Oligonucleotide sulfones

In the early solution phase syntheses of oligonucleotides, coupling of phosphate diesters was used. A mixed 3 -ester with one aryl substituent, usually o-chlorophenyl, was coupled with a deprotected 5 -OH nucleotide. The coupling reagents were sulfonyl halides, particularly 2,4,6-tri-i-propylbenzenesulfonyl chloride,53 and the reactions proceeded by formation of reactive sulfonate esters. Coupling conditions... 

Membranes offer a format for interaction of an analyte with a stationary phase alternative to the familiar column. For certain kinds of separations, particularly preparative separations involving strong adsorption, the membrane format is extremely useful. A 5 x 4 mm hollow-fiber membrane layered with the protein bovine serum albumin was used for the chiral separation of the amino acid tryptophan, with a separation factor of up to 6.6.62 Diethey-laminoethyl-derivatized membrane disks were used for high-speed ion exchange separations of oligonucleotides.63 Sulfonated membranes were used for peptide separations, and reversed-phase separations of peptides, steroids, and aromatic hydrocarbons were accomplished on C18-derivatized membranes. 

Phosphoric-sulfonic anhydrides are of special interest because they are presumed to be intermediates in oligonucleotide coupling reactions involving phosphordiester activation by arenesulfonyl derivatives (see Section 12.7). 

Cyanine dyes also are used as labels for oligonucleotide probes. Unlike the hydrophilic cyanine dyes valuable for protein labeling, the use of dye-phosphoramidite compounds to synthesize DNA or RNA probes typically requires the use of more hydrophobic dye structures to make them compatible with the solvents and reactions of oligonucleotide synthesis. Thus, indol cyanines containing few or no sulfonates are used in these applications to label oligos for applications such as array detection, hybridization assays, and RT-PCR. 

The fluorescence spectrum of the tris-acridine cryptand A-13 shows the characteristic monomer and excimer bands. Upon complexation with various organic anions (carboxylates, sulfonates, phosphates), the monomer band increases at the expense of the excimer band. The stability of the complexes depends on the contribution of the electrostatic and hydrophobic forces and on the structural complementarity. Stability constants of the complexes ranging from 103 to 107 have been measured. In particular, A-13 binds tightly to mono- and oligonucleotides, and it can discriminate by its optical response between a pyridimic and a purinic sequence. 

Addition of a nucleophile to the C-6 position of cytosine often results in fascile displacement reactions occurring at the N4 location. With hydroxylamine attack, nucleophilic displacement causes the formation of an N4-hydroxy derivative. A particularly important reaction for bioconjugate chemistry, however, is that of nucleophilic bisulfite addition to the C-6 position. Sulfonation of cytosine can lead to two distinct reaction products. At acid pH wherein the N-3 nitrogen is protonated, bisulfite reaction results in the 6-sulfonate product followed by spontaneous hydrolysis. Raising the pH to alkaline conditions causes effective formation of uracil. If bisulfite addition is done in the presence of a nucleophile, such as a primary amine or hydrazide compound, then transamination at the N4 position can take place instead of hydrolysis (Fig. 38). This is an important mechanism for adding spacer arm functionalities and other small molecules to cytosine-containing oligonucleotides (see Chapter 17, Section 2.1). 

Fig. 10.1 Rat colon tissue (A) or liver tissue (B) oligonucleotide concentrations as a percentage of administered radioactive dose for normal rats (filled symbols) or treated with trinitrobenzene sulfonic acid (open symbols) as a model for colitis. Solid lines represent intravenous route broken lines designate rectal dosing (both 100 mg/kg ISIS 2302 with nonexchangeable 3H label).

Fig. 3 TEM images. Left 1 1 molar ratio blend of poly(4-trimethylsilylstyrene) and deuterated polystyrene end-decorated with complementary oligonucleotides. Reprinted with permission from [72]. 2006 American Chemical Society. Right blend of 60wt% mono-end-aminated polyisoprene with di-end-sulfonated polystyrene [73]...

A method for the solid phase synthesis of 3 -modified oligonucleotides has been described. The general synthetic scheme involved the immobilisation of 5 -DMTr-T to CPG via a sulfonate linker, 218, oligonucleotide synthesis and... 

Fig. 14.4) were used to label oligonucleotides by Randolph et al [71]. While Cy3 contains a bis-sulfonate functionality for improved water-solubility, Cy3NOS is mono-sulfonated. The reaction of 14 and 15 produced the carboxy-substituted dye 16, which was further treated with N,N -disuccinimidyl carbonate in a mixture of DMF/pyridine to give the nonsymmetric N-hydroxysuccinimidyl substituted Cy dyes 17. Dyes 17 were then covalently linked via a short or long tether at the C-5 position of deoxyuridine to multiply-label DNA. The correlation study between the labeling density and the sensitivity of the DNA fluorescent probe demonstrated that labeling at every 6th base pair with Cy3 showed the optimal fluorescence. 

The homologated iodide 68, required for making sulfone-linked oligonucleotide analogues, has been prepared by the interesting sequence of reagents shown in Scheme... 

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