The Experts below are selected from a list of 300 Experts worldwide ranked by ideXlab platform
Richard T. Pon - One of the best experts on this subject based on the ideXlab platform.
-
Linker phosphoramidite reagents for Oligonucleotide Synthesis on underivatized solid-phase supports
Tetrahedron Letters, 2001Co-Authors: Richard T. PonAbstract:Abstract Linker phosphoramidite reagents containing a protected nucleoside with a cleavable 3′-ester linkage to either succinic acid, diglycolic acid, or hydroquinone-O,O′-diacetic acid (Q-Linker) allow the 3′-terminal nucleoside of an Oligonucleotide sequence to be attached to underivatized ‘Universal’ amino or hydroxyl supports. After solid-phase Oligonucleotide Synthesis, treatment with NH4OH cleaves the 3′-ester link to the support and produces Oligonucleotides with only 3′-OH ends. No changes to existing phosphoramidite Synthesis cycles, cleavage, or deprotection methods are required.
-
Current Protocols in Nucleic Acid Chemistry - Solid-Phase Supports for Oligonucleotide Synthesis
Current protocols in nucleic acid chemistry, 2000Co-Authors: Richard T. PonAbstract:This unit begins with a discussion of the advantages and disadvantages of Oligonucleotide Synthesis using solid supports. The physical and chemical properties of solid-phase supports are discussed in terms of their suitability for Oligonucleotide Synthesis. In addition, the unit outlines the properties of linkers used for transient or permanent attachment of properly protected nucleosides to the derivatized support, as well as strategies for coupling nucleosides to linkers and conditions for the release of synthetic Oligonucleotides from specific supports.
-
Reusable Solid-Phase Supports for Oligonucleotide Synthesis Using Hydroquinone-O,O'-diacetic Acid (“Q-Linker”)
Nucleosides and Nucleotides, 1999Co-Authors: Richard T. Pon, Z. Guo, X. Yang, Yogesh S. SanghviAbstract:Abstract Reusable solid-phase supports for large scale Oligonucleotide Synthesis have been prepared by converting amino derivatized supports into hydroxyl supports. Rapid nucleo side attachment, via a Q-linker arm, was automatically performed on the DNA synthesizer using HBTU and DMAP as the coupling reagents. All steps were suitable for automation and ∼ 1.5 h was required to prepare the supports for reuse. Up to twelve consecutive syntheses of a 20-mer phosphorothioate were performed on a Synthesis column.
-
Hydroquinone-O,O′-diacetic acid (‘Q-linker’) as a replacement for succinyl and oxalyl linker arms in solid phase Oligonucleotide Synthesis
Nucleic acids research, 1997Co-Authors: Richard T. PonAbstract:When hydroquinone-O,Ooffiacetic acid is used as a linker arm in solid phase Oligonucleotide Synthesis, the time for NH4OH cleavage of oligodeoxy- or oligoribonucleotides is reduced to only 2 min. This allows increased productivity on automated DNA synthesizers without requiring any other modifications to existing reagents or Synthesis and deprotection methods. The Q-linker may also be rapidly cleaved by milder reagents such as 5% NH4OH, potassium carbonate, anhydrous ammonia, t-butylamine or fluoride ion. However, the Q-linker is sufficiently stable for long-term storage at room temperature without degradation and no loss of material occurs during Synthesis. The linker is also reasonably resistant to 20% piperidine/DMF, 0.5 M DBU/pyridine and 1:1 triethylamine/ethanol. The Q-linker can therefore serve as a general replacement for both succinyl and oxalyl linker arms.
-
hydroquinone o o diacetic acid q linker as a replacement for succinyl and oxalyl linker arms in solid phase Oligonucleotide Synthesis
Nucleic Acids Research, 1997Co-Authors: Richard T. PonAbstract:When hydroquinone-O,Ooffiacetic acid is used as a linker arm in solid phase Oligonucleotide Synthesis, the time for NH4OH cleavage of oligodeoxy- or oligoribonucleotides is reduced to only 2 min. This allows increased productivity on automated DNA synthesizers without requiring any other modifications to existing reagents or Synthesis and deprotection methods. The Q-linker may also be rapidly cleaved by milder reagents such as 5% NH4OH, potassium carbonate, anhydrous ammonia, t-butylamine or fluoride ion. However, the Q-linker is sufficiently stable for long-term storage at room temperature without degradation and no loss of material occurs during Synthesis. The linker is also reasonably resistant to 20% piperidine/DMF, 0.5 M DBU/pyridine and 1:1 triethylamine/ethanol. The Q-linker can therefore serve as a general replacement for both succinyl and oxalyl linker arms.
