Effects of Intravenous Infusion of Phosphorothioate Oligonucleotides on Coagulation,Complement Activation and Hemodynamics

Abstract

Several acute toxicities in monkeys have been associated with administration of phosphorothioate oligonucleotides including effects on coagulation and complement cascades. These effects are transient in nature and the severity is closely associated with peak plasma concentrations of the oligonucleotide. Similar properties have been observed for several oligonucleotides with different base sequences.     

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.     

Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of CAc Derivatives

Abstract

We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dC^bz has been eliminated by the use of dC^Ac phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dC^Ac hydrogen phosphonate and DMT ribo C^Ac-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.     

A New Protecting Group Strategy for Amino Groups in Oligonucleotide Chemistry: CEOC Group

Abstract

A new protecting group, 2-cyanoethyloxycarbonyl, or CEOC, has been developed for amino groups and utilized in synthesizing modified oligonucleotides. (CEOC)-oxy-succinimide reagent has been synthesized to introduce this protecting group. The protecting group is removed by standard oligonucleotide deprotection protocols. Using this approach, oligonucleotides have been synthesized with various types of alkylamine substituents.     

New Pyrene Derivatives for Fluorescent Labeling of Oligonucleotides

Abstract

A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides.     

The Reactions of H-Phosphonates with Bifunctional Reagents. V. Functionalization of Support-Bound Oligonucleotides and Synthesis of Nonradioactive Hybridization Probes a

Abstract

Three methods for the functionalization of oligonucleotides with aminoalkyl moieties have been developed and their efficiencies were evaluated in the preparation of non-radioactive hybridization probes.

     

Evaluation of Oligonucleotides Containing Two Novel 2′-O-Methyl Modified Nucleotide Monomers: A 3′-C-Allyl and a 2′-O-3′-C-Linked Bicyclic Derivative

Abstract

The two ribo-configured nucleosides 1-(3-C-allyl-2–0-methyl-β-D-ribo-pentofuranosyl)thymine 3 and (1S,5R,6R,8R)-5-hydroxy-6-(hydroxymethyl)-1-methoxy-8-(thymin-1-yl)-2,7-dioxabicyclo[3.3.0]octane 6 have been transformed into their corresponding phosphoramidites, 5 and 8 respectively, and used as building blocks for the synthesis of modified oligonucleotides. The oligonucleotides were shown to hybridize with decreased binding affinity towards complementary single stranded DNA and RNA.     

Synthesis and Properties of New Fluorescein-Labeled Oligonucleotides

Abstract

2,4-Dinitroaniline is an efficient intramolecular fluorescence-quencher for fluorescein - labeled oligonucleotides and interacts with the heterocyclic bases on duplex formation. Consequently, intramolecular fluorescence quenching is disturbed in double labeled oligonucleotides of this type, and fluorescein shows strong fluorescence in a duplex form. There is a substential increase of the fluorescence-quantum yield when the marker and quencher is attached to a single guanosine residue. Two kinds of doubly labeled oligonucleotides have been synthesized, using the NPE/NPEOC strategy.     

The Synthesis of Branched Oligonucleotides as Signal Amplification Multimers for Use in Nucleic Acid Assays

Abstract

Branched oligonucleotides have been synthesized using phosphoramidite derivatives with two protected hydroxyl functions. These molecules are employed for a label amplification strategy used in DNA probe diagnostics.     

Dinucleoside Monophosphate Analogues Containing Disulfide Linkages

Abstract

Two dinucleoside monophosphate analogues containing disulfide linkages (1 and 2) have been prepared for incorporation into oligonucleotides. The modified oligomers will be tested for their potential as antisense agents.     

Thin Layer Chromatography of Radiolabeled Oligonucleotide Analogues: A Rapid and Sensitive Purity Assay

Abstract

Oligonucleotide analogues are being developed for use in cell culture, animals and for therapy. Prior to use it is important to have an indication of the oligomers' purity. Thin layer chromatography (TLC) has been applied to analyze hosphoromonothioate and phosphorodithioate oligonucleotides radiolabeled with either ³²P Or ¹⁴C. TLC coupled with radioactivity has been compared to Polyacrylamide Gel Electrophoresis (PAGE) and High Pressure Liquid Chromatography (HPLC). TLC is a rapid and sensitive alternative to these methods and is particularly suited for chemically modified oligonucleotides.     

Conjugated Antisense Oligonucleotides for Inhibition of Human Cytomegalovirus In Vitro

Abstract

Several thiono triester containing oligonucleotide phosphorothioates linked with a lipophilic group have been synthesized. Some of these modified antisense oligonucleotides show potent anti-HCMV activity as well as improved cellular association and nuclease resistance.     

Time-of-flight Secondary Ion Mass Spectrometry of Branched RNA Fragrants: Messenger RNA Splicing Intermedistes

Abstract

The negative ion mass spectra generated by a reflecting time-of-flight mass spectrometer are reported for a series of protected oligonucleotides. Quasimolecular and sequence ions have been detected, and the location and nature of protecting groups have been confirmed.     

Nuclease Stability of LNA Oligonucleotides and LNA-DNA Chimeras

Abstract

The stabilizing properties of LNA and α-l-LNA oligonucleotides against endo- and 3′-exonucleases have been evaluated.     

PHOSPHONOACETATE DERIVATIVES OF OLIGODEOXYRIBONUCLEOTIDES

Abstract

A deoxyribodinucleotide phosphonoacetate derivative has been prepared, separated into individual diastereomers, and incorporated into oligodeoxyribonucleotides possessing alternating phosphodiester and phosphonoacetate backbone linkages. The hybridization properties and enzymatic stabilities of these oligonucleotides have been studied.     

Oligonucleotides Labeled by Fluorophores at the Sugar 2′-Positions for Fluorescence Energy Transfer Study of Nucleic Acid Structure

Abstract

Oligonucleotides containing 2′-(6-dimethylamino-2-naphthamide)uridine have been shown to be useful as a donor fluorophore in FRET to oligonucleotides labeled with fluorescein at the 2′-position as an acceptor molecule.     

Cleavage of Leishmania Mini-exon Sequence by Oligonucleotides Conjugated to a Dimidazole Construction

Abstract

RNA sequences derived from the Leishmania amazonensis mini-exon and pre-mini-exon sequences have been targeted with complementary oligonucleotides bearing a diimidazole construction mimicking active center of ribonuclease A. The conjugates were shown to cleave the target RNAs at specific positions.     

Oligonucleotide Labeling Methods 4. Direct Labeling Reagents with a Novel,Non-Nucleosidic,Chirally Defined 2-Deoxy-β-D-Ribosyl Backbone.

Abstract

Novel solid supports and CE-phosphoramidite reagents have been prepared featuring a unique 2′-deoxyribosyl backbone. These chirally pure reagents form the basis of an oligonucleotide labeling system which provides diastereomerically pure oligonucleotides.     

In Search of Acyclic Analogues as Universal Nucleosides in Degenerate Probes

Abstract

Five acyclic nucleoside analogues with unnatural base moieties have been synthesized of which three successfully were incorporated into oligonucleotides. The acyclic analogue containing the base 5-nitroindazole was the least discriminating and should be further pursued for use as a universal nucleoside analogue.     

The Synthesis of Bicyclic N4-Amino-2′-deoxycytidine Derivatives

Abstract

A number of bicyclic N⁴-amino-2′-deoxycytidine derivatives have been prepared. Their ambivalent hydrogen bonding potential makes them of interest for mutagenesis studies, and for incorporation into oligonucleotides for probes and primers.