Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance

• Kristen K. Merritt,
• Kevin M. Bradley,
• Daniel Hutter,
• Mariko F. Matsuura,
• Diane J. Rowold and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 2348–2360, doi:10.3762/bjoc.10.245

• systems; solid-phase DNA synthesis; synthetic biology; Introduction It has been nearly 50 years since the first solid-phase synthesis of DNA by Letsinger and Mahadevan [1][2]. This work laid the platform for new strategies in oligonucleotide synthesis, culminating in the development of phosphoramidite

• exploit the phosphoramidite synthesis approach developed in the Caruther laboratory [3], and also the first to illustrate the ability of total synthesis to generate DNA products that are productively different from what might be found in nature. Total synthesis was used to introduce restriction sites to

• to assist in downstream processing. Thus, the complete target L-DNA sequence had 863 base pairs. Synthesis The oligonucleotides containing S and B shown in Table 1 were obtained from IDT, where they were prepared by automated solid phase phosphoramidite-based synthesis following the procedure of

Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining

• Emma Werz and
• Helmut Rosemeyer

Beilstein J. Org. Chem. 2014, 10, 2307–2321, doi:10.3762/bjoc.10.240

• immobilization of lipo-oligonucleotides carrying a racemic bis(hexadecyloxy)propan-1-yl tag (1a) at the 5’-termini at an artificial lipid bilayer–water phase boundary. These were prepared using the cyanoethyl phosphoramidite 1b. A specific duplex formation with complementary cyanine-5 (Cy5)-labelled DNA strands

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• in high yields. Keywords: nucleic acids; oligoribonucleotides; phosphoramidite; soluble support; synthesis; Introduction Recognition of short noncoding RNAs as regulatory elements of gene expression [1][2][3][4][5] has attracted interest in their physico-chemical properties, including structure

• solution phase approach, allowing assembly of short RNAs in a hundreds of milligrams scale. While several such methods for the synthesis of DNA, based either the phosphoramidite [11][12][13][14][15][16], H-phosphonate [17][18][19] or phosphotriester chemistry [20][21][22], have been introduced, none of

• support by a Cu(I) catalyzed click reaction and conventional phosphoramidite chemistry is then applied. The advantage of this support is that the small molecular reagents and byproducts are removed in each coupling cycle by two fully quantitative precipitations from MeOH, one after oxidation and the

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

• Keunsoo Kim,
• Venkateshwarlu Punna,
• Phaneendrasai Karri and
• Ramanarayanan Krishnamurthy

Beilstein J. Org. Chem. 2014, 10, 2131–2138, doi:10.3762/bjoc.10.220

• yield 16. The use of 16 in the subsequent Mitsunobu reaction afforded 68% of the desired product 17. With derivatives 11 and 17 in hand we proceeded to prepare the corresponding phosphoramidite derivatives 13 and 19, respectively, under standard conditions as outlined in Scheme 2. We proceeded to

• prepare the cytosine- and guanine-containing phosphoramidite by using the tritylated intermediate 10 as the starting point (Scheme 3). In the cytosine series we found that the normal N4-benzoyl or N4-acetyl protected cytosine did not give satisfactory yields under the Mitsunobu conditions. The best yields

• prepare the phosphoramidite 28, and proceeded with the oligomer synthesis for our studies. However, this was far from satisfactory, and the continued demand for isoGNA oligomers within our group and our collaborative work prompted us to look for an improvement of the preparation of the adenine building

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• bifunctionalized cytidine derivative and its successful conjugation to RNA. Results and Discussion Synthesis of the bifunctional cytidine derivative 1 started from uridine making use of four synthons: a protected hexaethylene glycol linker phosphoramidite 2 bearing a primary amine to be used later for RNA

• used for reaction with the triazolyl protected uridine derivative 3 to produce compound 9 in 85% yield. Upon removal of the Boc group and sugar deprotection, the remaining aliphatic amine should be used for conjugation to biotin, followed by coupling of the 5'-hydroxy group to a linker phosphoramidite

