Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• required to assemble oligonucleotides by phosphoramidite chemistry and to ligate them enzymatically, are known to partially degrade nitroxides. This problem can be reduced by postsynthetic introduction of the spin label [13][14][15][16][17][18][19][20][21][22][23][24]. Starting from convertible nucleotides

• oligonucleotides by phosphoramidite building blocks [27][28][29][30][31][32][33][34][35][36][37][38][39][40]. However, some degradation of the spin labels inevitably will occur. Nitroxide labeled DNA strands of the general structures 2 and 4 have been prepared by this way [30][34][37]. In recent years, we have

• therefore developed a third strategy based on photolabile protective groups [41][42][43] finally leading to phosphoramidite 6. This building block behaves in solid-phase RNA synthesis as any normal TOM protected amidite. It is completely stable against the conditions used for strand assembly, RNA

Oligonucleotide analogues with cationic backbone linkages

• Melissa Meng and
• Christian Ducho

Beilstein J. Org. Chem. 2018, 14, 1293–1308, doi:10.3762/bjoc.14.111

• supra). We have reported that partially zwitterionic NAA-modified DNA oligonucleotides can be obtained by standard solid phase-supported automated DNA synthesis if 'dimeric' phosphoramidite building blocks 49 and 50 are employed (Scheme 5) [72][73]. For the synthesis of 'dimeric' phosphoramidites 49 and

• cationic oligomers, i.e., oligonucleotide analogues with the cationic NAA-modification as their sole internucleotide linkage. The phosphoramidite-based synthetic strategy depicted in Scheme 5 was not suitable to reach this goal as it furnishes phosphate diester linkages at least at every second position

• accessible by means of chemical synthesis, which is either based on the application of H-phosphonate (for i) or phosphoramidite-based (for iv) DNA synthesis, or on a massively modified version of DNA synthesis (for ii and iii), or on solid phase-supported peptide synthesis (for iv). Studies on the properties

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• solubility of substrates in the ionic liquids (<10 mM) which rendered the phosphitylating agents prone to hydrolysis. Highly reactive phosphoramidite derivatives of low molecular weight amines could be isolated by this route (on 40–60 mg scales). Under the same conditions, coupling of bis(2-cyanoethyl

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• within a robust cyclic disulfide moiety [14]. Several modified ONs containing the cyclic disulfide trans-5-benzyl-1,2-dithiane-4-yl moiety have been synthesized using the corresponding thymidine phosphoramidite. Although they exhibited strong stability in serum and penetrated cells more efficiently

• synthesis and properties of 2’-O-alkyldithiomethyl-modified RNAs [15][16]. Previously, Urata had described a post-synthetic approach for the synthesis of 2’-O-methyldithiomethyl (MDTM) ONs [17] that was more practical than the phosphoramidite approach used initially for the chemical synthesis of RNAs using

• enzymolabile groups into phosphorothioate ONs by the reaction with alkyl iodides has been considered since the mid 90's [21][22][23][24], the use of phosphoramidite building blocks bearing the enzymocleavable group is the method of choice for synthesizing ON prodrugs regardless of the protected function

Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries

• Ruth Suchsland,
• Bettina Appel and
• Sabine Müller

Beilstein J. Org. Chem. 2018, 14, 397–406, doi:10.3762/bjoc.14.28

• , although using phosphite triester chemistry [27]. In this case, the synthesis started with the coupling of an N-acyl-5'-O-DMTr-protected nucleoside-3'-O-phosphoramidite to an N-acyl-3'-O-TBDMS-protected nucleoside, followed by oxidation of the internucleotide phosphorous. Upon cleavage of the 5'-O-DMTr

• group, the dimer was reacted with another N-acyl-5'-O-DMTr-protected nucleoside-3'-O-phosphoramidite to afford the trimer. The 3'-O-TBDMS group was selectively removed under mild conditions with trimethylamine/3HF (Figure 4B) with strict control of pH to leave the β-cyanoethyl groups at the

