Synthesis of PS/PO-chimeric oligonucleotides using mixed oxathiaphospholane and phosphoramidite chemistry

2015 ◽  
Vol 13 (1) ◽  
pp. 269-276 ◽  
Author(s):  
Ewa Radzikowska ◽  
Janina Baraniak
Keyword(s):  
Solid Phase ◽  
Phosphoramidite Chemistry ◽  
Chimeric Oligonucleotides

Chimeric oligonucleotides containing stereoregular phosphorothioate and natural phosphodiester linkages have been obtained on the solid phase support using nucleoside oxathiaphospholanes and commercially available nucleoside phosphoramidites.

Synthesis and sequencing of Informational Poly(amino phosphodiester)s

2021 ◽  
Author(s):  
Ian Roszak ◽  
Laurence Oswald ◽  
Abdelaziz AL-OUAHABI ◽  
Annabelle Bertin ◽  
Eline Laurent ◽  
...  
Keyword(s):  
Main Chain ◽  
Solid Phase ◽  
Tertiary Amines ◽  
Phosphoramidite Chemistry

Sequenced-defined poly(amino phosphodiester)s containing main-chain tertiary amines were synthesized by automated solid-phase phosphoramidite chemistry. These polymers were prepared using four monomers with different substituents. The formed polymers were characterized by...

scholarly journals Solid-Phase Synthesis of Phosphorothioate/Phosphonothioate and Phosphoramidate/Phosphonamidate Oligonucleotides

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1872 ◽  
Author(s):  
Ondřej Kostov ◽  
Radek Liboska ◽  
Ondřej Páv ◽  
Pavel Novák ◽  
Ivan Rosenberg
Keyword(s):  
Solid Phase Synthesis ◽  
Solid Phase ◽  
The Novel ◽  
Phase Synthesis ◽  
Chimeric Oligonucleotides ◽  
Modified Oligonucleotide

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.

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.

scholarly journals Targeting RNase L to Human Immunodeficiency Virus RNA with 2-5A-Antisense

1998 ◽  
Vol 9 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Player ◽  
RK Maitra ◽  
RH Silverman ◽  
PF Torrence
Keyword(s):  
Human Immunodeficiency Virus ◽  
Solid Phase ◽  
Rnase L ◽  
Hiv Rna ◽  
Cleavage Activity ◽  
Virus Rna ◽  
Phosphoramidite Chemistry ◽  
Immunodeficiency Virus ◽  
Antisense Approach ◽  
A Cell

In an attempt to develop a lead for the application of 2–5A-antisense to the targeted destruction of human immunodeficiency virus (HIV) RNA, specific target sequences within the HIV mRNAs were identified by analysis of the theoretical secondary structure. 2-5A-antisense chimeras were chosen against a total of 11 different sequences: three in the gag mRNA, three in the rev mRNA and five in the tat mRNA. 2-5A-antisense chimera synthesis was accomplished using solid-phase phosphoramidite chemistry. These chimeras were evaluated for their activity in a cell-free assay system using purified recombinant human RNase L to effect cleavage of 32P-labelled RNA transcripts of plasmids derived from HIV NL4-3. This screening revealed that of the three 2-5A-antisense chimeras targeted against gag mRNA, only one had significant HIV RNA cleavage activity, approximately10-fold-reduced compared to the parent 2-5A tetramer and comparable to that reported for the prototypical 2-5A-anti-PKR chimera, targeted against PKR mRNA. The cleavage activity of this chimera was specific, since a scrambled antisense domain chimera and a chimera without the key 5′-monophosphate moiety were both inactive. The 10 other 2-5A-antisense chimeras against tat and rev had significantly less activity. These results imply that HIV gag RNA, like PKR RNA and a model HIV tat-oligoA- vif RNA, can be cleaved using the 2-5A-antisense approach. The results further imply that not all regions of a potential RNA target are accessible to the 2-5A-antisense approach.

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>

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

Synthesis and hybridization of oligonucleotides modified at AMP sites with adenine pyrrolidine phosphonate nucleotides

2009 ◽  
Vol 74 (6) ◽  
pp. 935-955 ◽  
Author(s):  
Dominik Rejman ◽  
Petr Kočalka ◽  
Radek Pohl ◽  
Zdeněk Točík ◽  
Ivan Rosenberg
Keyword(s):  
Solid Phase ◽  
Thermal Characteristics ◽  
Stable Complex ◽  
Modified Oligonucleotides ◽  
Pyrrolidine Ring ◽  
Phosphonic Acids ◽  
Phosphoramidite Chemistry ◽  
Ring Nitrogen ◽  
Ring Nitrogen Atom ◽  
Phosphotriester Method

Three structurally diverse types of the protected pyrrolidine nucleoside phosphonates were prepared as the monomers for the introduction of pyrrolidine nucleotide units into modified oligonucleotides on the solid phase. Two different chemistries were used for incorporation of modified and natural units: the phosphotriester method for the former, i.e., monomers containing N-phosphonoalkyl and N-phosphonoacyl moieties attached to the pyrrolidine ring nitrogen atom, and phosphoramidite chemistry for the latter. Since the synthesized pyrrolidine nucleoside phosphonic acids are close mimics of the 3′-deoxynucleoside 5′-phosphates, the incorporation of one modified unit into oligonucleotides gives rise to one 2′,5′ internucleotide linkage. A series of nonamers containing two or three modified units, as well as the fully modified adenine 15-mer, were synthesized in reverse order, i.e., from the 5′ to the 3′ end of the strand. The measurement of thermal characteristics of the complexes of modified nonamers with the complementary strand revealed a destabilizing effect of the introduced modification. The modified adenine homooligonucleotide, was found to form the most stable complex with oligothymidylate of all the tested modified oligonucleotides in terms of ΔTm per modification.

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