• formation with biotin, provided for reaction as N-hydroxysuccinimidyl (NHS-) ester, and subsequently the 5'-O-phosphoramidite should be prepared. Unfortunately, preparation of 12 in the suggested one step procedure (Figure 4, upper path) was not possible. According to a previous report by Zhu et al. [36

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bc^en-T and iso-tricyclo-T nucleosides

• Branislav Dugovic,
• Michael Wagner and
• Christian J. Leumann

Beilstein J. Org. Chem. 2014, 10, 1840–1847, doi:10.3762/bjoc.10.194

• nucleosides with restricted conformation of the C6’–C7’ bond, namely bcen-T and iso-tc-T (Figure 1). Here we present the synthesis and X-ray structural characterization of the respective nucleosides, their incorporation into oligodeoxynucleotides by phosphoramidite chemistry as well as the DNA and RNA

• affinity profiles of the modified oligonucleotides. Results Synthesis of building blocks The synthesis of the phosphoramidite 10 started with the bicyclic intermediate 1 that had previously been described on the way to related bicyclo-DNA derivatives (Scheme 1) [30]. Following an obvious synthetic strategy

• ,β in a ratio of β:α = 1.2:1. After standard tritylation of 11α,β the anomeric mixture 12α,β became separable by flash chromatography and the corresponding β-nucleoside 12β could be smoothly converted into the phosphoramidite 13 by standard methods. Structural properties of nucleosides To get an

Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

• Christian B. Winiger,
• Simon M. Langenegger,
• Oleg Khorev and
• Robert Häner

Beilstein J. Org. Chem. 2014, 10, 1589–1595, doi:10.3762/bjoc.10.164

• total of four PDIs (blue) and/or pyrenes (green). Oligomers 1–7 consisting of varying numbers of pyrene or PDI moieties covalently linked to complementary DNA strands were prepared by automated oligonucleotide synthesis using the previously described phosphoramidite pyrene [53] and PDI [55] building

A new building block for DNA network formation by self-assembly and polymerase chain reaction

• Holger Bußkamp,
• Sascha Keller,
• Marta Robotta,
• Malte Drescher and
• Andreas Marx

Beilstein J. Org. Chem. 2014, 10, 1037–1046, doi:10.3762/bjoc.10.104

• way that all branches have the same sequence and terminate with a free 3'-OH group required for processing by DNA polymerases. This was achieved by the employment of standard phosphoramidites until the incorporation of the branching unit 6. Afterwards, the inverse-phosphoramidite strategy was used for

• branches in 5'–3' direction using inverse protected phosphoramidites. Thermal denaturation studies comparing linear and branched oligonucleotides hybridization. Incorporated phosphoramidite 6 is depicted as Bp for branched ODN I.a Supporting Information Experimental procedures and full characterization

Synthesis of nucleotide–amino acid conjugates designed for photo-CIDNP experiments by a phosphotriester approach

• Tatyana V. Abramova,
• Olga B. Morozova,
• Vladimir N. Silnikov and
• Alexandra V. Yurkovskaya

Beilstein J. Org. Chem. 2013, 9, 2898–2909, doi:10.3762/bjoc.9.326

• oligodeoxynucleotides and phosphorothioate hexa-2’-oligodeoxynucleotides by the phosphoramidite method [23][24]. Moreover, LPS was employed for preparing amino acid–nucleotide conjugates [25] and trinucleoside blocks [26] further used in SPSS. The method of nucleotide coupling in LPS presumably depends on the

• derivative [27], we used the LPS strategy in combination with the phosphotriester approach for the oligonucleotide synthesis to obtain target conjugates 1–8. The phosphoramidite condensation in LPS usually leads to the lower yields in these reactions due to insufficient stability of active phosphoramidites

