Synthesis of oligonucleotides carrying thiol groups using a simple reagent derived from threoninol

Oligonucleotides carrying thiol groups are useful intermediates for a remarkable number of applications involving nucleic acids. In this study, DNA oligonucleotides carrying tert-butylsulfanyl (t-BuS) protected thiol groups have been prepared. A building block derived from threoninol has been developed to introduce a thiol group at any predetemined position of an oligonucleotide. The resulting thiolated oligonucleotides have been used for the preparation of oligonucleotide conjugates and for the functionalization of gold nanoparticles using the reactivity of the thiol groups.     

Nucleotides. Part XLVI. The synthesis of phospholipid conjugates of antivirally active nucleosides by the improved phosphoramidite methodology

The application of the improved phosphoramidite strategy for the synthese of oligonucleotides using β-eliminating protecting groups to phospholipid chemistry offers the possibility to synthesize phospholipid conjugates of AZT ( 6 ) and cordycepin. The synthesis of 3′-azido-3′-deoxythymidine ( 6 ) was achieved by a new isolation procedure without chromatographic purification steps in an overall yield of 50%. Protected cordycepin ( = 3′-de-oxyadenosine) derivatives, the N⁶,2′-bis[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 12 ) and the N⁶,5′-bis[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 13 ) wre prepared by known methods and direct acylation of N⁶-[2-(4-nitrophenyl)ethoxycarbonyl]cordycepin ( 9 ), respectively. These protected nucleosides and the 3′-azido-3′-de-oxythymidine ( 6 ) reacted with newly synthesized and properly characterized lipid-phosphoramidites 21–25 , catalyzed by 1H-tetrazole, to the corresponding nucleoside-phospholipid conjugates 26–38 in high yield. The deprotection was accomplished via β-elimination with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in aprotic solvents to give analytically pure nucleoside-phospholipid diesters 39–51 as triethylammonium or sodium salts. The newly synthesized compounds were characterized by elemental analyses and UV and ¹H-NMR spectra.     

A simple methodology for the synthesis of heterotelechelic protein–polymer–biomolecule conjugates

A synthetic protocol for the preparation of hetero‐biofunctional protein–polymer conjugates is described. A chain transfer agent, S,S‐bis (α,α′‐dimethyl‐α″‐acetic acid) trithiocarbonate was functionalized with α,ω‐pyridyl disulfide (PDS) groups, Subsequently, one of the PDS groups was covalently attached to bovine serum albumin (BSA) at the specific free thiol group on the cysteine residue through a disulfide linkage. The second PDS group remained intact, as it was found to be inaccessible to further BSA functionalization. The BSA‐macro‐reversible addition‐fragmentation chain transfer (RAFT) agent was then used to prepare BSA‐polymer conjugates via in situ polymerization of oligo (ethyleneglycol) acrylate and N‐(2‐hydroxypropyl) methacrylamide using an ambient temperature initiator, 4,4′‐azobis [2,9‐imidazolin‐2‐ethyl)propane] dihydrochloride in an aqueous medium. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE) confirmed that the in situ polymerization occurred at the protein surface where the RAFT agent was attached and the molecular weights of the BSA–polymer conjugates were found to increase concomitantly with monomer conversion and polymerization time. After polymerization the remaining terminal PDS groups were then utilized to attach thiocholesterol and a flurophore, rhodamine B to the protein–polymer conjugates via disulfide coupling. UV–Vis and fluorescence analyses revealed that ～80% of the protein conjugates were found to retain integral PDS end groups for further attachment to free thiol‐tethered precursors. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1399–1405, 2010     

