RNase H Activation by Stereoregular Boranophosphate Oligonucleotide

Abstract

A stereoregular all-(S _p)-boranophosphate oligodeoxyribonucleotide (BH₃ ^?-ODN) 15-mer was synthesized using an enzymatic approach. The BH₃ ^?-ODN formed a hybrid with the complementary RNA 15-mer and induced RNase H hydrolysis of the RNA strand at ODN concentrations as low as 10 nM at 37°C, but with a lower efficiency than that of its natural phosphodiester analogue.     

Superactive Oligonucleotide Derivatives

Abstract

The conjugate of antitumor antibiotic bleomycin A5 with the tetranucleotide catalytically cleaves 20-mer ssDNA target in the presence of flanking octanucleotides. Each molecule of the conjugate cleaves on the average three molecules of the target.     

Tetraethylene Glycol-Derived Spacer for Oligonucleotide Synthesis

Abstract

3,6,9-Trioxaundecane-1,11-diisocyanate (6) was synthesised from tetraethylene glycol in 5 steps and 48 % overall yield. Spacer 6 was monofunctionalised with the fully protected adenosyl-3′-O-succinate derivative 7 and linked to aminomethyl polystyrene affording a solid support suitable for oligoribonucleotide synthesis (loading: ～20 μmol/g). The HPLC analysis of a crude oligoribonucleotide synthesis and the yield of the full-length product show that this spacer compares well to hexamethylene diamine.     

Synthesis of Circular Oligonucleotide Conjugates

Abstract

A new approach to the non-template synthesis of circular oligodeoxyribonucleotides containing flexible non-nucleotidic linkers has been developed. Using this technique a set of circular molecules representing triple helix forming, antisense and guanosine tetrad containing oligonucleotides has been obtained.     

Picomole Syntheses of High Quality Oligonucleotide Primers in Combination with the Preparation of Oligonucleotide Arrays

Abstract

The establishment of a new synthesis procedure for the preparation of oligonucleotide arrays is described. A modified phosphoramidite chemistry allowed the in situ synthesis of oligomer arrays on specially derivatized polypropylene membranes which can be used both for hybridisation experiments and for the isolation of the individual oligonucleotides.     

Synthesis of an Oligonucleotide Analogue of Ethenoadenosine

Abstract

A phosphoramidite building block derived from 11-carboxy-1,N ⁶-ethenoadenosine has been prepared to be used in a solid supported oligonucleotide synthesis.     

Improved Synthesis of Trinucleotide Phosphoramidites and Generation of Randomized Oligonucleotide Libraries

A new method to produce a set of 20 high quality trinucleotide phosphoramidites on a 5–10 g scale each was developed. The procedure starts with condensation reactions of P-components with N-acyl nucleosides, bearing the 3 ′-hydroxyl function protected with 2-azidomethylbenzoyl, to give fully protected dinucleoside phosphates 13. Upon cleavage of dimethoxytrityl group from 13, dinucleoside phosphates 16 are initially transformed into trinucleoside diphosphates 19 and then the 2-azidomethylbenzoyl is selectively removed under neutral conditions to generate trinucleoside diphosphates 5 in excellent yield. Subsequent 3 ′-phosphitylation affords target trinucleotide phosphoramidites 7. When mutagenic oligonucleotides are synthesized employing mixtures of building blocks 7 as well as following the new synthetic protocol, representative oligonucleotide libraries are generated in good yields.     

Synthesis of Oligonucleotide Prodrugs Bearing N-Acetyl Nucleobases

Abstract

N-Acetyl oligonucleotides and their prodrugs were synthesized on photolabile solid support. Tm studies showed a decrease of hydridization for N-acetyl A and G and an increase for N-acetyl C. In cells extract, acetyl groups were hydrolysed.     

Stereochemical Problems in Oligonucleotide Synthesis

Abstract

The phosphoramidites of protected cordycepin, thymidine and deoxyadenosine were prepared and the two isomers were well separated by medium-pressure chromatography. Condensations were performed in solution to dimers and on solid support to oligomers. The stereochemical consequences will be discussed.     