Yogesh S. Sanghvi - One of the best experts on this subject based on the ideXlab platform.
-
Liquid-Phase Oligonucleotide Synthesis: Past, Present, and Future Predictions.
Current protocols in nucleic acid chemistry, 2019Co-Authors: Alejandro Gimenez Molina, Yogesh S. SanghviAbstract:Therapeutic Oligonucleotides have emerged as a powerful paradigm with the ability to treat a wide range of the human diseases. As a result, we have witnessed more than one hundred Oligonucleotides currently in active clinical trials and eight Food and Drug Administration (FDA)-approved drugs. Until now, the demand for Oligonucleotide-based drugs has been fulfilled by conventional solid-phase Synthesis in an effective manner. However, there are products in advanced stages of clinical trials projecting a collective demand of metric ton quantities in the near future. Therefore, large-scale manufacturing of these products has become a high priority for process chemists. This article summarizes the advances in liquid-phase Oligonucleotide Synthesis (LPOS) as a possible alternative strategy to meet the scale-up challenge. A review of the literature describing major efforts in developing LPOS technologies is presented. Gratifyingly, serious attempts are under way to develop an efficient environmentally benign green chemistry protocol that is scalable and cost effective for the manufacturing of Oligonucleotides. A summary of the most innovative LPOS protocols has been included to provide a glimpse of what may be possible in the future for large-scale production of Oligonucleotides. © 2019 by John Wiley & Sons, Inc.
-
Dimethylthiarum disulfide: new sulfur transfer reagent in phosphorothioates Oligonucleotide Synthesis.
Methods in molecular biology (Clifton N.J.), 2005Co-Authors: Zhiwei Wang, Quanlai Song, Yogesh S. SanghviAbstract:Dimethylthiarum disulfide (DTD) has been developed as a new and efficient sulfur-transfer reagent for automated Synthesis of phosphorothioate Oligonucleotides using phosphoramidite chemistry. The traditional four-step automated Oligonucleotide Synthesis has been compressed to three-step protocol using DTD. This improvement allowed an overall 20% reduction in the solvent consumption and reduced the total Synthesis time by 25%. The large-scale application of DTD has been successfully demonstrated by Synthesis of therapeutically useful 20-mer phosphorothioate antisense Oligonucleotides with excellent yield and purity.
-
Tandem Oligonucleotide Synthesis on solid-phase supports for the production of multiple Oligonucleotides.
Journal of Organic Chemistry, 2002Co-Authors: Shuyuan Yu, Yogesh S. SanghviAbstract:More than one Oligonucleotide can be synthesized at a time by linking multiple Oligonucleotides end-to-end in a tandem manner on the surface of a solid-phase support. The 5‘-terminal hydroxyl position of one Oligonucleotide serves as the starting point for the next Oligonucleotide Synthesis. The two Oligonucleotides are linked via a cleavable 3‘-O-hydroquinone-O,O‘-diacetic acid linker arm (Q-linker). The Q-linker is rapidly and efficiently coupled to the 5‘-OH position of immobilized Oligonucleotides using HATU, HBTU, or HCTU in the presence of 1 equiv of DMAP. This protocol avoids introduction of phosphate linkages on either the 3‘- or 5‘-end of Oligonucleotides. A single NH4OH cleavage step can simultaneously release the products from the surface of the support and each other to produce free 5‘- and 3‘-hydroxyl termini. Selective cleavage of one Oligonucleotide out of two sequences has also been accomplished via a combination of succinyl and Q-linker linker arms. Tandem Synthesis of multiple oligonucle...
-
Reusable Solid-Phase Supports for Oligonucleotide Synthesis Using Hydroquinone-O,O'-diacetic Acid (“Q-Linker”)
Nucleosides and Nucleotides, 1999Co-Authors: Richard T. Pon, Z. Guo, X. Yang, Yogesh S. SanghviAbstract:Abstract Reusable solid-phase supports for large scale Oligonucleotide Synthesis have been prepared by converting amino derivatized supports into hydroxyl supports. Rapid nucleo side attachment, via a Q-linker arm, was automatically performed on the DNA synthesizer using HBTU and DMAP as the coupling reagents. All steps were suitable for automation and ∼ 1.5 h was required to prepare the supports for reuse. Up to twelve consecutive syntheses of a 20-mer phosphorothioate were performed on a Synthesis column.
