiation factor eIF4E, susceptibility to enzymatic hydrolysis, and translational efficiency in vitro. The results indicate that modification in the phosphate chain can increase binding to cap-interacting proteins and provides higher resistance to degradation. Furthermore, modified derivatives of m(7)GTP were found to be potent inhibitors of cap-dependent translation in cell free systems.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Katarzyna Wnek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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