Patent ID: 7511125

Claim:
An oligonucleotide having the formula: wherein: D is hydroxyl, protected hydroxyl, an oligonucleotide coupling group or a solid support; D 1 is an oligonucleotide coupling group, hydroxyl, protected hydroxyl or a solid support, provided that D and D 1 are not both an oligonucleotide coupling group and they are not both a solid support; each R 4 is, independently, a phosphodiester linkage or a phosphodiester substitute linkage; n is an integer from 0 to 98; 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: wherein R 34 is independently â€”Oâ€”, â€”Sâ€” or â€”N(CH 3 )â€”; R 2 is â€”R 6 â€”(CH 2 ) t N(R 5 )C(NR 5 )N(R 3 ) 2 , â€”R 6 â€”CH 2 â€”CHR 31 â€”N(R 3 ) 2 , â€”R 6 â€”(R 7 ) v â€”N(R 3 ) 2 , â€”R 6 â€”(CH 2 ) t â€”N(R 3 ) 2 , or â€”(CH 2 ) 1-2 â€”O(CH 2 ) t â€”N(R 3 ) 2 ; R 3 is â€”H, â€”CH 3 , â€”C 2 H 5 or a protecting group; R 5 is independently â€”H or a protecting group; R 6 is independently â€”Sâ€”, â€”NR 5 , â€”Oâ€” or â€”CH 2 â€”; R 7 is independently linear alkyl having 1 to 4 carbon atoms optionally including one â€”CHâ•CHâ€”, â€”Câ•Câ€” or â€”CH 2 â€”Oâ€”CH 2 â€” moiety, or R 7 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€”CH 3 , â€”CN, â•O, â€”OH or protected hydroxyl, provided that the carbon atoms in any â€”CHâ•CHâ€” or â€”CH 2 â€”Oâ€”CH 2 â€” moiety are not substituted with â•O, â€”OH or protected hydroxyl; R 31 is the side chain of an amino acid; t is 1, 2, 3, or 4, but when R 6 is â€”Oâ€”, â€”Sâ€”, or â€”NR 5 â€”, t is not 1; and v is independently 0, 1, or 2.