Mitsuo Sekine - One of the best experts on this subject based on the ideXlab platform.
-
A new protecting group for 5′-hydroxyl function of nucleotides in Oligonucleotide Synthesis without acid treatment utilizing unique properties of tritylthio group
Nucleic Acids Symposium Series, 2002Co-Authors: Kohji Seio, Eri Utagawa, Mitsuo SekineAbstract:New protecting groups having a 2-aminomethylbezoyl skeleton, in which the reactive amino functions were blocked further by a tritylthio-type protecting group, were developed for the protection of the 5'-hydroxyl function of nucleosides during the Oligonucleotide Synthesis. These benzoate-type protecting groups were designed to be removed via an intramolecular cyclization following the removal of the tritylthio-type protecting group under mild oxidative conditions using diluted aqueous iodine solution. The new protecting groups would enable us to synthesize Oligonucleotides without using any acid treatment. Furthermore, they can reduce the reaction steps required for a chain elongation cycle from four to three because the deprotection of the 5'-hydroxyl protecting group and the oxidation of the phosphite intermediate can be performed simultaneously by a single aqueous iodine treatment.
-
A new protecting group for 5'-hydroxyl function of nucleotides in Oligonucleotide Synthesis without acid treatment utilizing unique properties of tritylthio group.
Nucleic acids research. Supplement (2001), 2002Co-Authors: Kohji Seio, Eri Utagawa, Mitsuo SekineAbstract:New protecting groups having a 2-aminomethylbezoyl skeleton, in which the reactive amino functions were blocked further by a tritylthio-type protecting group, were developed for the protection of the 5'-hydroxyl function of nucleosides during the Oligonucleotide Synthesis. These benzoate-type protecting groups were designed to be removed via an intramolecular cyclization following the removal of the tritylthio-type protecting group under mild oxidative conditions using diluted aqueous iodine solution. The new protecting groups would enable us to synthesize Oligonucleotides without using any acid treatment. Furthermore, they can reduce the reaction steps required for a chain elongation cycle from four to three because the deprotection of the 5'-hydroxyl protecting group and the oxidation of the phosphite intermediate can be performed simultaneously by a single aqueous iodine treatment.
-
Synthesis of pentathymidylate using a 4-monomethoxytritylthio (MMTrS) group as a 5′-hydroxyl protecting group: toward Oligonucleotide Synthesis without acid treatment
Tetrahedron Letters, 2001Co-Authors: Kohji Seio, Mitsuo SekineAbstract:Abstract A phosphoramidite unit having 4-monomethoxytritylthio as a new 5′-hydroxyl protecting group was prepared and employed in Oligonucleotide Synthesis. The new phosphoramidite enabled the Synthesis of Oligonucleotides without the use of acids such as TFA or DCA.
-
2-(Trimethylsilyl)ethyl as a phosphate protecting group in Oligonucleotide Synthesis
Tetrahedron Letters, 1994Co-Authors: Takeshi Wada, Mitsuo SekineAbstract:Abstract The 2-(trimethylsilyl)ethyl (TSE) group was found to be effective as a protecting group for the internucleotidic phosphate in Oligonucleotide Synthesis. Phosphoramidite building blocks having the TSE group were prepared in good yields. In the case of deoxyguanosine, a 2-N-unprotected phosphoramidite building block was synthesized. These compounds were applied to the solid-phase Synthesis of oligodeoxyribonucleotides. A side reaction associated with the unprotected guanine moiety was elucidated by means of 31P NMR.
Andreas Walther - One of the best experts on this subject based on the ideXlab platform.
-
Scalable One-Pot-Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels.
Journal of the American Chemical Society, 2020Co-Authors: Guido Creusen, Cecilia Oluwadunsin Akintayo, Katja Schumann, Andreas WaltherAbstract:Solid-phase Oligonucleotide Synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA Synthesis but suffers from scalability limitations and hig...