Synthesis and Properties of Some Morpholino Oligonucleotide Analogues

Abstract

The solid phase synthesis of the three types of morpholino analogues of nucleic acids has been accomplished and their hybridization properties were evaluated.     

Oligonucleotide Analogues with Dialkyl Silyl Internucleoside Linkages

Abstract

Oligonucleotide analogues with dialkyl-silyl inter-nucleoside linkages were prepared by “one pot” reactions starting from dialkyl-dichloro- resp. chloro-dialkylamino-silane derivatives.     

Synthesis of 3′-Azido-3′-Deoxythymidine-Terminated Oligonucleotide

Abstract

A method of completely chemical synthesis of 3′-azido-3′-deoxythymidine-terminated oligonucleotides via 5′-H-phosphonate of AZT is described.     

Chemical and Photochemical Ligation of Oligonucleotide Blocks

Abstract

Several efficient means for joining oligonucleotides in dilute solution by non-natural internucleotide bridges are discussed. It is also shown that an oligonucleotide containing a -OP(O)(O^?)S- link can hnction as an effective template in PCR amplification and that oligonucleotide probes containing stilbenedicarboxamide groups can serve in monitoring the presence of mismatched bases in an oligonucleotide target.     

A New Approach to Oligonucleotide Synthesis in Solution

Abstract

A new approach, based on the use of 3′-H-phosphonate building blocks, is described for the synthesis of oligonucleotides and their phosphorothioate analogues in solution.

     

NMR Study and Improvement of H-Phosphonate Oligonucleotide Synthesis

Abstract

The mechanism of the internucleotide condensation and side-reactions in H-phosphonate approach has been investigated. The modification of this method allowed to minimize side-reactions during the preactivation of the nucleotidic component has been developed.     

Solid-Supported Oligonucleotide Systems for Special Biomedical Applications

Abstract

The use of composite beads consisting of a 6 μm polystyrene core with 30 nm surface-bound silica particles to routine automatic oligodeoxynucleotide (ODN) synthesis is described.     

Concept of “Binary Oligonucleotide Reagent”

Abstract

A new strategy for site-directed chemical modification of NA is described. NA-target-driven autoligation reaction between two oligonucleotide derivatives with N-(2-chloroethyl)-N-(p-formylphenyl)-N-propyl-N-3 -ydeneamino and 4-carbohydrazidephenyl groups at their opposing termini results in the NA-target modification, which is several times more effective than modification by one of the derivatives.     

Semi-Mechanized Simultaneous Synthesis of Multiple Oligonucleotide Fragments

Abstract

A new strategy for the simultaneous synthesis of multiple oligonucleotides is described, which is based on asynchronous chain growth and use of a maximum number of support segments in each elongation. An approach to the mechanization of this strategy and applications to the preparation of gene fragments and sequentially variant probes are discussed.     

Synthesis and Hybridization Studies of Oligonucleotide Sequences with Modified Fluorescent Nucleoside Analogs

Abstract

Two complementary oligodeoxynucleotide hexamers CATGAA and TTCATG and a pentamer with a fluorescent nucleoside analog viz. 9-N-(2′-deoxy-β-D-ribofuranosyl) carbazole (C*) incorporated into it, TTC*ATG were synthesized and characterised by spectroscopic and chromatographic studies. The comparative fluorescent studies of the two nucleoside analogs viz. 9-N-(2′-deoxy-β-D-ribofuranosyl) acridone and its carbazole analog (C*) have been carried out under different experimental conditions. The effect on fluorescence by incorporation of (C*) into the sequence and its subsequent hybridization with the complementary sequence have been studied.     

Oligonucleotide Labeling: Synthesis of a New Spin-Labeled 2′-Deoxyguanosine Analogue

Abstract

in order to achieve an EPR sensitive probe for DNA, 3-carboxy-Proxyl free radical was linked to O-6 of dG through a five-atoms-tether. The modified base was incorporated into a 30-mer ODN, then annealed to its complementary DNA strand. Hydrodinamic parameters show only a slight destabilization with respect to the equivalent unlabeled hybrid. EPR could monitor the hybrid formation showing a progressive enlargement of the upfield signal in passing from the labeled ss- to the ds-30-mer.