Synthesis and Hybridization Properties of an Oligonucleotide Consisting of 1′,4′‐Anhydro‐2′,5′‐dideoxy‐2′‐(thymin‐1‐yl)‐D‐altritol

The novel oligonucleotide analogue 7 , consisting of 1′,4′‐anhydro‐2′,5′‐dideoxy‐2′‐(thymin‐1‐yl)‐D ‐altritol ( 4 ), residues was synthesized by the phosphoramidite approach on an automated DNA synthesizer. The phosphoramidite building block 6 was obtained by phosphitylation of the corresponding isonucleoside 5 . Oligoisonucleotide 7 contains an extended phosphodiester linkage with a higher flexibility. Oligoisonucleotide 7 was studied with respect to hybridization properties, enzymatic stability, and CD spectra. It exhibits a high stability towards snake‐venom phosphodiesterase and an acceptable hybridization to complementary single‐stranded DNA and RNA.     

Oligodeoxynucleotide analogues containing 3′-deoxy-3′-C-threo-hydroxymethylthymidine: Synthesis, hybridization properties and enzymatic stability

Novel Oligodeoxynucleotide analogues containing 3′-C-threo-methylene phosphodiester internucleoside linkages were synthesized on automated DNA-synthesizers using the phosphoramidite approach. The sugar modified phosphoramidite building block 5 was obtained by phosphitylation of 1-(2,3-dideoxy-5-O-(4,4′-dimethoxytrityl)-3-C-hydroxymethyl-β-D-threo-pentofuranosyl)thymine (4) which was synthesized in only three steps from 5′-O-(4,4′-dimethoxytrityl)thymidine (1). The hybridization properties and enzymatic stability of the oligonucleotide analogues were studied by UV experiments. 17-Mers having one or three modifications in the middle or two modifications in each end hybridized to DNA with moderate lowered affinity compared to unmodified 17-mers (ΔT_m 1–3°C per modification). Furthermore, the end-modified and all-modified oligonucleotides were stable towards snake venom phosphodiesterase.     

Oligonucleotides Functionalized by Fluorescein and Rhodamine Dyes: Michael Addition of Methyl Acrylate to 2′‐Deoxypseudouridine

The 2′‐deoxypseudouridine ( 5 ) was functionalized at N(1) with methyl acrylate by Michael addition. The resulting methyl 2′‐deoxypseudouridine‐1‐propanoate ( 6 ) was converted to the phosphoramidite 8 and to the amino‐functionalized derivative 9 , which was transformed into the fluorescein‐labeled phosphoramidites 14 and 16 . Fluorescent oligonucleotides were synthesized either from these building blocks or by post‐synthetic modification of oligomers containing 2′‐deoxypseudouridine subunits. The stability of oligonucleotide duplexes was determined from the melting profiles, measured by UV‐ or VIS‐light absorbance, as well as from the fluorescence emission spectra. While small spacer residues did not affect the thermal stability of the 2′‐deoxypseudouridine‐containing duplexes, large dye residues led to destabilization.     

Synthesis and properties of novel l-isonucleoside modified oligonucleotides and siRNAs

Antisense oligonucleotides and siRNAs are potential therapeutic agents and their chemical modifications play an important role to improve the properties and activities of oligonucleotides. Isonucleoside is a type of nucleoside analogue, in which the nucleobase is moved from C-1 to other positions of ribose. In this report, a novel isonucleoside containing a 5'-CH(2)-extended chain at the sugar moiety was synthesized, thus isoadenosine and isothymidine were incorporated into a DNA single strand and siRNA. It was found that isonucleoside modified oligonucleotides can form stable double helical structures with their complementary DNA and RNA and the stability towards nuclease and ability to activate RNase H are more promising compared with the unmodified, natural analogues. In siRNA, passenger strand modified with isonucleoside () at 3' or 5' terminal can retain the silencing activity and minimize the passenger strand specific off-target effect.     