甾体磷酰胺类缀合物在电喷雾质谱中的裂解特征

Novel steroidal phosphoramidate conjugates of 3'-azido-2',3'-dideoxythymidine(AZT)and amino acid esterswere synthesized and determined by positive and negative ion electrospray ionization mass spectrometry.The MSfragmentation behaviors of the steroidal phosphoramidate conjugates have been investigated in conjunction withtandem mass spectrometry of ESI-MS/MS.There were three characteristic fragment ions in the positive ion ESImass spectra,which were the Na adduct ions with loss of steroidal moiety,amino acid ester moiety from pseudomolecular ion(M Na)~ ,and the phosphoamino acid methyl ester Na adduct ion by α-cleavage of the phosphora-midate respectively.The main fragment ions in negative ion ESI mass spectra were the ion(M-HN_3)~-,the ion(M-AZT-H)~-,and the ion(M-steroidal moiety-H)~- besides the pseudo molecular ion(M-H)~-.Thefragmentation patterns did not depend on the attached amino acid ester moiety.     

Hybridization and Melting Behavior of Peptide Nucleic Acid (PNA) Oligonucleotide Chimeras Conjugated to Gold Nanoparticles

Peptide nucleic acids (PNA) and PNA–DNA chimeras carrying thiol groups were used for surface functionalization of Au nanoparticles. Conjugation of PNA to citrate‐stabilized Au nanoparticles destabilized the nanoparticles causing them to precipitate. Addition of a tail of glutamic acid to the PNA prevented destabilization of the nanoparticles but resulted in loss of interaction with complementary sequences. Importantly, PNA–DNA chimeras gave stable conjugates with Au nanoparticles. The hybridization and melting properties of complexes formed from chimera–nanoparticle conjugates and oligonucleotide–nanoparticle conjugates are described for the first time. Similar to oligonucleotide–nanoparticle conjugates, conjugates with PNA–DNA chimeras gave sharper and more‐defined melting profiles than those obtained with unmodified oligonucleotides. In addition, mismatch discrimination was found to be more efficient than with unmodified oligonucleotides.     

Synthesis and Base Pairing Properties of 1′,5′‐Anhydro‐L‐Hexitol Nucleic Acids (L‐HNA)

Oligonucleotides composed of 1′,5′‐anhydro‐arabino‐hexitol nucleosides belonging to the L series (L ‐HNA) were prepared and preliminarily studied as a novel potential base‐pairing system. Synthesis of enantiopure L ‐hexitol nucleotide monomers equipped with a 2′‐(N⁶‐benzoyladenin‐9‐yl) or a 2′‐(thymin‐1‐yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar‐modified oligonucleotides. In many cases stable homo‐ and heterochiral associations were found. Besides T_m measurements, detection of heterochiral complexes was unambiguously confirmed by LC‐MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L ‐HNA form left‐handed helices with both D and L oligonucleotides.     

Base‐Pairing Properties of 8‐Aza‐7‐deazaadenine Linked via the 8‐Position to the DNA Backbone

The base‐pairing properties of oligonucleotides containing the unusual N⁸‐linked 8‐aza‐7‐deazaadenine 2′‐deoxyribonucleoside ( 2a ) as well as its 7‐bromo derivative 2b are described. The oligonucleotides were prepared by solid‐phase synthesis employing phosphoramidite chemistry. Compound 2a forms a strong base pair with T_d for which a reverse Watson‐Crick pair is suggested (Fig. 9). Compound 2a displays a lower N‐glycosylic‐bond stability than its N⁹‐nucleoside and shows strong stacking interactions when incorporated into oligonucleotides. The replacement of 2′‐deoxyadenosine by 2a does not significantly influence the duplex stability. However, this behavior depends on the position of the incorporation.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Preparation and some properties of maleimido acids and maleoyl derivatives of peptides.

N-Alkoxycarbonylmaleimides 3 have been prepared and used to convert amino acids to maleimido acids (6–8) in aqueous solution. The carboxyl group of maleimido acids can be activated for amide or peptide synthesis (e.g., in the N-succinimidyl esters 10); t-butyl-based protecting groups can be cleaved without damage to the maleimide moiety. Peptides carrying maleimide groups are accessible either from the maleimido acids (e.g., 11b, 15) or by direct maleoylation (e.g., 16b). The maleoyl group can be cleaved off by successive mild alkaline and acid hydrolysis or by hydrazinolysis. The reactivity of maleimides toward thiol groups suggests the use of maleimido acids and maleoylpeptides for preparing a wide range of conjugates of biochemical interest.     

