Synthesis of DNA-peptide conjugates by solid-phase fragment condensation

[reaction: see text] DNA-peptide conjugates were synthesized by condensing partially protected peptide fragments and oligonucleotides on a CPG support using diisocyanatoalkane as a linker. After cleavage and deprotection with aqueous ammonia, pure products were obtained by single RPHPLC purification in satisfactory yields and identified by a MALDI-TOF MS spectrometer. This method allows one to prepare DNA-peptide conjugates with any components and sequences of DNA and peptides.     

Efficient Automated Solid‐Phase Synthesis of DNA and RNA 5′‐Triphosphates

A fast, high‐yielding and reliable method for the synthesis of DNA‐ and RNA 5′‐triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5‐chloro‐saligenyl‐N,N‐diisopropylphosphoramidite was coupled to the 5′‐end. Oxidation of the formed 5′‐phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5′‐cycloSal‐oligonucleotides. Reaction of the support‐bonded 5′‐cycloSal‐oligonucleotide with pyrophosphate yielded the corresponding 5′‐triphosphates. The 5′‐triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.     

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides

The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using ³¹P NMR at room temperature showed less than 10% degradation after 6?h. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.     

Site-specific DNA photocleavage by rhodium intercalators analyzed by MALDI-TOF mass spectrometry

The DNA photocleavage reaction of mismatch-selective Rh complexes has been analyzed by MALDI-TOF mass spectrometry as well as gel electrophoresis analysis of radioactively tagged oligonucleotides. Analogous results are obtained with these two techniques showing site-specific cleavage neighboring the mismatch to yield primarily 5'- and 3'-phosphate termini. Additional intermediates and products are observed, however, using MALDI-TOF analysis. MALDI-TOF mass spectrometry is seen to be particularly powerful in the analysis of DNA cleavage by site-specific molecules. The method requires no radioactive labeling, only little material, and analysis can be accomplished within minutes. Moreover, this mass spectral analysis of DNA cleavage yields direct information regarding products rather than simply the base pair site of cleavage.     

Acid-catalyzed cyclization of alkoxyacryloylureas to 2,4(1H,3H)pyrimidinediones

1-Phenylthymine and the carbocyclic analog of thymidine were obtained in yields of 84-87% by cyclizing the appropriate 3-methoxy-2-methylacryloylureas in dilute sulfuric acid. High yields of 1-phenylthymine also resulted when the cyclization was carried out in trifluoroacetic acid, in acetic acid containing toluenesulfonic acid (TSA), or by fusion of the urea with a catalytic amount of TSA. In comparison, the typical aqueous-alkali catalyzed cyclizations gave lower yields of the two thymines, and cleavage of the acryloylureas was shown to occur. However, cyclization in concentrated aqueous ammonia produced high yields of both thymine derivatives.     

Glycosylidene Carbenes. Part 5. Synthesis of Glycono-1,5-lactone Tosylhydrazones as Precursors of Glycosylidene Carbenes

The benzyl- and the acyl-protected glyconolactone tosylhydrazones 6 , 9 , 12 , 16 , and 19 (Scheme 1) were prepared in good yields by treating the hemiacetals 4 , 7 , 10 , 14 , and 17 with N-tosylhydrazine, to give the N-glycosylhydrazines 5 , 8 , 11 , 15 , and 18 , and by oxidizing these hydraz tries with N-bromosuccinimide (NBS) in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU), with CrO₃–dipyridine complex or with pyridinium dichromate. Photolysis of the sodium sail 20 of 6 (Scheme 2) in the presence of N-phenylmaleimide, dimethyl fumarate, or acrylonitrile gave the corresponding cyctopropanes 21 – 28 in satisfactory yields. Phololytic or thermolytic glycosidation of phenol and 4-melhoxyphenol by 20 yielded the anomeric glycosides 29 / 30 and 31 / 32 , yields being marginally higher for the Ihermolytic process. Phololytic glycosidation of propan-2-ol gave the glycosides 33 and 34 in low yields only. Yields and ratios of products were compared to those obtained with the diazirine 1 as a source of glycosylidene carbenes. While the yields from 20 are lower, the ratios of products obtained in the photolytic reactions are in agreement with the formation of a common intermediate from both carbene precursors.     