Synthesis, structure and thermal stability of fully hydrophobic porphyrin-DNA conjugates

The DNAs modified with tetraphenyl porphyrin at the center of 13mer oligonucleotide were synthesized using phosphoramidite chemistry and automated DNA synthesis. When the porphyrin modified oligonucleotide was annealed with its complementary strand, they formed a standard B-form duplex. The porphyrin moiety intercalated in the duplex, and moderately lowered the thermal stability.     

pH‐Independent Recognition of the dG ⋅ dC Base Pair in Triplex DNA: 9‐Deazaguanine N7‐(2′‐Deoxyribonucleoside) and Halogenated Derivatives Replacing Protonated dC

Triplex-forming oligonucleotides (TFOs) containing 9-deazaguanine N⁷-(2′-deoxyribonucleoside) 1a and halogenated derivatives 1b,c were synthesized employing solid-phase oligonucleotide synthesis. For that purpose, the phosphoramidite building blocks 5a – c and 8a – c were synthesized. Multiple incorporations of 1a – c in place of dC were performed within TFOs, which involved the sequence of five consecutive 1a – c ⋅ dG ⋅ dC triplets as well as of three alternating 1a – c ⋅ dG ⋅ dC and dT ⋅ dA ⋅ dT triplets. These TFOs were designed to bind in a parallel orientation to the target duplex. Triplex forming properties of these oligonucleotides containing 1a – c in the presence of Na⁺ and Mg²⁺ were studied by UV/melting-curve analysis and confirmed by circular-dichroism (CD) spectroscopy. The oligonucleotides containing 1a in the place of dC formed stable triplexes at physiological pH in the case of sequence of five consecutive 1a ⋅ dG ⋅ dC triplets as well as three alternating 1a – c ⋅ dG ⋅ dC and dT ⋅ dA ⋅ dT triplets. The replacement of 1a by 9-halogenated derivatives 1b,c further enhanced the stability of DNA triplexes. Nucleosides 1a – c also stabilized duplex DNA.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone,Part 5, 2′‐Deoxy‐8‐(hydroxymethyl)adenosine‐ and 2′‐Deoxy‐6‐(hydroxymethyl)uridine‐Derived Phosphoramidites: Synthesis and Incorporation into 14‐Mer DNA Strands

The pairing propensity of new DNA analogues with a phosphinato group between O−C(3′) and a newly introduced OCH₂ group at C(8) and C(6) of 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively, was evaluated by force‐field calculations and Maruzen model studies. These studies suggest that these analogues may form autonomous pairing systems, and that the incorporation of single modified units into DNA 14mers is compatible with duplex formation. To evaluate the incorporation, we prepared the required phosphoramidites 3 and 4 from 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively. The phosphoramidite 5 was similarly prepared to estimate the influence of a CH₂OH group at C(8) on the duplex stability. The modified 14‐mers 6 – 9 were prepared by solid‐phase synthesis. Pairing studies show a decrease of the melting temperature by 2.5° for the duplex 13 ⋅ 9 , and of 6 – 8° for the duplexes 10 ⋅ 6 , 11 ⋅ 6 , 13 ⋅ 7 , and 14 ⋅ 8 , as compared to the unmodified duplexes.     

New synthesis of (+/-)-isonucleosides

[Structure: see text] A novel method for synthesizing isonucleosides, a new class of anti-HIV nucleosides, is described. 2,2-Dimethyl-1,3-dioxan-5-one was converted into a dioxabicyclohexane derivative in six steps. After cleaving the epoxide group with thiophenol, the resulting product was subjected to the Mitsunobu reaction in the presence of a nucleobase to give the desired isonucleoside derivative via migration of the thiophenyl group. Removal of the thiophenyl group under radical conditions followed by deprotection led to the 4'-substituted 2',3'-dideoxyisonucleosides as a racemic mixture.     

Reversible diselenide cross-links are formed between oligonucleotides containing 2′-deoxy-6-selenoinosine

We have synthesized and characterized a phosphoramidite derivative of 2′-deoxy-6-selenoinosine (d^6SeI) and incorporated this modification into an oligonucleotide by solid-phase synthesis. During cleavage from the solid-support and deprotection, spontaneous dimerization of this oligonucleotide occurs via formation of a diselenide cross-link between the modified nucleobases. This cross-link can be readily reduced to restore the single-stranded oligonucleotide. UV thermal denaturation and circular dichroism spectroscopy of duplexes with d^6SeI paired against all four native nucleobases revealed minor differences in stability and structure relative to 2′-deoxyinosine. This selenium containing nucleobase modification may be useful for applications in DNA nanomaterials and X-ray crystallography.     

