Abstract: This invention provides dye phosphoramidites, particularly phosphoramidites of substituted cyclic bridged cyanine and related dyes, of the general formula: In this formula, each dotted line represents carbon atoms necessary to form a fused substituted or unsubstituted aromatic ring; m is an integer from 1 to 18; Y and Z are independently selected from the group consisting of S, O, N, CH2 and C(CH3)2; R1 is an alkyl; (PAM) is a phosphoramidite group; X{circle around (?)} is a negative ion; and Q is L-W, wherein L is a conjugated cyclic moiety and W is OR2, wherein R2 is a second alkyl. Methods of making and using the dye phosphoramidites are also provided.

Abstract: A compound of the general formula ##STR1## wherein R is alkyl of 1 to about 10 carbons and R' is selected from the group consisting of trityl and pixyl, for use in the synthesis of 2'-OMe RNA sequences. Fast cleavage and deprotection of oligonucleotides is facilitated by the use of a reagent comprising methylamine as active component in place of the traditional reagent ammonium hydroxide.

Abstract: Oxidizing compositions particularly for use in automated oligonucleotide synthesis containing a mixture of KI and I.sub.2 in solution, in equilibrium with KI.sub.3. One preferred composition contains 1.75% KI.sub.3 (providing 0.69% KI and 1.06% I.sub.2) in tetrahydrofuran/pyridine/water (93/5/2, v/v). These formulations enable synthesis of oligonucleotides of significantly higher quality than the currently employed formulation comprising 3% I.sub.2 in tetrahydrofuran/pyridine/water (74/21/2, v/v).

Abstract: A compound of general formula ##STR1## wherein R is methyl R' is selected from the group consisting of trityl and pixyl, and R" is H or OMe. These compounds may advantageously be employed in the synthesis of oligonucleotides by conventional methods, such as automated solid phase synthesis. Use of ethylene diamine in the cleavage and deprotection procedure substantially eliminates the formation of undesirable side products.