A Novel Radical-Based Synthesis of Valerolactones

The photolytic radical addition of phenylselenomalonates to allylic alcohols, followed by acid-catalyzed cyclization yields valerolactones incorporating a phenylseleno substituent.     

Insertion of Chemical Handles into the Backbone of DNA during Solid-Phase Synthesis by Oxidative Coupling of Amines to Phosphites

Conjugation of molecules or proteins to oligonucleotides can improve their functional and therapeutic capacity. However, such modifications are often limited to the 5′ and 3′ end of oligonucleotides. Herein, we report the development of an inexpensive and simple method that allows for the insertion of chemical handles into the backbone of oligonucleotides. This method is compatible with standardized automated solid-phase oligonucleotide synthesis, and relies on formation of phosphoramidates. A unique phosphoramidite is incorporated into a growing oligonucleotide, and oxidized to the desired phosphoramidate using iodine and an amine of choice. Azides, alkynes, amines, and alkanes have been linked to oligonucleotides via internally positioned phosphoramidates with oxidative coupling yields above 80 %. We show the design of phosphoramidates from secondary amines that specifically hydrolyze to the phosphate only at decreased pH. Finally, we show the synthesis of an antibody-DNA conjugate, where the oligonucleotide can be selectively released in a pH 5.5 buffer.     

Ion trap collision-induced dissociation of locked nucleic acids

Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3′C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics.     

Photooxidation Of Arsenobetaine And Arsenocholine To Generate Arsines Previous To Icp-Oes Measurement

Abstract

A photolytic method, which uses UV irradiation (254 nm) and K₂S₂O₈ in alkaline media has been optimized for the speciation of arsenite, arsenate, monomethylarsonic and dimethylarsinic acid, arsenobetaine and arsenocholine. Under these conditions it is possible to obtain not only simple species from arsenobetaine and arsenocholine with good yields, but also to establish the optimum conditions to carry out the process on-line with HG-ICP/OES for the determination of these species.

The products obtained in the photolytic reaction are introduced into the reduction chamber to form arsines. According to the results obtained from the ICP measurements, the recoveries obtained are about 100% and the procedure has a good reproducibility.     

Synthesis of labeled oligonucleotides through a new chemically cleavable linker

A synthesis of labeled oligonucleotides incorporating a new chemically cleavable linker (III) via a two-step method is described. The labeled oligomers obtained after cleavage and deprotection reactions [treatment with anhydrous tert-butylamine and dry methanol, 1:1 (v/v) for 12 h at room temperature, and lyophilization followed by subsequent reaction with aq NH₄OH and methylamine (40%), 1:1 (v/v) for 5 min at 65 °C] were analyzed by RP-HPLC. A distinctive feature of this protocol is that free oligomers can be recovered from their labeled analogs under mild conditions (0.2 M NaOH containing 0.5 M NaCl over 30 min at room temperature) and are comparable to the corresponding standard oligonucleotides (HPLC).     

High-sensitivity detection of biological amines using fast Hadamard transform CE coupled with photolytic optical gating

Here, we report the first utilization of Hadamard transform CE (HTCE), a high-sensitivity, multiplexed CE technique, with photolytic optical gating sample injection of caged fluorescent labels for the detection of biologically important amines. Previous implementations of HTCE have relied upon photobleaching optical gating sample injection of fluorescent dyes. Photolysis of caged fluorescent labels reduces the fluorescence background, providing marked enhancements in sensitivity compared to photobleaching. Application of fast Hadamard transform CE (fHTCE) for fluorescein-based dyes yields a ten-fold higher sensitivity for photolytic injections compared to photobleaching injections, due primarily to the reduced fluorescent background provided by caged fluorescent dyes. Detection limits as low as 5 pM (ca. 18 molecules per injection event) were obtained with on-column LIF detection using fHTCE in less than 25 s, with the capacity for continuous, online separations. Detection limits for glutamate and aspartate below 150 pM (1-2 amol/injection event) were obtained using photolytic sample injection, with separation efficiencies exceeding 1 x 10(6) plates/m and total multiplexed separation times as low as 8 s. These results strongly support the feasibility of this approach for high-sensitivity dynamic chemical monitoring applications.     