• -phosphonate and the release of the oligomer with the free 3'-OH group leaving all other protecting groups intact. This strategy has been shown to be compatible with phosphoramidite chemistry and β-cyanoethyl protection of the internucleotide phosphates [33]. A more recent report describes the preparation of a

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• functionalized with a phosphoramidite and incorporated into oligonucleotides [30]. However, the fully detailed synthesis with complete characterization was published in 2007 as a Nature Protocol paper [37]. The aromatic core of tC was prepared according to the procedure of Roth et al. (Scheme 1), followed by a

• glycosylation using the sodium-salt method as later also performed in the synthesis of tCnitro in 2009 (reaction c, Scheme 3) [14][42]. The synthesis was finished by standard DMTr protection and phosphitylation furnishing tC deoxyribose phosphoramidite in a total of 2.1% yield over 6 steps [43][44]. In 2008

• sodium methoxide in MeOH, which yielded the free nucleoside 15 in 71%. Standard DMTr protection furnished compound 16 which was then activated for oligonucleotide solid-phase synthesis (SPS) by phosphitylation using CEP-Cl. The total yield of tCnitro deoxyribose phosphoramidite was 0.8% over 6 steps

Aminosugar-based immunomodulator lipid A: synthetic approaches

• Alla Zamyatina

Beilstein J. Org. Chem. 2018, 14, 25–53, doi:10.3762/bjoc.14.3

• deprotection by catalytic hydrogenation furnished lipid A 31. Alternatively, the lactol 30 was phosphitylated by application of the phosphoramidite procedure with (benzyloxy)[(N-Cbz-3-aminopropyl)oxy](N,N-diisopropylamino)phosphine in the presence of 1H-tetrazole and subsequent oxidation with dimethyldioxirane

• lactol was phosphorylated via phosphoramidite procedure to furnish fully protected trisaccharide phosphodiester 40, which was deprotected by hydrogenolysis on Pd(OH)2/C in THF/H2O/AcOH to give H. pylori lipid A 41. The availability of pure homogeneous synthetic compounds allowed for extensive

• -benzyl ether. The liberated 4’-OH group was phosphorylated via phosphoramidite procedure to furnish 56. Next, both 2- and 2’-N-Troc groups were reductively cleaved using Zn in acetic acid and the resulting 2’- and 2-amino groups were acylated with (R)-3-dodecanoyltetradecanoic acid to give 57. Three

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• ′-phosphorylated trimer synthesized by standard phosphoramidite chemistry. To address the problem of m7G instability under basic conditions, the TMG-capping reaction was carried out upon deprotection of all base-labile groups. Utilization of a novel, acid labile linker to the solid support allowed for subsequent

• . A combination of chemical synthesis and enzymatic modification was also used by Thillier et al. for the large scale synthesis of capped RNA. Herein, to circumvent the problem of m7G instability, non-methylated capped RNAs were first synthesized using the phosphoramidite 2′-O-pivaloyloxymethyl method

Synthesis of oligonucleotides on a soluble support

• Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

• byproducts after each coupling, oxidation and deprotection step. The techniques applied so far include precipitation, extraction, chromatography and nanofiltration. As regards coupling, all conventional chemistries, viz. phosphoramidite, H-phosphonate and phosphotriester strategies, have been attempted

• . While P(III)-based phosphoramidite and H-phosphonate chemistries are almost exclusively used on a solid support, the “outdated” P(V)-based phosphotriester chemistry still offers one major advantage for the synthesis on a soluble support; the omission of the oxidation step simplifies the coupling cycle

• with acyl chlorides or chlorophosphates [11][12][13]. On applying the phosphoramidite chemistry, the phosphite triesters obtained are oxidized to phosphate triesters in each coupling cycle, whereas the H-phosphonate diesters may be stable enough to become oxidized only at the end of chain assembly

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

A postsynthetically 2’-“clickable” uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA

• Heidi-Kristin Walter,
• Bettina Olshausen,
• Ute Schepers and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2017, 13, 127–137, doi:10.3762/bjoc.13.16

