Conjugation reagents and methods using 1,2-cyclohexanediones

A composition comprising a peptide-polynucleotide conjugate, wherein a covalent linkage connecting a peptide and a polynucleotide of the peptide-polynucleotide conjugate comprises the following substructure (D):

• or a tautomer thereof, wherein:
• the dashed bond to Nuc represents where substructure (D) is covalently linked to the polynucleotide;
• the dashed bond to Pep represents where substructure (D) is covalently linked to the peptide;
• R4 is an optional substituent on the cyclopentyl ring, and
• each R4 is independently selected from the group consisting of C1-2 alkyl, C1-2 alkoxy, C1-2 haloalkyl, —COOR, SO3R, halo, hydroxy, and C(O)NR2;
• each R is independently H or C1-4 alkyl optionally substituted with up to three groups selected from the group consisting of halo, OH, C1-2 alkyl, C1-2 haloalkyl, C1-2 alkoxy, and carbonyl (oxo), or two R groups on one N are forming a 4-8 membered ring optionally containing an additional one or two heteroatoms selected from N, O and S as ring members and optionally substituted with one or two groups selected from halo, C1-2 alkyl, C1-2 haloalkyl, C1-2 alkoxy, hydroxy, and carbonyl (oxo);
• and n is 0, 1, 2 or 3.