Nucleotides,Part LXII,Pyridinium Salts – An Effective Class of Catalysts for Oligonucleotide Synthesis

Various pyridinium salts (see 1 – 9 ) have been tested as catalysts for the condensation step in the phosphoramidite approach of oligonucleotide synthesis. Pyridinium chloride ( 1 ) turned out to be the most effective activator, speeding up the condensation tremendously. Pyridinium bromide ( 2 ) and 4-methylbenzenesulfonate ( 4 ) can also be regarded as powerful substitutes for the commonly used 1H-tetrazole. The acidic pK_a of the pyridinium cation provides an optimal range for phosphoramidite activation, which is followed by a nucleophilic attack of the pyridine ring to give the P-pyridinio intermediate 11 as the most likely precursor of phosphite ester formation (Scheme). ³¹P-NMR Studies support this proposal indirectly.     

Preparation of High‐Loading Polymer Supports by Polymerization Reaction Useful for Oligonucleotide Synthesis

A simple protocol based on polymerization reactions has been developed for the preparation of high‐loading polymer supports, useful for large‐scale synthesis of oligonucleotides. Polymer supports of different pore sizes have been employed in the present investigation to improve the functional‐group density on them. A ten‐ to twelvefold increase in the loading of the functional groups, after the polymerization reaction, has been observed. The support was then used in the subsequent reaction to attach the leader nucleoside to obtain fully functionalized supports 6a – 6c by oligonucleotide synthesis in an automated DNA synthesizer. The aminoalkylated‐supports 5a – 5c were directly employed for the synthesis of oligonucleotide 3′‐phosphates. The oligonucleotides and oligonucleotide 3′‐phosphates synthesized on these supports were compared with the corresponding standard oligomers with respect to their retention time on HPLC. These were further characterized on MALDI‐TOF mass spectrometry.     

8-Aza-7-deaza-2′-deoxyguanosine: Phosphoramidite synthesis and properties of octanucleotides

Base-modified octanucleotides derived from d(G1–G2–A–A–T–T–C–C–) ( 11 ) but containing 8-aza-7-deaza-2′-deoxyguanosine ( 2 ) instead of 2′-deoxyguanosine ( 1 ) have been prepared by solid-phase synthesis employing P(III) chemistry. Isobutyrylation of 2 , followed by 4, 4′-dimethoxytritylation and subsequent phosphitylation yielded the methyl or the cyanoethyl phosphoramidites 6a or 6b , respectively. They were used as building blocks in automated DNA synthesis. The resulting octanucleotides 12–14 containing 2 showed increased T_m values compared to the parent oligomer 11 . The oligomers 11 – 14 were employed as sequence-specific probes in endo-deoxyribonuclease Eco RI oligonucleotide recognition. Whereas displacement of dG-2 (enzymic cleavage site of 11 ) abolished phosphodiester hydrolysis, replacement of dG-1 enhanced the cleavage rate compared to 11 .     

以核酸为作用靶的内源性活性物质的研究

(Sp)-8-Cl-cAMP-辛酯通过调节细胞信号传导系统而抑制肿瘤细胞生长,其代谢产物8-Cl-腺苷也同样具有诱导分化和启动肿瘤细胞程序死亡的作用。从D(L)-木糖、D-葡萄糖和2-氨基-2-脱氧-D-葡萄糖出发合成了五种不同形式的异核苷,由异核苷组成的反义寡核苷酸能有效拮抗磷酸二酯酶的降解,它们对互补序列的杂交能力与异核苷的结构及磷酸二酯键的连接方式密切相关。     

Syntheses of pyrido[1,2-a][1,3,5]triazin-4-one C-deoxyribonucleosides

We achieved the syntheses of new C-deoxyribonucleosides bearing pyrido[1,2-a][1,3,5]triazin-4-one derivatives using palladium-catalyzed Heck-type coupling. Some of these C-deoxyribonucleosides were able to convert to phosphoramidite reagents, which can be used for DNA synthesizer. DNA oligomers including pyrido[1,2-a][1,3,5]triazin-4-one C-deoxyribonucleoside, which had 2-amino group were synthesized, and T_m values with a natural nucleoside were measured.     

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.     

