202719-41-3Relevant academic research and scientific papers
NBS-DMSO as a nonaqueous nonbasic oxidation reagent for the synthesis of oligonucleotides
Uzagare, Matthew C.,Padiya, Kamlesh J.,Salunkhe, Manikrao M.,Sanghvi, Yogesh S.
, p. 3537 - 3540 (2003)
A new method for the oxidation of nucleoside phosphite triester into phosphate triester under nonbasic and nonaqueous conditions using NBS-DMSO in CH3CN has been developed. The utility of this method for solution- and solid-phase synthesis of oligonucleotide is demonstrated.
Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA
Paul, Sibasish,Roy, Subhadeep,Monfregola, Luca,Shang, Shiying,Shoemaker, Richard,Caruthers, Marvin H.
, p. 3253 - 3264 (2015)
The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2′-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.
Correction to: Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA (Journal of the American Chemical Society (2015) 137 (3253-3264) DOI: 10.1021/ja511145h)
, p. 13586 - 13586 (2017)
Supporting Information. In Figure S19, the LC-MS profile for ODN 15 as obtained from 37 scans has been added as part B. The ESI scans shown in parts A and B were obtained from the same sample. These ESI scans (16 and 37, respectively) generate essentially the same results. In Figure S21, the LC-MS profile for ODN 17 as obtained from 34 scans has been added as part B. The ESI scans as shown in parts A and B were obtained from the same sample. These ESI scans (78 and 37, respectively) generate essentially the same conclusions. As expected with more scans, several additional minor side products/impurities were observed with the profile from 78 scans as published. These LC-MS profiles were obtained from unpurified reaction mixtures as obtained from the controlled pore glass supports following synthesis. The quality of these products should be compared to the results obtained when the same crude reaction mixtures were analyzed by denaturing polyacrylamide gel electrophoresis (see Figure 2 in the original article). These additions do not alter any of the results or conclusions as presented in original publication.
Studies on the synthesis of neamine-dinucleosides and neamine-PNA conjugates and their interaction with RNA
Mei, Hui,Xing, Lei,Cai, Li,Jin, Hong-Wei,Zhao, Peng,Yang, Zhen-Jun,Zhang, Liang-Ren,Zhang, Li-He
supporting information; scheme or table, p. 5355 - 5358 (2009/07/18)
Two types of neamine derivatives, neamine-dinucleotide conjugates 8a-g and neamine-PNA conjugates 12a-c and 14a-d, were synthesized. Compound 8a-g were synthesized by the condensation of azido-neamine with dinucleotide-5′-carboxylic acids, followed by reduction and deprotection. Compound 12a-c and 14a-d were synthesized by the similar strategy. The binding affinities of conjugates 8a-g, 12a-c, and 14a-d towards 16S RNA, 18S RNA, and TAR RNA were evaluated by SPR. It indicates that conjugates 12a-c and 14a-d interact with 16S, 18S RNA at the same level as that of neamine, 14a and 14d show about twofold binding affinities to TAR RNA compared to that of neamine. However, the neamine-dinucleotide conjugates 8a-g exhibit very weak binding affinities to 16S, 18S, and TAR RNA, computer modelling results that negative-negative electrostatic repulsion of phosphate group in compound 8a-g and RNA leads to a sharp decrease of the binding affinities compared with that of neamine, neamine-nucleoside and neamine-PNA conjugates.
Synthesis of analogues of oligonucleotides; synthesis of unprotected C-linked di- and tri-nucleotides
Mellor, Ben J.,Thomas, Eric J.
, p. 747 - 757 (2007/10/03)
The Wittig reaction between the N-benzyloxymethylthymidine-derived ylide 25 and the aldehyde 16 followed by hydrogenolysis gives access to the unprotected C-linked dinucleotide 20 on a multi-gram scale. Oxidation of the dinucleotide gives the aldehyde 27 which is condensed with the ylide 25 to give the unprotected bis-C-linked trinucleotide 29 after hydrogenolysis. The mono-C-linked trinucleotide 44 is prepared by oxidation of the dinucleotide ester 34 to the aldehyde 36 which is condensed with the ylide 25 followed by hydrogenolysis to give the mono-C-linked trinucleotide ester 38. This intermediate is also prepared from the C-linked dinucleotide 20 by conversion into the phosphoramidite 41 which is coupled with 3-acetylthymidine 15 to give the mono-C-linked trinucleotide phosphite 42. Oxidation and deprotection give the phosphate triester 38. Treatment of 38 with methanolic ammonia gives the fully unprotected mono-C-linked trinucleotide 44.