• phosphoramidite chemistry. The alkyne groups as reactive precursors are attached to the oligonucleotide [13], especially at the 5-position of pyrimidines [13], the 7-position of 7-deazapurines [14], and the 2’-position of ribofuranosides [11][15]. These positions were chosen since they are typically accepted by

• developed and synthesized the 2’-propargyl-modified arabino-configured uridine analog 2, incorporated it into DNA by automated phosphoramidite chemistry, “clicked” it to a variety of our recently established, photostable cyanine-styryl dyes and probed the fluorescence and energy transfer properties by

• determination of quantum yields and emission color contrasts. Results and Discussion The synthesis of the phosphoramidite 7 (Scheme 2) was straightforward and includes mainly protecting group chemistry since it starts with the commercially available arabino-configured uridine analog 3. The 3’- and 5’-hydroxy

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

• Elisabeth Mairhofer,
• Elisabeth Fuchs and
• Ronald Micura

Beilstein J. Org. Chem. 2016, 12, 2556–2562, doi:10.3762/bjoc.12.250

• modern RNA research, in particular for atomic mutagenesis experiments to explore mechanistic aspects of ribozyme catalysis. Here, we report the 5-step synthesis of a c3A phosphoramidite from cost-affordable starting materials. The key reaction is a silyl-Hilbert–Johnson nucleosidation using unprotected 6

• , prices in the hundreds of Euro range for low milligram amounts make this source unsatisfying. The previously reported c3A phosphoramidite synthesis from our laboratory [16], which took older reports by Matsuda, Piccialli, McLaughlin, Watanabe, Robins, and co-workers into account [17][18][19][20][21

• . Because of this frustrating situation, we set out to develop an efficient and easy-to-handle synthesis of a 3-deazaadenosine phosphoramidite building block. Results and Discussion Previously described synthetic routes to c3A via nucleosidation In 1966, Rousseau, Townsend, and Robins reported the

DNA functionalization by dynamic chemistry

• Zeynep Kanlidere,
• Oleg Jochim,
• Marta Cal and
• Ulf Diederichsen

Beilstein J. Org. Chem. 2016, 12, 2136–2144, doi:10.3762/bjoc.12.203

• libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer

• oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was

• ][18][19][20][21] constitutes an attractive choice for oligonucleotide functionalization. Threoninol can be introduced in oligonucleotides via the corresponding phosphoramidite generating a ribose-free abasic site on the backbone that provides the amine group for later functionalization [22][23][24][25

Chiral cyclopentadienylruthenium sulfoxide catalysts for asymmetric redox bicycloisomerization

• Barry M. Trost,
• Michael C. Ryan and
• Meera Rao

Beilstein J. Org. Chem. 2016, 12, 1136–1152, doi:10.3762/bjoc.12.110

• functionality on the substrate in question. For example, Hayashi has shown that a rhodium/phosphoramidite catalysis is particularly effective for asymmetric [5 + 2] cycloaddition reactions (Scheme 2b). The (S,R,R)-diastereomer of the Feringa-style phosphoramidite ligand proved to be crucial to both the yield

1H-Imidazol-4(5H)-ones and thiazol-4(5H)-ones as emerging pronucleophiles in asymmetric catalysis

• Antonia Mielgo and
• Claudio Palomo

Beilstein J. Org. Chem. 2016, 12, 918–936, doi:10.3762/bjoc.12.90

• bearing the quinoyl moiety provided once again better stereochemical results than 2-naphthylthiazolones. 2.2.3 Iridium-catalyzed allylic substitution reactions. Allylic substitution reactions catalyzed by cyclometalated iridium phosphoramidite complexes constitute a powerful tool for the construction of C

Synthesis of cyclic N¹-pentylinosine phosphate, a new structurally reduced cADPR analogue with calcium-mobilizing activity on PC12 cells

