Modified oligonucleotides and methods for their synthesis

A compound of Formula (I)

• wherein
• Z is selected from —O−, —S−, —Se−, —N−RN, or —BH3−, wherein RN is H, C1-4alkyl, or a protecting group;
• X is selected from the 5′ end of a nucleoside, nucleoside analogue, oligonucleotide, or oligonucleotide analogue and Y is selected from the 3′ end of a nucleoside, nucleoside analogue, oligonucleotide, or oligonucleotide analogue;
• —H, —OH, —SH, NHRN, —O-PG, S-PG, wherein PG is a protecting group;
• a linker, a monophosphate or diphosphate, or a label or quencher;
• or
• Y is selected from the 3′ end of a nucleoside, nucleoside analogue, oligonucleotide, or oligonucleotide analogue and X is selected from the 5′ end of a nucleoside, nucleoside analogue, oligonucleotide, or oligonucleotide analogue, —H, —OH, —SH, NHRN, —O-PG, or S-PG, wherein PG is a protecting group;
• a linker, a monophosphate or diphosphate, or a label or quencher;
• R1 is selected from —NR1AR1B, —OR3, —SR3, —H, —S(O)H, —S(O)R3, —S(O)2H, —S(O)2R3, —S(O)2NH2, —S(O)2NHR3, —S(O)2NR32, —C1-10alkyl, —C2-10alkenyl, —C2-10alkynyl, —C6-10aryl, or —C5-10heteroaryl;
• R2 is selected from —H, —NR2AR2B, —OR3, —SR3,
• halogen, —CN, —S(O)H, —S(O)R3, —S(O)2H, —S(O)2R3, —S(O)2NH2, —S(O)2NHR3, —S(O)2NR32, —C1-10alkyl, C2-10alkenyl, C2-10alkynyl, —C6-10aryl, or —C5-10heteroaryl;
• wherein each R1A, R1B, R2A, and R2B is independently selected from
• —H, —C1-10alkyl, C2-10alkenyl, C2-10alkynyl, —C6-10aryl, or —C5-10heteroaryl;
• optionally wherein R1A and R2A together form an alkylene or heteroalkylene chain of 2-4 atoms in length;
• optionally wherein R1A and R1B, together with the atom to which they are bound, form a 5-8 membered heterocycle;
• optionally wherein R2A and R2B, together with the atom to which they are bound, form a 5-8 membered heterocycle;
• R3 is selected from —C1-10alkyl, —C2-10alkenyl, —C2-10alkynyl, —C6-10aryl, or —C5-10heteroaryl;
• wherein each alkyl, aryl, heteroaryl, alkylene or heteroalkylene is optionally substituted.