Oligonucleotides Containing Novel 4′‐C‐ or 3′‐C‐(Aminoalkyl)‐Branched Thymidines

The synthesis of four novel 3′‐C‐branched and 4′‐C‐branched nucleosides and their transformation into the corresponding 3′‐O‐phosphoramidite building blocks for automated oligonucleotide synthesis is reported. The 4′‐C‐branched key intermediate 11 was synthesized by a convergent strategy and converted to its 2′‐O‐methyl and 2′‐deoxy‐2′‐fluoro derivatives, leading to the preparation of novel oligonucleotide analogues containing 4′‐C‐(aminomethyl)‐2′‐O‐methyl monomer X and 4′‐C‐(aminomethyl)‐2′‐deoxy‐2′‐fluoro monomer Y (Schemes 2 and 3). In general, increased binding affinity towards complementary single‐stranded DNA and RNA was obtained with these analogues compared to the unmodified references (Table 1). The presence of monomer X or monomer Y in a 2′‐O‐methyl‐RNA oligonucleotide had a negative effect on the binding affinity of the 2′‐O‐methyl‐RNA oligonucleotide towards DNA and RNA. Starting from the 3′‐C‐allyl derivative 28 , 3′‐C‐(3‐aminopropyl)‐protected nucleosides and 3′‐O‐phosphoramidite derivatives were synthesized, leading to novel oligonucleotide analogues containing 3′‐C‐(3‐aminopropyl)thymidine monomer Z or the corresponding 3′‐C‐(3‐aminopropyl)‐2′‐O,5‐dimethyluridine monomer W (Schemes 4 and 5). Incorporation of the 2′‐deoxy monomer Z induced no significant changes in the binding affinity towards DNA but decreased binding affinity towards RNA, while the 2′‐O‐methyl monomer Z induced decreased binding affinity towards DNA as well as RNA complements (Table 2).     

Nucleotides. Part LIV. Synthesis of condensed N1-(2′-deoxy-β-D-ribofuranosyl)lumazines,New fluorescent building blocks in oligonucleotide synthesis

Various condensed areno[g]lumazine derivatives 2 , 3 , and 5 – 7 were synthesized as new fluorescent aglycones for glycosylation reactions with 2-deoxy-3, 5-di-O-(p-toluoyl)-α/β-D -erythro-pentofuranosyl chloride ( 10 ) to form, in a Hilbert-Johnson-Birkofer reaction, the corresponding N¹-(2′-deoxyribonucleosides) 15 – 21 . The β-D -anomers 15 , 17 , 19 , and 21 were deblocked to 24 – 27 and, together with N¹-(2′-deoxy-β-D -ribofuranosyl)lumazine ( 22 ) and its 6, 7-diphenyl derivative 23 , dimethoxytritylated in 5′-position to 28–33. These intermediates were then converted into the 3′-(2-cyanoethyI diisopropylphosphoramidites) 34 – 39 which function as monomeric building block in oligonucleotide syntheses as well as into the 3′-(hydrogen succinates) 40 – 45 which can be used for coupling with the solid-support material. A series of lumazine-modified oligonucleotides were synthesized and the influence of the new nucleobases on the stability of duplex formation studied by measuring the T_m values in comparison to model sequences. A substantial increase in the T_m is observed on introduction of areno[g]lumazine moieties in the oligonucleotide chain stabilizing obviously the helical structures by improved stacking effects. Stabilization is strongly dependent on the site of the modified nucleobase in the chain.     

Comparative electrochemical properties of fluorinated endoperoxides related to the G-factor series

Fluorinated analogues of natural product G3-factor were synthesized and evaluated for their antiplasmodium activity. Electrochemical studies allowed us to measure the reduction potential E_p of the new compounds and to compare the effect of fluorine atoms on peroxo bridge stability.     

Diels--Alder bioconjugation of diene-modified oligonucleotides

In an effort to offer complementary technology for covalent biomolecule modification (bioconjugation), we have developed a method that exploits the aqueous acceleration of Diels--Alder reactions for this purpose. Three different diene phosphoramidite reagents have been synthesized that enable diene modification of synthetic oligonucleotides prepared by the phosphoramidite method. Clean and efficient Diels--Alder cycloaddition of these diene oligonucleotides with maleimide dieneophiles was carried out, and the labeled oligonucleotide bioconjugates were characterized by HPLC and electrospray mass spectrometry. Dieneophile stoichiometry, temperature, and pH are all parameters that were shown to influence the efficiency of the process.     

An efficient reagent for 5′-azido oligonucleotide synthesis

A new bromohexyl phosphoramidite was synthesized and used for the introduction of an azide function at the 5′-end of oligonucleotides after a treatment on solid support with sodium azide and sodium iodide. The corresponding 5′-azido oligonucleotide could be further used for ‘Click’ conjugation with alkyne derivatives or by Staudinger ligation.