• -elimination. It is worthy to notice that the TBAF treatment is essential when the phosphotriester group contains the aromatic residue (p-chlorophenyl in our case), which is much more stable to ammonia than the 2-cyanoethyl group usually used in the phosphoramidite oligodeoxynucleotide synthesis. After the

Advancements in the mechanistic understanding of the copper-catalyzed azide–alkyne cycloaddition

• Regina Berg and
• Bernd F. Straub

Beilstein J. Org. Chem. 2013, 9, 2715–2750, doi:10.3762/bjoc.9.308

• additives in combination with copper(II) salts has been reported. In 2009, Feringa used phosphoramidite ligands to accelerate CuAAC reactions in aqueous media (Scheme 4) [85]. With the traditional Sharpless–Fokin system copper(II) sulfate pentahydrate (1 mol %) plus ascorbate (5 mol %) as reducing agent

• , the reaction of phenylacetylene (1.2 equivalents) with benzyl azide gave 98% yield within two hours when the monodentate phosphoramidite ligand MonoPhos (1.1 mol %) was present in the aqueous reaction mixture (DMSO/H2O 1:3). In the absence of MonoPhos, the reaction was only completed after 30 hours

• one hour at room temperature). The effect of the phosphine ligand is generally attributed to an increase in the copper(I) salt’s solubility in organic media. Feringa et al. used copper(I) salts in combination with phosphoramidite ligands such as MonoPhos. With copper(I) chloride (1 mol %) and MonoPhos

Gold(I)-catalyzed enantioselective cycloaddition reactions

• Fernando López and
• José L. Mascareñas

Beilstein J. Org. Chem. 2013, 9, 2250–2264, doi:10.3762/bjoc.9.264

• phosphoramidite–gold complex, such as Au7, could eventually solve this limitation, leading to a complementary reactivity to that exhibited by DTBM-Segphos(AuCl)2/AgBF4 in terms of substrate scope, and affording enantioselectivities up to 97% (Scheme 6) [51]. Additionally, Fürstner and co-workers have also

• demonstrated that a phosphoramidite–gold complex like Au8, containing an acyclic Taddol-based backbone, was also an excellent catalyst to perform the same type of [2 + 2] cycloadditions of allenenes 11 [52][53]. This catalyst performs equally well with carbon-based and nitrogen-based tethers, and excellent

• [4 + 2] cycloaddition (Scheme 9, R1, R2 = alkyl groups). This turned out to be the case and, gratifyingly, we showed that it is possible to perform highly enantioselective allenediene [4 + 2] cycloadditions by using gold complexes derived from a bulky phosphoramidite equipped with anthracenyl

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The

• representative oligonucleotides by using automated phosphoramidite chemistry, and characterized with respect to its photochromism in DNA. Results and Discussion Design and synthesis of diarylethene-modified 2’-deoxyuridines 4–6 The typical way to tether fluorophores to oligonucleotides is to use an alkyl chain

• nm, outside of the absorption range of DNA. The preparation of the corresponding phosphoramidite 17 as an artificial DNA building block follows standard procedures (Scheme 3) [30]: Protection of the 5’-OH group of nucleoside 4 by DMT-chloride is followed by phosphitylation of the 3’-OH group of the

Recent developments in gold-catalyzed cycloaddition reactions

• Fernando López and
• José L. Mascareñas

Beilstein J. Org. Chem. 2011, 7, 1075–1094, doi:10.3762/bjoc.7.124

• and 3' positions of the binaphthol moiety (Au9, Scheme 29) [102]. Almost simultaneously, the group of Toste reported that related phosphoramidite–gold complexes, such as Au10, and the chiral gold catalyst Au11 [104], derived from a C3-symmetric phosphite ligand previously developed by Reetz and

• coworkers [105], are also capable of inducing excellent enantioselectivities in these (4 + 2) cycloaddition reactions of allenedienes. More recently, the group of Fürstner has also reported that Taddol-based phosphoramidite–gold complexes such as Au12 (Scheme 29) are excellent catalysts for these (4 + 2