Synthesis,Characterization and Application of Some Axially Chiral Binaphthyl Phosphoric Acids in Asymmetric Mannich Reaction

Two novel chiral Br?nsted acids 3b and 3c were prepared without involving the complexity of Suzuki coupling. Catalyst 3c bearing two additional hydroxyl groups at 3 and 3′ positions of axially chiral 1,1‐binaphthalene‐2,2′‐diol phosphoric acid was applied in a model Mannich reaction to afford β‐amino ester in high yield (92%) and enantiomeric excess (91%) at low reacting temperature of ?40°C. In addition, those β‐amino ester derivatives with high yields and excellent enatioselectivities were obtained in the presence of catalyst 3c under the above condition.     

Oligonucleotides Containing 7‐Deaza‐2′‐deoxyinosine as Universal Nucleoside: Synthesis of 7‐Halogenated and 7‐Alkynylated Derivatives,Ambiguous Base Pairing,and Dye Functionalization by the Alkyne–Azide ‘Click’ Reaction

Oligonucleotides containing 7‐deaza‐2′‐deoxyinosine derivatives bearing 7‐halogen substituents or 7‐alkynyl groups were prepared. For this, the phosphoramidites 2b – 2g containing 7‐substituted 7‐deaza‐2′‐deoxyinosine analogues 1b – 1g were synthesized (Scheme 2). Hybridization experiments with modified oligonucleotides demonstrate that all 2′‐deoxyinosine derivatives show ambiguous base pairing, as 2′‐deoxyinosine does. The duplex stability decreases in the order C_d>A_d>T_d>G_d when 2b – 2g pair with these canonical nucleosides (Table 6). The self‐complementary duplexes 5′‐d(F⁷c⁷I‐C)₆, d(Br⁷c⁷I‐C)₆, and d(I⁷c⁷I‐C)₆ are more stable than the parent duplex d(c⁷I‐C)₆ (Table 7). An oligonucleotide containing the octa‐1,7‐diyn‐1‐yl derivative 1g , i.e., 27 , was functionalized with the nonfluorescent 3‐azido‐7‐hydroxycoumarin ( 28 ) by the Huisgen–Sharpless–Meldal cycloaddition ‘click’ reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme 3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal C?C bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ‘click’ chemistry. ii) Space demanding residues introduced in the 7‐position of the 7‐deazapurine base does not interfere with duplex structure and stability (Table 8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology.     

1‐Methoxyhexane‐3‐thiol,a Powerful Odorant of Clary Sage (Salvia sclarea L.)

The peculiar and highly diffusive odor signal of flowering clary‐sage plants (Salvia sclarea L.) was identified to derive from trace amounts of 1‐methoxyhexane‐3‐thiol ( 1 ) by mass‐spectrometry analysis and confirmed by comparison with synthetic racemic thiol (±)‐ 1 . The enantiomers (S)‐ and (R)‐ 1 were prepared by enantioselective synthesis, and the absolute configuration of (S)‐ 1 was fully corroborated by X‐ray‐diffraction analysis of the crystalline thioester (1′S,1S)‐ 2 . Compound (S)‐ 1 is one of the most powerful odorants known, with a detection threshold of 0.04⋅10⁻³ ng/l air, and is, with its herbaceous‐green, alliaceous, and perspiration profile, key to the fragrance of clary‐sage flowers and of the freshly distilled essential oil. As a consequence of its unique odor, 1 was also suspected to be part of the volatiles of a Ruta species where it was subsequently identified together with its homologue, 1‐methoxyheptane‐3‐thiol ( 3 ), 1‐methoxy‐4‐methylpentane‐3‐thiol ( 4 ), and the known 4‐methoxy‐2‐methylbutane‐2‐thiol ( 5 ). The syntheses of (±)‐ 3 and (±)‐ 4 as well as of the enantiomer (R)‐ 4 are described. In both natural fractions, the ratio (S)‐ 1 /(R)‐ 1 was slightly in favor of the (S)‐enantiomer. Natural 4 has (R)‐configuration.     

