Patent ID: 6639061
Filing Date: 2003-10-28
Classification: A61K,C07B,C07H

Abstract:
A method of preparing an oligomer of formula II: wherein:Bx is a protected or unprotected heterocyclic base moiety; T1 is an oligonucleotide, oligonucleoside, nucleoside, nucleotide, H or a hydroxyl protecting group; each X1, X2 and X3 is, independently, O, S or NH; L is C(Y1)(Y2) or O, provided that at least one L is C(Y1)(Y2); R1 is Z0â€”(C2-C20 alkynyl); or R1 has one of formulas XI or XII: â€ƒwherein: Z0 is O, S or NH; E is C1-C10 alkyl, N(Q1)(Q2) or N&boxH;C(Q1)(Q2); each Q1, and Q2 is, independently, H, C1-C10 alkyl, substituted alkyl, dialkylaminoalkyl, a nitrogen protecting group, a tethered or untethered conjugate group, a linker to a sold support; or Q1 and Q2, together, are joined in a nitrogen protecting group or a ring structure that can include at least one additional heteroatom selected from N and O; q1 is from 1 to 10; q2 is from 1 to 10; q3 is zero or 1; q4 is zero, 1 or 2; q5 is 1 to 10; each M1 is, independently, H, C1-C8 alkyl, C1-C8 haloalkyl, C(&boxH;NH)N(H)M2, C(&boxH;O)N(H)M2 or OC(&boxH;O)N(H)M2; M2 is H or C1-C8 alkyl; Z1, Z2 and Z3 comprise a ring system having from about 4 to about 7 carbon atoms or having from about 3 to about 6 carbon atoms and 1 or 2 heteroatoms wherein said heteroatoms are selected from oxygen, nitrogen and sulfur and wherein said ring system is aliphatic, unsaturated aliphatic, aromatic, or saturated or unsaturated heterocyclic; and Z4 is OM1, SM1, or N(M1)2; Z5 is alkyl or haloalkyl having 1 to about 10 carbon atoms, alkenyl having 2 to about 10 carbon atoms, alkynyl having 2 to about 10 carbon atoms, aryl having 6 to about 14 carbon atoms, N(Q1)(Q2), OQ1, halo, SQ1 or CN; m is 0 or 1; p is 0 or an integer from 1 to 50; and each of Y1 and Y2 is, independently, H, alkyl, substituted alkyl, aryl, substituted aryl, heterocyclyl, substituted heterocyclyl, cyano, carboxyl, ester or a cyclic moiety; comprising the steps of: (a) providing a 5â€²-protected nucleoside attached to a solid support; (b) cleaving the 5â€²-protecting group in the presence of an acid solution to form a 5â€²-deprotected nucleoside; (c) coupling said 5â€²-deprotected nucleoside with a monomer of formula I: â€ƒwherein: Z6 is OH, OCH2CH2CN, N(i-Pr)2, dialkylamino, disubstituted alkylamino or Oâˆ’HBy+; and By is an organic base moiety; in the presence of an condensing reagent to form a compound having an H-phosphonate linkage; (d) optionally capping said 5â€²-deprotected nucleoside with isopropylphosphite and pivaloyl chloride in acetonitrile and pyridine; (e) repeating steps (b) to (d) to form an oligomer of desired length and sequence; (f) oxidizing said H-phosphonate linkage with an oxidizing reagent to form an oxidized methylenephosphonate linkage; (g) repeating steps (b) to (f) to form an oligomer of desired length and sequence; and (h) cleaving said oligomer with aqueous ammonia.