Chiral gold(I) vs chiral silver complexes as catalysts for the enantioselective synthesis of the second generation GSK-hepatitis C virus inhibitor

• María Martín-Rodríguez,
• Carmen Nájera,
• José M. Sansano,
• Abel de Cózar and
• Fernando P. Cossío

Beilstein J. Org. Chem. 2011, 7, 988–996, doi:10.3762/bjoc.7.111

• ; phosphoramidite; silver; viral inhibitor; Introduction The prevalence of chronic hepatitis C virus (HCV) infection is such that it is estimated to be suffered by around 200 million people worldwide [1]. This enveloped single-stranded RNA virus (belonging to the Flaviviridae family) is present in six major

• , approach to the enantiomeric formation of this non-nucleosidic antiviral agent 1 is based on a catalytic enantioselective 1,3-DC [20][21][22][23][24]. The first reported enantioselective overall synthesis of the structure 1 was catalyzed by a chiral phosphoramidite and AgClO4 [25][26], although the

• , generated from chiral phosphoramidites or BINAP as ligands, in order to prepare antiviral agent 2a. Results and Discussion The efficiency of the chiral phosphoramidite/silver(I) salts [25][26][29] and BINAP/Ag(I) salts [30][31] in 1,3-DC, following the general pattern shown in Scheme 1, has been

Synthesis, reactivity and biological activity of 5-alkoxymethyluracil analogues

• Lucie Brulikova and
• Jan Hlavac

Beilstein J. Org. Chem. 2011, 7, 678–698, doi:10.3762/bjoc.7.80

• oligodeoxynucleotides containing 5-formyl-2'-deoxyuridine have been published. Sugiyama and co-workers reported a seven-step synthesis of phosphoramidite 134 (Scheme 23, reaction conditions 1) starting with readily available 5-iodo-2'-deoxyuridine (14) [36]. The first two steps of the synthesis involved the protection

• of 3',5'-dihydroxyl groups with the TBDMS group followed by a Pd-catalyzed coupling reaction with vinyl acetate to give the protected 5-vinyluridine 129 in 68% yield. Oxidation with OsO4 with subsequent acetylation with acetic anhydride in pyridine gave nucleoside 131. The target phosphoramidite 134

• was obtained after the standard phosphoramidite synthesis starting with the protection of the 5'-OH group with dimethoxytrityl chloride and final phosphitylation. Later, Kittaka and co-workers reported the synthesis of phosphoramidite 134 under different conditions [37]. The protected 5-iodo-2

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• been synthesised [99]. Phosphoramidite 56 (Figure 24) was used as a building block to introduce guanidinium linkages at desired positions in the chimeric oligonucleotides. The biological properties were evaluated using the bcr-abl oncogene (the cause of chronic myeloid leukaemia) as the target. The

• groove. As in the case of RNG, a 20 base pair DNG/DNA chimera has been synthesised [106]. Phosphoramidite 66 (Figure 26) was used as the starting material for the introduction of guanidinium linkages at desired positions in the chimeric oligonucleotides. The biological properties were evaluated using the

• derivatives 51–55. Phosphoramidite building block 56. Structures of DNGs 57–65. Structure of the phosphoramidite building block 66. Synthetic route to the target amide-linked sialooligomers. (a) Fmoc-Cl, NaHCO3, H2O, dioxane, 0 °C. (b) Ac2O, Pyridine, 0 °C. (c) BOP, DIPEA. (d) NH2NH2·H2O, MeOH. Strategy for

Synthetic incorporation of Nile Blue into DNA using 2′-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker

• Daniel Lachmann,
• Sina Berndl,
• Otto S. Wolfbeis and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2010, 6, No. 13, doi:10.3762/bjoc.6.13

• was supported by geometrically optimized DNA models. Keywords: cycloaddition; fluorescence; glycol; oligonucleotide; phenoxazinium; phosphoramidite; Introduction Chemical bioanalysis and imaging of nucleic acids require synthetic incorporation of fluorescent DNA probes for an optical readout [1][2

