scholarly journals A P(V)-Platform for Oligonucleotide Synthesis

2021 ◽  
Author(s):  
Phil Baran ◽  
Kyle W. Knouse ◽  
Yazhong Huang ◽  
Shenjie Qiu ◽  
wei hao ◽  
...  
Keyword(s):  
Solid Phase ◽  
High Reactivity ◽  
Oligonucleotide Synthesis ◽  
Complex Molecules ◽  
Phase Synthesis ◽  
Disease States ◽  
Racemic Form ◽  
Phosphoramidite Chemistry ◽  
Sustainability Challenges ◽  
Phosphate Diesters

<div><div><div><p>The early promise of gene-based therapies is currently being realized at an accelerated pace with over 155 active clinical trials for antisense compounds and multiple FDA-approved oligonucleotide therapeutics. Fundamental advances in this area are vital and present an unprecedented opportunity to both address disease states that have been resistant to other common modalities and improve the significant sustainability challenges associated with production of these complex molecules on a commercial scale. The advent of phosphoramidite coupling chemistry and solid-phase synthesis 40 years ago democratized oligonucleotide synthesis to the scientific community, paving the way for many of these stunning developments. The reliability and generality of this approach for the preparation of native phosphate-diesters is attributed to the high reactivity of phosphorus when in the P(III)-oxidation state versus the desired P(V), as it enables rapid P-heteroatom bond formation. However, the growing demand for more diverse phosphorus-based linkages has challenged the limits of this technology. For example, the phosphorothioate (PS) linkage, which stabilizes oligonucleotides towards nuclease cleavage, is universally employed in current oligonucleotide therapeutics but is generally incorporated in racemic form. Stereodefined PS oligonucleotides may have desirable biological and physical properties but are accessed with difficulty using phosphoramidite chemistry. Here we report a flexible and efficient [P(V)]-based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can efficiently install not only stereodefined or racemic thiophosphates, but can install any combination of (S, R or rac)-PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotides. Importantly this platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable, P(V) reagents.</p></div></div></div>

scholarly journals A P(V)-Platform for Oligonucleotide Synthesis

2021 ◽  
Author(s):  
Phil Baran ◽  
Kyle W. Knouse ◽  
Yazhong Huang ◽  
Shenjie Qiu ◽  
wei hao ◽  
...  
Keyword(s):  
Solid Phase ◽  
High Reactivity ◽  
Oligonucleotide Synthesis ◽  
Complex Molecules ◽  
Phase Synthesis ◽  
Disease States ◽  
Racemic Form ◽  
Phosphoramidite Chemistry ◽  
Sustainability Challenges ◽  
Phosphate Diesters

<div><div><div><p>The early promise of gene-based therapies is currently being realized at an accelerated pace with over 155 active clinical trials for antisense compounds and multiple FDA-approved oligonucleotide therapeutics. Fundamental advances in this area are vital and present an unprecedented opportunity to both address disease states that have been resistant to other common modalities and improve the significant sustainability challenges associated with production of these complex molecules on a commercial scale. The advent of phosphoramidite coupling chemistry and solid-phase synthesis 40 years ago democratized oligonucleotide synthesis to the scientific community, paving the way for many of these stunning developments. The reliability and generality of this approach for the preparation of native phosphate-diesters is attributed to the high reactivity of phosphorus when in the P(III)-oxidation state versus the desired P(V), as it enables rapid P-heteroatom bond formation. However, the growing demand for more diverse phosphorus-based linkages has challenged the limits of this technology. For example, the phosphorothioate (PS) linkage, which stabilizes oligonucleotides towards nuclease cleavage, is universally employed in current oligonucleotide therapeutics but is generally incorporated in racemic form. Stereodefined PS oligonucleotides may have desirable biological and physical properties but are accessed with difficulty using phosphoramidite chemistry. Here we report a flexible and efficient [P(V)]-based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can efficiently install not only stereodefined or racemic thiophosphates, but can install any combination of (S, R or rac)-PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotides. Importantly this platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable, P(V) reagents.</p></div></div></div>

Improved Conditions for Solid Phase Synthesis of Oligonucleotides on PS-PEG Copolymers

1995 ◽  
Vol 50 (7) ◽  
pp. 1096-1100 ◽  
Author(s):  
Ernst Bayer ◽  
Konrad Bleicher ◽  
Martin Maier
Keyword(s):  
Electrospray Mass Spectrometry ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Chemical Properties ◽  
Oligonucleotide Synthesis ◽  
Phase Synthesis ◽  
Controlled Pore Glass ◽  
Product Identification ◽  
Pore Glass ◽  
And Chemical Properties