-
Scalable One-Pot - Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels
2020Co-Authors: Guido Creusen, Katja Schumann, Cecilia Oluwadunsin Akintayo, Andreas WaltherAbstract:Solid-phase Oligonucleotide Synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA Synthesis, but suffers from scalability limitations and high reagent consumption. Liquid-phase Oligonucleotide Synthesis (LPOS) uses soluble polymer supports and has the potential of being scalable. However, at present, LPOS requires 3 separate reaction steps and 4-5 precipitation steps per nucleotide addition. Moreover, long acid exposure times during the deprotection step degrade sequences with high A-content (adenine) due to depurination and chain cleavage. In this work, we present the first one-pot liquid-phase DNA Synthesis technique, which allows the addition of one nucleotide in a one-pot reaction of sequential coupling, oxidation and deprotection, followed by a single precipitation step. Furthermore, we demonstrate how to suppress depurination during the addition of adenine nucleotides. We showcase the potential of this technique to prepare high-purity 4-arm PEG‑T<sub>20</sub> (T = thymine) and 4-arm PEG-A<sub>20</sub>building blocks in multi-gram scale. Such complementary 4-arm PEG-DNA building blocks reversibly self-assemble into supramolecular model network hydrogels, and facilitate the elucidation of bond lifetimes. These model network hydrogels exhibit new levels of mechanical properties, high stability at room temperature (melting at 44 °C), and thus open up pathways to next-generation, scalable DNA-materials programmable through sequence recognition and available for macroscale applications<i>.</i>
Andrei P Guzaev - One of the best experts on this subject based on the ideXlab platform.
-
Solid-phase supports for Oligonucleotide Synthesis.
Current protocols in nucleic acid chemistry, 2013Co-Authors: Andrei P GuzaevAbstract:This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to Oligonucleotide chemists for preparation of natural and 3'-modified Oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in Oligonucleotide Synthesis and deprotection is discussed wherever the relevant observations are available.
-
Current Protocols in Nucleic Acid Chemistry - Solid‐Phase Supports for Oligonucleotide Synthesis
Current Protocols in Nucleic Acid Chemistry, 2013Co-Authors: Andrei P GuzaevAbstract:This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to Oligonucleotide chemists for preparation of natural and 3′-modified Oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in Oligonucleotide Synthesis and deprotection is discussed wherever the relevant observations are available. Curr. Protoc. Nucleic Acid Chem. 53:3.1.1-3.1.60. © 2013 by John Wiley & Sons, Inc. Keywords: nucleic acid chemistry; Oligonucleotides; solid-phase Synthesis; molecular biology
-
A conformationally preorganized universal solid support for efficient Oligonucleotide Synthesis.
Journal of the American Chemical Society, 2003Co-Authors: Andrei P Guzaev, Muthiah ManoharanAbstract:A novel, conformationally preorganized nonnucleosidic universal solid support for Oligonucleotide Synthesis was developed. The solid support featured two chemically equivalent hydroxy groups locked in syn-periplanar orientation and orthogonally protected with 4,4‘-dimethoxytrityl and acetyl groups. The solid support was extensively tested in the preparation of Oligonucleotides and their phosphorothioate analogues containing 2‘-deoxy, 2‘-O-methyl, and 2‘-O-methoxyethylnucleoside residues at the 3‘-terminus. Upon completion of Oligonucleotide chain assembly, the support-bound Oligonucleotide material was treated with concentrated ammonium hydroxide, which removed the O-acetyl protection. The deprotected hydroxy group then effected the transesterification of a phosphate linkage between the solid support and the 3‘-terminal nucleoside residue to result in a facile release of the Oligonucleotide to solution. The kinetics of the release process was studied in a continuous flow of concentrated aqueous ammonium h...
-
A novel phosphate protection for Oligonucleotide Synthesis: the 2-[(1-naphthyl)carbamoyloxy]ethyl (NCE) group
Tetrahedron Letters, 2000Co-Authors: Andrei P Guzaev, Muthiah ManoharanAbstract:Abstract The utility of the 2-(arylcarbamoyloxy)ethyl group for protection of internucleosidic phosphate linkages in Oligonucleotide Synthesis was studied. Of the three protecting groups tested, the 2-[(1-naphthyl)carbamoyloxy]ethyl demonstrated high coupling yields, favorable deprotection kinetics and the highest hydrolytic stability of the thymidine phosphoramidite building block. The mechanism of deprotection was confirmed by deprotecting a model phosphate triester and synthetic dodecathymidylate.