Nucleotides,Part LXV,Synthesis of 2′‐Deoxyribonucleoside 5′‐Phosphoramidites: New Building Blocks for the Inverse (5′‐3′)‐Oligonucleotide Approach

The syntheses of the 3′‐O‐(4,4′‐dimethoxytrityl)‐protected 5′‐phosphoramidites 25 – 28 and 5′‐(hydrogen succinates) 29 – 32 , which can be used as monomeric building blocks for the inverse (5′‐3′)‐oligodeoxyribonucleotide synthesis are described (Scheme). These activated nucleosides and nucleotides were obtained by two slightly different four‐step syntheses starting with the base‐protected nucleosides 13 – 20 . For the protection of the aglycon residues, the well‐established 2‐(4‐nitrophenyl)ethyl (npe) and [2‐(4‐nitrophenyl)ethoxy]carbonyl (npeoc) groups were used. The assembly of the oligonucleotides required a slightly increased coupling time of 3 min in application of the common protocol (see Table 1). The use of pyridinium hydrochloride as an activator (instead of 1H‐tetrazole) resulted in an extremely shorter activation time of 30 seconds. We established the efficiency of this inverse strategy by the synthesis of the oligonucleotide 3′‐conjugates 33 and 34 which carry lipophilic caps derived from cholesterol and vitamin E, respectively, as well as by the formation of (3′‐3′)‐ and (5′‐5′)‐internucleotide linkages (see Table 2).     

Synthesis of oligonucleotides containing 7-(2-deoxy-β-d-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine

The synthesis of oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine was accomplished. The viable intermediate N²-isobutyryl-7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine ( 6 ) was prepared via a four step deoxygenation procedure from 7-β-D-ribofuranosylguanine ( 1 ). The 5′-hydroxyl group of 6 was protected as 4,4′-dimethoxytrityl ether and then converted to the target phosphoramidite ( 8 ) via conventional phosphitylation procedure. The amino groups of 8-amino-2′-deoxyguanosine ( 9 ) were protected in the form of N-(dimethylainino)methylene functions to give the protected nucleoside 10 , which was subsequently converted to the target phosphoramidite 12 via dimethoxytritylation followed by phosphitylation. The phosphoramidites 8 and 12 were incorporated into a 26-mer and a 31-mer G-rich oligonucleotide using solid-support, phosphoramidite methodology. Analysis of antiparallel triplex formation by the oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofura-nosyl)guanine in place of 2′-deoxyguanosine showed no enhancement in triple helix formation.     

Stable and Rapid Thiol Bioconjugation by Light‐Triggered Thiomaleimide Ring Hydrolysis

Maleimide‐mediated thiol‐specific derivatization of biomolecules is one of the most efficacious bioconjugation approaches currently available. Alarmingly, however, recent work demonstrates that the resulting thiomaleimide conjugates are susceptible to breakdown via thiol exchange reactions. Herein, we report a new class of maleimides, namely o ‐CH₂NHⁱ Pr phenyl maleimides, that undergo unprecedentedly rapid ring hydrolysis after thiol conjugation to form stable thiol exchange‐resistant conjugates. Furthermore, we overcome the problem of low shelf lives of maleimide reagents owing to their propensity to undergo ring hydrolysis prior to bioconjugation by developing a photocaged version of this scaffold that resists ring hydrolysis. UV irradiation of thiol bioconjugates formed with this photocaged maleimide unleashes rapid thiomaleimide ring hydrolysis to yield the desired stable conjugates within 1 h under gentle, ice‐cold conditions.     