Polystyrene-polyethylene glycol (PS-PEG) tentacle polymers with loadings of up to 60/<μmol/g were used for standard oligonucleotide synthesis. As these resins are easy to handle and stable under reaction and cleavage conditions they may be used alternatively to controlled pore glass (CPG) as the most commonly used solid support for oligonucleotide synthesis. However, structural and chemical properties of the PS-PEG resins require modified conditions to guarantee syntheses with high coupling efficiencies. Oligonucleotides (ODN ) of various sequences and lengths have successfully been synthesized using HPLC and capillary electrophoresis (CE) for purity control. Additionally, electrospray mass spectrometry (ES-MS) was used for product identification.

Solid-Phase Synthesis of DNA Chemical Sensor

2013 ◽  
Vol 815 ◽  
pp. 305-311 ◽  
Author(s):  
Hui Yong Zhang
Keyword(s):  
Nucleic Acid ◽  
Chemical Sensor ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Acid Synthesis ◽  
Synthetic Approach ◽  
Biological Interactions ◽  
Oligonucleotide Synthesis ◽  
Phase Synthesis ◽  
Essential Components

Oligonucleotides are essential components of many applications in molecular biology. The synthesis chemistry is robust and commercial oligonucleotide synthesizers have taken advantage of the chemistry to provide oligonucleotides of high quality and purity. This paper established nucleic acid synthesis platform to carry out the synthesis of the labeled nucleic acid probes based on the DNA synthesizer and solid-phase synthesis technology. We chose to study the automated synthesis starting from DMT protected FAM labeled amidite attached to controlled pore glass (CPG) support and the standard trityl-off oligonucleotide synthesis cycle was performed, yielding the solid-supported oligonucleotide. The reported automated solid-phase oligonucleotide synthesis procedure successfully employs the common iterative synthesis, deblocking, activation, coupling, capping, oxidation, and isolation steps in standard oligonucleotide synthesis. The automated synthetic approach can also be applied to oligonucleotides of different length, composition of nucleotide, demonstrating the universality of the method. Moreover, the synthesis involved the use of commercially available, safe, stable, and inexpensive reagents, particularly advantageous and attractive for their use in automated solid-phase synthesis. The synthesis allows custom tailoring of their structure to the requirements of biological assays within hours, as opposed to traditional approaches that require weeks or months of work in the laboratory. Therefore it will become much easier to investigate biological interactions and optimize for objectives such as the receptor mediated targeting of oligonucleotides.

Solid-phase synthesis of phosphorylated peptides by phosphoramidite chemistry

Peptides 1992 ◽  
1993 ◽  
pp. 334-335 ◽  
Author(s):  
Elizabeth A. Ottinger ◽  
Nuria A. Solé ◽  
Zhenping Tian ◽  
David A. Bernlohr ◽  
George Barany
Keyword(s):  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Phase Synthesis ◽  
Phosphoramidite Chemistry ◽  
Phosphorylated Peptides

scholarly journals 8-Fluoro-N-2-isobutyryl-2′-deoxyguanosine: Synthesis and Reactivity

Molbank ◽  
10.3390/m1119 ◽  
2020 ◽  
Vol 2020 (1) ◽  
pp. M1119 ◽  
Author(s):  
Andrei Solodinin ◽  
James Helmkay ◽  
Samuel Ollivier ◽  
Hongbin Yan
Keyword(s):  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Ammonium Hydroxide ◽  
Dichloroacetic Acid ◽  
Protecting Group ◽  
Phase Synthesis ◽  
Phosphoramidite Chemistry ◽  
Acidic Conditions

3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2′-deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2′-deoxyguanosine and C8:5′-O-cyclo-2′-deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis.

Solid-phase synthesis of 5′-triantennary N-acetylgalactosamine conjugated antisense oligonucleotides using phosphoramidite chemistry

2015 ◽  
Vol 25 (19) ◽  
pp. 4127-4130 ◽  
Author(s):  
Thazha P. Prakash ◽  
W. Brad Wan ◽  
Audrey Low ◽  
Jinghua Yu ◽  
Alfred E. Chappell ◽  
...  
Keyword(s):  
Antisense Oligonucleotides ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Phase Synthesis ◽  
Phosphoramidite Chemistry
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