• Ahmed Mahal,
• Stefano D’Errico,
• Nicola Borbone,
• Brunella Pinto,
• Agnese Secondo,
• Valeria Costantino,
• Valentina Tedeschi,
• Giorgia Oliviero,
• Vincenzo Piccialli and
• Gennaro Piccialli

Beilstein J. Org. Chem. 2015, 11, 2689–2695, doi:10.3762/bjoc.11.289

• regioisomer 7 equipped with the reactive phosphorous(III) group. Unfortunately, the activation of the phosphoramidite function with 1H-tetrazole aimed at inducing the cyclization on the 5’-OH ribose function produced only a complex mixture. No traces of the target cyclic compound were detected after the usual

• phosphorous oxidation step. This failure prompted us to use the alternative phosphitylating reagent bis(cyanoethyl)phosphoramidite 8, which, after the regioselective reaction with the 5’-hydroxyalkyl function of 5 led to the phosphotriester product 9 after the phosphorous oxidation with t-BuOOH. Starting from

Copper-catalysed asymmetric allylic alkylation of alkylzirconocenes to racemic 3,6-dihydro-2H-pyrans

• Emeline Rideau and
• Stephen P. Fletcher

Beilstein J. Org. Chem. 2015, 11, 2435–2443, doi:10.3762/bjoc.11.264

• examination of phosphoramidite ligands (for example, Table 1, entries 2 and 11–13) did not improve the ee. We then tested many different additives (TMSCl, AgOTf, borates, ZrCl4, Si(OEt)4, etc, for example Table 1, entries 14–18). Using B(OiPr)3, which presumably acts as a Lewis acid, improved the ee to 80

Copper-catalyzed asymmetric conjugate addition of organometallic reagents to extended Michael acceptors

• Thibault E. Schmid,
• Sammy Drissi-Amraoui,
• Christophe Crévisy,
• Olivier Baslé and
• Marc Mauduit

Beilstein J. Org. Chem. 2015, 11, 2418–2434, doi:10.3762/bjoc.11.263

• co-workers discovered in 2001 the first example of copper-catalyzed enantioselective 1,6-conjugate addition [16]. Using phosphoramidite ligand (S,R,R)-L1 and Cu(OTf)2 as the copper source, diethylzinc was added to dienone 16 with a full 1,6-regioselectivity, and an ee of 35% (Scheme 1). In 2006

• polyenic Michael acceptors and various nucleophiles [18]. In this study, the addition of diethylzinc was notably investigated on cyclic dienone 20 (Scheme 3). As regards the 1,6-conjugate addition, the highest enantioselectivity was achieved with the bulky phosphoramidite (S,R,R)-L2, to afford 21 in 66

• efficiently 1,6-ACA reactions using trialkylaluminium reagents as nucleophiles. In 2008, Alexakis, Mauduit and co-workers described the copper-catalyzed 1,6-ACA of triethylaluminium on cyclic α,β,γ,δ-unsaturated ketones using the phosphoramidite (S,R,R)-L2 ligand [18]. The reaction of the cyclic dienone 20

DNA display of glycoconjugates to emulate oligomeric interactions of glycans

• Alexandre Novoa and
• Nicolas Winssinger

Beilstein J. Org. Chem. 2015, 11, 707–719, doi:10.3762/bjoc.11.81

• conjugate, the same group reported the synthesis of phosphoramidite derivatized with an acetyl-protected monosaccharide 3 and its incorporation into DNA to access well-defined DNA conjugates 4 (Scheme 2). Cleavage of the acetate groups occurs upon ammonia treatment for DNA cleavage/deprotection [19][20][21

• available N-hydroxysuccinimide (NHS)-carboxy-dT phosphoramidite 5 (Scheme 3). This method allows the sequential introduction of any amine-functionalized glycan during DNA synthesis and was shown to be compatible with more complex glycans such as Lewis X trisaccharide. The capping step in DNA synthesis