Semisynthesis of 3′(2′)‐O‐(Aminoacyl)‐tRNA Derivatives as Ribosomal Substrate

An efficient synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated pCpA derivatives is described, which could lead to the production of (aminoacyl)‐tRNAs following T4 RNA ligase mediated ligation. The tetrahydrofuranyl (thf) group was used as a permanent protective group for the 2′‐OH of the cytidine moiety which can be removed during the purification of the 3′(2′)‐O‐aminoacylated‐pCpA. This approach allowed for a general synthesis of (3′‐terminally) 3′(2′)‐O‐aminoacylated oligonucleotides. The fully protected pCpA 14 was synthesized by phosphoramidite chemistry and treated with NH₃ solution to remove the 2‐cyanoethyl and benzoyl groups (→ 15 ; Schemes 1 and 2). The 2′‐O‐thf‐protected‐pCpA 15 was coupled with α‐amino acid cyanomethyl esters, and the products 20a – c were deprotected and purified with AcOH buffer to afford 3′(2′)‐O‐aminoacylated pCpA 21a – c in high yields. The 3′(2′)‐O‐aminoacylated pCpA were efficiently ligated with tRNA(? CA) to yield (aminoacyl)‐tRNA which was an active substrate for the ribosome.     

Nucleotides. Part XXXI. Modified Oligomeric 2′–5′ A Analogues: Synthesis of 2′–5′ oligonucleotides with 9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine and 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)adenine as modified nucleosides

A series of new 2′–5′ oligonucleotides carrying the 9-(3′-azido-3′deoxy-β-D-xylofuranosyl)adenine moiety as a building block has been synthesized via the phosphotriester method. The use of the 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) blocking groups for phosphate, amino, and hydroxy protection guaranteed straightforward syntheses in high yields and easy deblocking lo form the 2′–5′ trimers 21 , 22 , and 25 and the tetramer 23 . Catalytic reduction of the azido groups in [9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine]2′-yl-[2′-(O^p-ammonio)→ 5′]-[9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenin]-2′-yl-[2′-(O^p-ammonio)→ 5′]-9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine ( 21 ) led to the corresponding 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)-adenine 2′–5′ trimer 26 in which the two internucleotidic linkages are formally neutralized by intramolecular betaine formation.     

Synthesis of New Conjugates of Modified Podophyllotoxin and Stavudine

To find podophyllotoxin compounds with superior bioactivitiy and less toxicity, a series of novel conjugates of ring‐A‐modified 4‐epipodophyllotoxin and stavudine with amino acids as spacers were synthesized, i.e., the N‐[(2′,3′‐didehydro‐3′‐deoxythymidin‐5′‐O‐yl)carbonyl]‐substituted L ‐amino acid rel‐(3aR,4S,9R,9aR)‐1,3,3a,4,9,9a‐hexahydro‐6,7‐dimethoxy‐1‐oxo‐9‐(3,4,5‐trimethoxyphenyl)naphtho[2,3‐c]furan‐4‐yl esters 8a – 8f .     

Simple Methods for Preparing Oligonucleotides Containing 1) Thiol Groups at their 5′-Termini, 2) 5′-Phosphates

Abstract

A simple method has been developed for synthesising oligonucleotides containing a thiol group at their 5′-termini. The sequence required is prepared using standard solid phase phosphoramidite methods and an extra round of synthesis is then performed with S-triphenylmethyl O-methoxymorpholino-phosphinyl 3-mercaptopropan (1) ol. After normal deblocking this gives an oligonucleotide containing a tritylthiol group attached to the 5′-phosphate of an oligonucleotide via a 3-carbon spacer arm. The trityl group can be removed with AgNO₃ at pH 5 to give the free thiol. This compound is stable at pH 8 and reacts cleanly and rapidly with sulphydryl specific probes (eg fluorescent iodoacetates) at this pH value. This method can be used to prepare a wide variety of usefully labelled oligonucleotides and it is envisaged that fluorescent oligonucleotides will be useful in the study of protein nucleic acid interactions and to replace ³²P labelled hybridisation probes.