A convenient procedure for the deprotection of silylated nucleosides and nucleotides using triethylamine trihydrofluoride

Pirrung, Michael C.; Shuey, Steven W.; Lever, Davic C.; Fallon, Lara

doi:10.1016/s0960-894x(01)80358-9

Cited by 54 publications

(53 citation statements)

References 19 publications

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“…The solid support was removed by filtration and the filtrate was lyophilized. Removal of the silyl-protecting groups on the 29-hydroxyls was achieved by incubation in a 9:1 (v/v) TEA-3HF (triethylamine trihydrofluoride)/DMF mixture at 55°C for 2 h or at room temperature for 24 h, followed by 1-butanol precipitation (Pirrung et al 1994). The sample was lyophilized before redissolving in 5 mM ammonium bicarbonate (pH 7).…”

Section: Oligonucleotide Synthesis and Purificationmentioning

confidence: 99%

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Lerman

Kennedy²,

Shankar³

et al. 2011

RNA

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The NMR solution structure is reported of a duplex, 59GUGAAGCCCGU/39UCACAGGAGGC, containing a 4 @ 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 59GAA/39AGG, 59GAG/39AGG, 59GAA/39AAG, and 59AAG/39AGG. The structural information is compared with predictions made with the MC-Sym program.

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Section: Oligonucleotide Synthesis and Purificationmentioning

confidence: 99%

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Lerman

Kennedy²,

Shankar³

et al. 2011

RNA

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“…When the reaction was run at 0°C, a 1:1 mixture of anomers was formed. The once troublesome anomeric desilylation step, 39,49 that was later optimized on a related analogue by SchmidtÕs group, 45 was refined by the use of triethylamine/trihydrofluoride complex in THF, 50 which removed the TBDMS group cleanly and quantitatively to give 13, which was subsequently converted to the trichloroacetimidate 14 7 in 95% yield by the procedure of Ren and Liu. 27 Glycosylations with serine and threonine derivatives 15a and 15b 44 proceeded with excellent yield and stereoselectivity, but under strictly optimized conditions.…”

Section: Tf-glycopeptide Precursors For Multivalent Assembly On Goldmentioning

confidence: 99%

“…This glycopeptide 18 was previously designed to bind to MHC-I isotypes where the carbohydrate was placed in an anchor position known to bind in a pocket of the T-cell receptor (TcR). 51 Glycopeptide 18 was shown to inhibit binding of a well-characterized K b -binding peptide with a 4 nM IC 50 and elicits a strong cytotoxic T-lymphocyte (CTL) response against the TF disaccharide. 51 We reasoned that a multivalent presentation of this glycopeptide may lead to an enhanced immune response and possibly more powerful glycopeptide-restricted CTL.…”

Section: Attempt At Glycopeptide-coated Nanoparticle Synthesismentioning

confidence: 99%

Synthesis of gold nanoparticles bearing the Thomsen–Friedenreich disaccharide: a new multivalent presentation of an important tumor antigen

Svarovsky

Székely

Barchi

2005

Tetrahedron: Asymmetry

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“…Deprotonation of 8 with excess LDA [26], followed by formylation with DMF [27] [28], hydrolysis, and reduction [29] of the resulting aldehyde [7] yielded 80% of the hydroxymethylated uridine 11. Mesylation of 11 yielded 82% of 12, while 4monomethoxytritylation gave 80% of 13 that was desilylated [30] to the alcohol 14 (84%). The desired C(5')-S-acetates 9 [31] (70%) and 15 (75%) were obtained by substitution of the crude C(5')-O-p-toluenesulfonates obtained from 7 and 14 with excess potassium thioacetate in DMF [32].…”

mentioning

confidence: 99%

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

Ritter

Egli

Bernet

et al. 2008

Helvetica Chimica Acta

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The formation of cyclic duplexes (pairing) of known oxymethylene‐linked self‐complementary U*[o]A(*) dinucleosides contrasts with the absence of pairing of the ethylene‐linked U*[ca]A(*) analogues. The origin of this difference, and the expected association of U*[x]A(*) and A*[x]U(*) dinucleosides with x=CH2, O, or S was analysed. According to this analysis, pairing occurs via constitutionally isomeric Watson–Crick, reverse Watson–Crick, Hoogsteen, or reverse Hoogsteen H‐bonded linear duplexes. Each one of them may give rise to three diastereoisomeric cyclic duplexes, and each one of them can adopt three main conformations. The relative stability of all conformers with x=CH2, O, or S were analysed. U*[x]A(*) dinucleosides with x=CH2 do not form stable cyclic duplexes, dinucleosides with x=O may form cyclic duplexes with a gg‐conformation about the C(4′)C(5′) bond, and dinucleosides with x=S may form cyclic duplexes with a gt‐conformation about this bond. The temperature dependence of the chemical shift of HN(3) of the self‐complementary, oxymethylene‐linked U*[o]A(*) dinucleosides 1–6 in CDCl3 in the concentration range of 0.4–50 mM evidences equilibria between the monoplex, mainly linear duplexes, and higher associates for 3, between the monoplex and cyclic duplexes for 6, and between the monoplex, linear, and cyclic duplexes as well as higher associates for 1, 2, 4, and 5. The self‐complementary, thiomethylene‐linked U*[s]A(*) dinucleosides 27–32 and the sequence isomeric A*[s]U(*) analogues 33–38 were prepared by S‐alkylation of the 6‐(mesyloxymethyl)uridine 12 and the 8‐(bromomethyl)adenosine 22. The required thiolates were prepared in situ from the C(5′)‐acetylthio derivatives 9, 15, 19, and 25. The association in CHCl3 of the thiomethylene‐linked dinucleoside analogues was studied by 1H‐NMR and CD spectroscopy, and by vapour‐pressure osmometric determination of the apparent molecular mass. The U*[s]A(*) alcohols 28, 30, and 31 form cyclic duplexes connected by Watson–Crick H‐bonds, while the fully protected dimers 27 and 29 form mainly linear duplexes and higher associates. The diol 32 forms mainly cyclic duplexes in solution and corrugated ribbons in the solid state. The nucleobases of crystalline 32 form reverse Hoogsteen H‐bonds, and the resulting ribbons are cross‐linked by H‐bonds between HOCH2C(8/I) and N(3/I). Among the A*[s]U(*) dimers, only the C(8/I)‐hydroxymethylated 37 forms (mainly) a cyclic duplex, characterized by reverse Hoogsteen base pairing. The dimers 34–36 form mainly linear duplexes and higher associates. Dimers 34 and particularly 38 gelate CHCl3. Temperature‐dependent CD spectra of 28, 30, 31, and 37 evidence π‐stacking in the cyclic duplexes. Base stacking in the particularly strongly associating diol 32 in CHCl3 solution is evidenced by a melting temperature of ca. 2°.

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A convenient procedure for the deprotection of silylated nucleosides and nucleotides using triethylamine trihydrofluoride

Cited by 54 publications

References 19 publications

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Synthesis of gold nanoparticles bearing the Thomsen–Friedenreich disaccharide: a new multivalent presentation of an important tumor antigen

Oligonucleotide Analogues with Integrated Bases and Backbone. Part 17

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