Optimization and Mechanistic Analysis of Oligonucleotide Cleavage from Palladium-Labile Solid-Phase Synthesis Supports1
摘要:
Pd(0)-labile solid-phase synthesis supports have been used to produce oligonucleotides containing S'-alkyl carboxylic acid and 3'-hydroxy termini in quantitative yields. Optimization of the cleavage reaction conditions using tetrabutylammonium formate buffer resulted in quantitative yields of oligonucleotides using 4 molar equiv of Pd-2(dba)(3).CHCl3 in 1 h at 55 degrees C. A proton source facilitates cleavage of the oligonucleotide from the supports. Trace amounts of water, acting as a nucleophile on the eta(3)-complex, presumably preventing back biting by the initially released oligonucleotide, are required to obtain reproducibly high yields of cleaved oligonucleotides during a 1 h reaction. The previously observed lability of beta-cyanoethyl groups to the Pd(0) conditions has been examined using a mononucleotide substrate. Cleavage of the beta-cyanoethyl group was shown to proceed to the exclusion of other alkyl groups. A mechanism involving initial insertion by Pd(0) into the carbon-oxygen bond of the beta-cyanoethyl group is suggested to account for the cleavage of this group.
Tuning DNA Stability To Achieve Turnover in Template for an Enzymatic Ligation Reaction
作者:Abu Kausar、Rosalie D. McKay、Jade Lam、Rohan S. Bhogal、Alexandra Y. Tang、Julianne M. Gibbs-Davis
DOI:10.1002/anie.201102579
日期:2011.9.12
destabilizing modifications into a DNAtemplate leads to turnover in a DNA‐templatedligationreaction. By incorporating a cross‐catalytic cycle, self‐replication was also achieved, with one target able to make 32 copies of itself (see picture). This destabilization approach represents a general method for incorporating amplification into DNAligation processes using T4 DNA ligase.
Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives
作者:Yu-Cheng Chang、Jayatilake Herath、Tony H.-H. Wang、Christine S. Chow
DOI:10.1016/j.bmc.2007.11.039
日期:2008.3
A series of 3-substituted uridine and pseudouridine derivatives, based on the naturally occurring 3-(3-amino-3-carboxypropyl) modification, were synthesized. Their aqueous solution conformations were determined by using circular dichroism and NMR spectroscopy. Functional group composition and chain length were shown to have only a subtle influence on the distribution of syn/anti conformations of the
OLIGONUCLEOTIDE DERIVATIVE, OLIGONUCLEOTIDE CONSTRUCT USING THE SAME, AND METHODS FOR PRODUCING THEM
申请人:GIFU UNIVERSITY
公开号:US20180094017A1
公开(公告)日:2018-04-05
The oligonucleotide derivative of the present invention is represented by Formula (1). This derivative is considered to be introduced into cells by binding of its amino sugar chain moiety to a ligand on cell surfaces, and have selective drug delivery function. The oligonucleotide derivative can be easily synthesized and introduced into cells without using a lipofection reagent.
wherein—A and B are independently modified or unmodified oligonucleotides whose total chain length is 3 or more, and A and B do not contain hydroxyl groups at 3′ and 5′ ends of the oligonucleotide; S represents a sugar substituent, a peptide chain, or a tocopherol-binding group; and an alkyl group may be bound instead of hydrogen bound to a benzene ring.
TFFH as an Excellent Reagent for Acylation of Alcohols, Thiols and Dithiocarbamates
作者:Jørn B. Christensen、Michael Pittelkow、Fadhil S. Kamounah、Ulrik Boas、Brian Pedersen
DOI:10.1055/s-2004-831250
日期:——
A convenient and easy procedure to synthesize esters and thioesters from the corresponding carboxylic acid using TFFH as the coupling reagent is described. The preparation of N-acyl-dithiocarbamates from carboxylic acids and 1,3-thiazolidine-2-thione with TFFH as the coupling reagent is also described.
Hydroxyalkylated phosphoramidate, phosphoramidothioate and phosphorodiamidothioate derivatives as thiophosphate protecting groups in the development of thermolytic DNA prodrugs
作者:Andrzej Grajkowski、Jacek Cieślak、Alexei Gapeev、Serge L. Beaucage
DOI:10.1039/b9nj00692c
日期:——
The hydroxyalkylated phosphoramidate 4a, phosphoramidothioates 4b, 4e–j, and phosphorodiamidothioates 4c and 4d have been identified as a new class of heat-sensitive thiophosphate protecting groups in the development of thermolytic immunomodulatory DNA prodrugs. These alcohols are converted to their deoxyribonucleoside phosphoramidite derivatives 6a–j, which are then used in the preparation of the thermosensitive dinucleoside phosphorothioates 7a–j. The negatively charged thiophosphate protecting groups of 7a–b and 7e–j presumably undergo thermolytic cyclodeesterification at elevated temperature under essentially neutral conditions. The thiophosphate protecting groups of 7e and 7f show relatively rapid deprotection kinetics at 37 °C (t½ = 20 and 42 h, respectively) and are therefore suitable for the protection of phosphodiester functions flanking the CpG motifs of immunomodulatory DNA sequences, whereas the thiophosphate protecting groups of 7g–j with thermolytic deprotection half-lives in the range of 94–265 h at 37 °C are more appropriate for the thiophosphate protection of CpG motifs. Furthermore, the thermostability of the group protecting the thiophosphate function of 7a (t½ = 82 min at 90 °C) should offer adequate protection of the 5′- and/or 3′-terminal phosphodiester functions of DNA prodrugs against ubiquitous extracellular and intracellular exonucleases.