A new photocleavable linker in solid-phase chemistry for ether cleavage

We have designed a new linker (1) for the solid-phase synthesis that cleaves ether bonds photolytically. The linker was prepared in nine steps and anchored to the support via an amide bond. Photocleavage is a two-step process in which the immobilized alcohols are released by photolytic generation of a radical that undergoes a spontaneous beta-bond scission. The pivaloyl linker (1) was found to cleave off alcohols in high yields and purities. Only traces of acid (pH approximately 5.5) are necessary for an efficient cleavage.     

A novel approach to oligonucleotide synthesis using an imidazolium ion tag as a soluble support

The synthesis of oligonucleotides in solution using a soluble, ionic liquid based support is described. Short oligomers of varying base composition were synthesized using this method in high yields and high purity, requiring no chromatography for purification prior to cleavage from the support. The solution-phase-synthesized oligomers were compared to the same sequences prepared using standard gene machine techniques by LCMS. This methodology may provide a cheaper route for the large-scale synthesis of oligonucleotides.     

Stereospecific syntheses of 3'-deuterated pyrimidine nucleosides and their site-specific incorporation into DNA

[reaction: see text] 2'-Deoxy-3'-deutero pyrimidines have been synthesized in high yields and incorporated into deoxyoligonucleotides using standard phosphoramidite chemistry. A key synthetic step is a stereospecific reduction of 3'-keto nucleosides using sodium triacetoxyborodeuteride to give 3'-deuterated thymidine and 2'-deoxy uridine nucleosides. Conversion of the corresponding phorphoramidites 7a and 7b to 4-triazolo derivatives has, for the first time, enabled incorporation of 2'-deoxy-3'-deutero cytidine and 2'-deoxy-3'-deutero-5-methyl cytidine into oligonucleotides.     

Synthesis of a new family of acyclic nucleoside phosphonates, analogues of TPases transition states

A 6-step procedure was developed for the synthesis of a new family of acyclic nucleoside phosphonates (ANPs), "PHEEPA" [(2-pyrimidinyl-2-(2-hydroxyethoxy)ethyl)phosphonic acids] in overall yields ranging from 4.5% to 32%. These compounds, which possess on one side a hydroxy function and on the other side a phosphonate group, can be considered either as potential antiviral agents or as transition state analogues of nucleoside phosphorylases such as thymidine phosphorylase.     

An efficient reagent for the phosphorylation of deoxyribonucleosides, DNA oligonucleotides, and their thermolytic analogues

[reaction: see text] The phosphoramidite 11 was prepared in three steps from methyl 2-mercaptoacetate and demonstrated efficiency in the synthesis of conventional 5'-/3'-phosphate/thiophosphate monoester derivatives of 2'-deoxyribonucleosides and DNA oligonucleotides. Moreover, the use of 11 has enabled the preparation of the dinucleoside phosphorothioate analogue 26 in high yields (>95%) with minimal cleavage (<2%) of the thermolytic thiophosphate protecting group.     

Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides.

A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.     

Photolytic behavior of copolyamides from adipic and truxillic acids

The synthesis of copolyamides from adipic and truxillic acids with piperazine was undertaken to include photoreactive units in aliphatic polyamides and to throw light on the factors that control the photolytic rates and photochromic behavior of these materials. The results indicate that the introduction of variable amounts of truxillic units (photodegradable) induces a measurable increment in the photolytic rate of the aliphatic polyamide. Moreover, it has been found that the addition of strong acids induces a higher photolytic cleavage of the polyamides, which may allow a further reduction in the amount of truxillic units in the copolyamides.     

Oligonucleotides containing arylacetylene residues: Synthesis and post-synthetic modification via [3+2] cycloaddition

The synthesis of a phosphoramidite reagent for 5′-modification of oligonucleotides by introducing an arylacetylene residue has been described. Using the reaction with 3-(perylen-3-yl)propyl azide as an example, it was shown that the acetylene derivatives of oligonucleotides synthesized using this reagent undergo Cu^I-catalyzed [3+2] dipolar cycloaddition. Fluorescent conjugates were obtained in high yields and characterized by mass spectra. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1220–1226, July, 2006.