• density. Synthesis of glycoconjugate DNA by diazo-coupling. β-Galactose-modified deoxyuridine phosphoramidite used for solid-phase DNA synthesis and DNA display of glycan. (NHS)-carboxy-dT phosphoramidite as a general entry for the solid-phase synthesis of glycan–DNA conjugates. Preparation of the DNA

Diastereoselective and enantioselective conjugate addition reactions utilizing α,β-unsaturated amides and lactams

• Katherine M. Byrd

Beilstein J. Org. Chem. 2015, 11, 530–562, doi:10.3762/bjoc.11.60

• to excellent yields and enantioselectivities. In 2006, Pineschi and co-workers reported the copper-catalyzed asymmetric 1,4-addition of alkylzinc reagents to acyclic α,β-unsaturated imides [95]. In this case, the authors used a phosphoramidite as the chiral ligand. They were also able to obtain the

TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy

• Dnyaneshwar B. Gophane and
• Snorri Th. Sigurdsson

Beilstein J. Org. Chem. 2015, 11, 219–227, doi:10.3762/bjoc.11.24

• deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; TA directly and UA as well as UC through a urea linkage. TA and UC showed a minor destabilization of a DNA duplex, as registered by a small decrease

• nucleoside TA and its corresponding phosphoramidite were prepared by a previously reported procedure [74] with minor modifications. The synthesis started with the reaction between 3′,5′-diacetyl-2′-deoxyinosine (1) and 2,4,6-triisopropylbenzenesulfonyl chloride to obtain compound 2 (Scheme 1). Coupling of 2

• gave compound 8 in low yields (Scheme 2). Cleavage of the TBDMS groups using TBAF gave spin-labeled nucleoside UA, which was tritylated to give compound 9 and phosphitylated to give phosphoramidite 10. The synthesis of UC, the urea-cytidine analogue, started by reaction of 3′,5′-TBDMS-protected 2

NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks

• Boris Schmidtgall,
• Claudia Höbartner and
• Christian Ducho

Beilstein J. Org. Chem. 2015, 11, 50–60, doi:10.3762/bjoc.11.8

• of the NAA-linkage at T–T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X–T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A–T phosphoramidite building blocks for automated DNA

• synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step

• physiological pH values, thus leading to a (partially) zwitterionic backbone structure in NAA-modified oligonucleotides. We have previously described that NAA-modified DNA oligonucleotides can be obtained by standard solid phase-supported automated DNA synthesis, using the 'dimeric' phosphoramidite building

Nucleic acid chemistry

• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2014, 10, 2928–2929, doi:10.3762/bjoc.10.311

• cases, postsynthetic strategies can allow for the desired oligonucleotides modification. This becomes an even more important issue for functionalities, probes or biologically relevant molecules that are incompatible with routine phosphoramidite chemistry. Although nucleic acid chemistry appears to be a

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

• Vicky Gheerardijn,
• Jos Van den Begin and
• Annemieke Madder

Beilstein J. Org. Chem. 2014, 10, 2566–2572, doi:10.3762/bjoc.10.268

• [64], only one extra deprotection step is needed after incorporation. After transformation of the modified nucleosides into the corresponding phosphoramidite building blocks 5, 9 and 13 are amenable to incorporation in nucleic acids through standard DNA synthesis methodology. The described protocol

Phosphinocyclodextrins as confining units for catalytic metal centres. Applications to carbon–carbon bond forming reactions

• Matthieu Jouffroy,
• Rafael Gramage-Doria,
• David Sémeril,
• Dominique Armspach,
• Dominique Matt,
• Werner Oberhauser and
• Loïc Toupet

Beilstein J. Org. Chem. 2014, 10, 2388–2405, doi:10.3762/bjoc.10.249

• differs from that of the only other reported trans-[RhH(CO)3L] complex (where L is a bulky phosphoramidite), the observed three carbonyl bands (2055 (sh), 2022 (w) and 1998 (s) cm−1) being here spread over a larger frequency range [31]. Note that the related cobalt complex trans-[CoH(CO)3(PCy3)] displays