Patent ID: 6800743
Filing Date: 2004-10-05
Classification: C07H,C12Q,Y02P

Abstract:
A compound having the formula: wherein:D is hydroxyl, protected hydroxyl, an oligonucleotide coupling group or a solid support; D1 is an oligonucleotide coupling group, hydroxyl, protected hydroxyl or a solid support, wherein D1 is bonded to one 2â€² or 3â€² position in the oligonucleotide and another 2â€² or 3â€² position is substituted with R21, provided that D and D1 are not both an oligonucleotide coupling group and they are not both a solid support; each R4 is, independently, a phosphodiester linkage or a phosphodiester substitute linkage; each R21 is, independently, hydroxyl, protected hydroxyl, halogen or a moiety that enhances nuclease resistance; n is an integer from 0 to 98; each B, independently, is a naturally occurring or non-naturally occurring base, or an analog or a protected derivative thereof, provided that at least one B is a base of structure II: â€ƒwherein R34 is independently â€”Oâ€”, â€”Sâ€” or â€”N(CH3)â€”, R2 is â€”R6â€”(CH2)tN(R5)C(NR5)N(R3)2, â€”R6â€”CH2â€”CHR31â€”N(R3)2, â€”R6â€”(R7)vâ€”N(R3)2, â€”R6â€”(CH2)tâ€”N(R3)2, â€”(CH2)1-2â€”O(CH2)tâ€”N(R3)2, or A(Z)x1; A is a spacer and Z independently is a label bonding group optionally bonded to a detectable label, but R2 is not amine, protected amine, nitro or cyano; x1 is 1, 2, or 3; R3 is â€”H, â€”CH3, â€”C2H5 or a protecting group; R5 is independently â€”H or a protecting group; R6 is independently â€”Sâ€”, â€”N(R5)â€”, â€”Oâ€” or â€”CH2â€”; R7 is independently linear alkyl having 1 to 4 carbon atoms optionally including one â€”CH&boxH;CHâ€”, â€”C&boxH;Câ€” or â€”CH2 â€”Oâ€”CH2â€” moiety, or R7 is cyclic alkyl having 3, 4 or 5 carbon atoms, wherein one of the linear alkyl carbon atoms is optionally substituted with a single â€”CH3, â€”CN, &boxH;O, â€”OH or protected hydroxyl, provided that the carbon atoms in any â€”CH&boxH;CHâ€” or â€”CH2â€”Oâ€”CH2â€” moiety are not substituted with &boxH;O, â€”OH or protected hydroxyl; R31 is the side chain of an amino acid; t is 1, 2, 3, or 4, but when R6 is â€”Oâ€”, â€”Sâ€”, or â€”N(R5)â€”, t is not 1; and v is independently 0, 1, or 2.