Biological Activities of Oligonucleotides Linked to Poly(L-Lysine)

Abstract

We have developped a method to couple oligonucleotides to poly(L-lysine). This tool has been tested with anti m-RNA synthetic oligodeoxyribonucleotides and 2′-5′(A)_n and allows oligonucleotides to enter intact cells.     

Intercalating Insert into Internucleotide Linkages as Way for Stabilization and Detection of of Short DNA Duplexes

Abstract

Simple and convenient method for stabilization and detection of duplexes of short oligonucleotides with DNA was developed. This method is based on use of oligonucleotides containing inercalating insert in internucleotide linkage. The linker is so long that dye can intercalate only into the same stacking contact. Additionally the method allows to introduce into oligonucleotide as one intercalator as well as several identical or different intercalating dye.     

Protection of 2,6-Diaminopurine 2′-Deoxyriboside

Abstract

Protection of both mine moieties of 2, 6-diaminopurine 2′-deoxyriboside as a dimethylformamidine group did not proove feasable, while protection with a phenoxyacetyl group afforded only a mono-protected analogue 5. This analogue can be incorporated into oligonucleotides without difficulties. However, oligonucleotides with diaminopurine substituted for adenine did not yield more stable duplexes for the two sequences tested here.     

Quantitative One Step Derivatization of Oligonucleotides by a Fluorescent Label Through Abasic Site Formation

Abstract

Reaction of abasic site-containing oligonucleotides with an oxyamino fluorescent label is described. The reaction represents an efficient method to functionalize oligonucleotides at preselected positions.     

3′-Terminal Modification of Oligonucleotides Using a Universal Solid Support

Abstract

A practical method to prepare 3′-terminally labeled oligonucleotides using a universal solid support (1) was developed. This novel method was demonstrated by incorporating thirteen different label moieties on the 3′-terminus of a common (dT)₇ sequence. Label incorporations were verified by ion exchange HPLC analysis and MALDI TOF mass spectrometry.     

Fluorescent Labelling of Oligodeoxyribonucleotides by the Oxyamino-Aldehyde Coupling Reaction

Abstract

We describe the reaction of oligonucleotides containing an aldehydic group at the 5′-end or inside the sequence with an oxyamino label. The reaction was found to be highly selective and represents an efficient method for derivatization of oligonucleotides.     

Biotin-Labeled Synthetic Oligodeoxyribonucleotides: Chemical Synthesis and Uses as Hybridization Probes

Abstract

Several biotinylated synthetic oligodeoxyribonucleotides have been selectively prepared by a simple and efficient chemical method. This procedure allows the specific and covalent coupling of one biotinmoiety to any 5′-kinased unprotected oliqodeoxyribonucleotide through an aminoalkylphosphoramide linker arm. The reactions are performed in aqueous solutions on unprotected oligonucleotides and proceed cleanly with good yields. This method is insensitive of the length of the polynucleotide, of the nucleotide sequence and of the nature of the 5′-terminal nucleotide.     

Novel Method for the Covalent Immobilization of Oligonucleotides via Diels-Alder Bioconjugation

Abstract

The synthesis of cyclohexadiene and maleimide derivatives and their use for the functionalization of oligonucleotides and the coating of glass surfaces is reported. A method for the covalent attachment of diene or maleimide modified oligonucleotides to the coated glass surfaces via aqueous Diels-Alder reactions is presented.     

Oligonucleotide Conjugates Derived from an Electrophilic Site: Conjugation to Baseless Carbohydrate Residue. Synthesis,Hybridization and Modeling Studies

Abstract

Conjugation of electrophiles to oligonucleotides via tethers camying nucleophilic sites well-known. However, for the rever.se reaction, the availahlc methods to generate electrophilic sites in oligonucleotides are not many: (e.g., periodate oxidation of terminal rihose sugar followed by reductive amination).     

New Strategies for the Chemical Synthesis of Biologically Important Nucleic Acid Derivatives

Abstract

This paper describes general methods for the synthesis of N-phosphorylated ribonucleosides and oligonucleotides containing a 2′-O-phosphorylated or 2′-O-thiophosphorylated ribonucleoside. The NMR-based conformational analysis and computational molecular dynamics simulation of the 2′-O-phosphorylated ribonucleoside residue in such modified oligonucleotides suggested that the ribose residue existed preferentially in a C2′-endo conformation. It was also found that simple heating of 2′-O-phosphorylated oligonucleotides resulted in rapid dethiophosphorylation.     

A Rapid Solid Phase Method for the Synthesis of 3′-Thiol Group Containing Oligonucleotides

Abstract

A rapid solid phase method for the synthesis of 3′-thiol group containing oligonucleotides is described.     

Characterization of Oligonucleotide Sequence Isomers in Mixtures Using HPLC/MS

Abstract

A method is described for the analysis of mixtures containing sequence isomers of oligonucleotides. The approach consists of an electrospray ionization mass spectrometric analysis in direct combination with HPLC separation. Mass spectrometry can provide sequence information based on the fragmentation patterns of oligonucleotides allowing the simultaneous characterization of sequence isomers. An example is shown for the characterization of a mixture of dCAGT, dCGTA, dTCAG, dAGTC and dTCGA.     

A New Solid Phase Method for the Synthesis of Oligonucleotides with Terminal -3′-Phosphate

Abstract

A novel method for the synthesis of oligonucleotides with terminal-3′-phosphate using universal CPG polymer support is described.     

Use of [4,6-Di-14C]-5′-DMT-thymidine Phosphoramidite Reagent for the Radiolabeling of Synthetic Oligonucleotides

Abstract

A novel synthesis of 5′-radiolabeled oligonucleotides is described. The labeling is carried out by the phosphoramidite method with the aid of building block 1. The feasibility of the method is demonstrated by preparation of 5′-radiolabeled 3′-phosphorylated dodecathymidylate phosphorothioate.     

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.     

A Rapid Method for Simultaneous Chemical Synthesis of Oligonucleotides in Large Nufiber

Abstract

A rapid manual method i s described for simultaneous synthem o v e r one hundred oligonucleotides on a microscale by the phosphotriester approach on cellulose paper.     

A General Procedure for Assigning the 31P Spectra of Drug-Oligonucleotide Complexes

Abstract

Taking advantage of the slow exchange at the NMR time scale occurring in drug oligonucleotides complexes the ³P signals in the bound forms are assigned by using ³¹PNMR two dimensional chemical exchange. This technique was applied to complexes between Actinomycin D and d[C_pG_pC_pG] or d[m⁵C_pG_pm ⁵C_pG], As compared to the labelled ¹⁷O,¹⁸O this method proved to be a powerful and unique way to assign ³¹P in broad spectrum or with long oligonucleotides.     

Base-Labile Group Protected Biotinphosphoramidite Reagents for Solid Phase Biotinylation of Oligonucleotides

Abstract

A general and rapid method is described for the synthesis of N¹ -base labile group protected biotinphosphoramidite reagents, useful for the synthesis of biotinylated oligonucleotides in automated DNA synthesizer.     

Oligodeoxyribonucleosides Containing 1-β-D-Glucopyranosylthymine Synthesis and Substrate Properties

Abstract

Regioselective method for 1-β-D-glucopyranosylthymine incorporation into oligonucleotides has been developed and substrate properties of the latters in DNA synthesis and hydrolysis reactions were investigated.     

Efficient Chemical Synthesis of Oligonucleotides Containing the 2-Deoxyribonolactone Site

Abstract

A highly efficient synthetic method for incorporation of the deoxyribonolactone lesion into oligonucleotides was developed using the photochemical properties of 7-nitroindole.