• ][3][4][5][6][7][8][9]. A large variety of organic fluorophores can be incorporated routinely at specific positions within the oligonucleotide using standard phosphoramidite DNA chemistry and commercially available DNA building blocks. However, problems can arise if labels or probes are chemically

• basic conditions of automated DNA phosphoramidite chemistry and/or DNA workup. We recently presented the postsynthetic incorporation of Nile Blue and a coumarin dye as representatives of base-labile fluorophores by the “click” ligation strategy [17]. Several other fluorophores (spanning the whole

Investigation of acetyl migrations in furanosides

• O. P. Chevallier and
• M. E. Migaud

Beilstein J. Org. Chem. 2006, 2, No. 14, doi:10.1186/1860-5397-2-14

• acetyl moieties. Such direct transesterification is intermolecular and while it has been observed in nucleoside-phosphoramidite and glycoside chemistry,[20][21][22][23] this alkoxide-promoted intermolecular acetyl migration process has been overlooked in furanosides. The isolated quantities of 1c and 1d

A superior P-H phosphonite: Asymmetric allylic substitutions with fenchol- based palladium catalysts

• Bernd Goldfuss,
• Thomas Löschmann,
• Tina Kop-Weiershausen,
• Jörg Neudörfl and
• Frank Rominger

Beilstein J. Org. Chem. 2006, 2, No. 7, doi:10.1186/1860-5397-2-7

• Leeuwen's bulky, monodentate TADDOL based phosphoramidite gave rise to intriguing memory effects [28b] and yielded 6% branched product with 25% ee (Scheme 2) [9]. We have recently employed modular, chelating fencholates, [10][11][12][13][14] in enantioselective organozinc catalysts, [15][16][17][18][19] and

• , reflecting the effect of steric demanding and electron donating pyridine groups on enantioselectivity. The surprisingly stable halogen phosphites BIFOP-Cl and BIFOP-Br yield even higher enantioselectivities (39% and 37% ee) than the corresponding phosphite BIFOP-OPh or the phosphoramidite BIFOP-NEt2 (10% and

• ). Bidentate P, N-ligands and a monodentate phosphoramidite for Pd-catalyzed allylic substitutions with unsymmetric substrates, cf. Scheme 1. Fenchole-based phosphorus ligands (i.e. FEENOPs and BIFOPs) for Pd-catalyzed allylic substitutions. Pd-π arene or Pd-N coordinations give rise to different

An exceptional P-H phosphonite: Biphenyl- 2,2'-bisfenchylchlorophosphite and derived ligands (BIFOPs) in enantioselective copper- catalyzed 1,4-additions

• T. Kop-Weiershausen,
• J. Lex,
• J.-M. Neudörfl and
• B. Goldfuss

Beilstein J. Org. Chem. 2005, 1, No. 6, doi:10.1186/1860-5397-1-6

• as well as hydridic and organometallic nucleophiles. Chloride substitution in BIFOP-Cl proceeds only under drastic conditions. New enantiopure, sterically demanding phosphorus ligands such as a phosphoramidite, a phosphite and a P-H phosphonite (BIFOP-H) are hereby accessible. In enantioselective Cu

• -catalyzed 1,4-additions of ZnEt2 to 2-cyclohexen-1-one, this P-H phosphonite (yielding 65% ee) exceeds even the corresponding phosphite and phosphoramidite. Keywords: phosphorus ligands; chirality; biaryls; asymmetric conjugate additions; phosphoramidites; phosphites; phosphonites; X-ray analyses

• and LiNEt2. While no hydrolysis of 1 is observed at ambient temperature, only reflux and basic conditions (KOH) yield complete hydrolysis of 1 to BIFOP(O)-H, 8 (98%, Table 1, entry 14, Figure 5). [79][80] The phosphite BIFOP-OPh, 6 (40%, Figure 6) and the phosphoramidite BIFOP-NEt2, 7 (47%, Figure 7