Enzymatic modification of nucleic acids

A compound with structure of Formula (I):

• wherein
• L1 is a bond, —C(O)—, —C(O)O—, —C(O)NR2—, —O—, —S(O)n—, —S(O)NR2—, —C(O)NR2S(O)2—, substituted or unsubstituted alkylene, or substituted or unsubstituted heteroalkylene, substituted or unsub stituted cycloalkylene, substituted or unsub stituted heterocycloalkylene, substituted or unsubstituted aryl ene, or substituted or unsubstituted heteroaryl ene;
• R1 is substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl,
• R2 is independently hydrogen, halogen, —N3, —NO2, —CF3, —CCl3, —CBr3, —CI3, —CN, —OH, —NH2, —COOH, —CONH2, —NO2, —SH, —SO2Cl, —SO3H, —SO2Ph, —SO2NH2, —NHNH2, —ONH2, —OCH3, —NHCNHNH2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl, and n is 0, 1, or 2.

A compound of structural Formula II:

• or a salt thereof,
• wherein:
• L1 is a bond, substituted or unsubstituted alkylene or substituted or unsubstituted heteroalkylene, a detectable moiety, —CX1.13, —CHX1.12, —CH2X1.1, —CN, —SOn1R1A, —SOv1NR1BR1C, —NHNR1BR1C, —ONR1BR1C, —NHC(O)NHNR1BR1C, —NHC(O)NR1BR1C, —N(O)m1, —NR1BR1C, —C(O)R1D, —C(O)OR1D, —C(O)NR1BR1C, —OR1A, —NR1BSO2R1A, —NR1BC(O)R1D, —NR1BC(O)R1D, —NR1BOR1D, —OCX1.13, —OCHX1.12, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
• L2 is a bond, substituted or unsubstituted alkylene or substituted or unsubstituted heteroalkylene, a detectable moiety, —CX2.13, —CHX2.12, —CH2X2.1, —CN, —SOn1R2A,
• —SOv1NR2BR2C, —NHNR2BR2C, —ONR2BR2C, —NHC(O)NHNR2BR2C, —NHC(O)NR2BR2C, —N(O)m1, —NR2BR2D, —C(O)R2D, —C(O)OR2D, —C(O)NR2BR2C, —OR2A, —NR2BSO2R2A, —NR2BC(O)R2D, —NR2BC(O)OR2D, —NR2BOR2D, OCX2.13, —OCHX2.12, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene;
• n1 is an integer from 0 to 4;
• m1 and v1 are independently 1 or 2;
• R3 is a detectable moiety, a biomolecule, hydrogen, halogen, —CX3.13, —CHX3.12, —CH2X3.1, —CN, —SOn1R3A,
• —SOv1NR3BR3C, NHNR3BR3C, —ONR3BR3C, —NHC(O)NHNR3BR3C, —NHC(O)NR3BR3C, —N(O)m1, —NR3BR3C, —C(O)R3D, —C(O)OR3D, —C(O)NR3BR3C, OR3A, —NR3BSO2R3A, —NR3BC(O)R3D, —NR3BC(O)OR3D, —NR3BOR3D, —OCX3.13, —OCHX3.12, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
• R4 is hydrogen or a ribose, wherein the ribose is part of a modified or unmodified RNA molecule, and further wherein the ribose comprises a guanine;
• R1A, R1B, R1C, R1D, R2A, R2B, R2C, R3D, R3A, R3B, R3C and R3D are independently hydrogen, halogen, —CF3, —CCl3, —CBr3, —CI3, —OH, —NH2, —COOH, —CONH2, —NO2, —SH, —SO3H, —SO4H, —SO2NH2, —NHNH2, —NHC(O)NHNH2, —NHC(O)NH2, —NHSO2H, —NHC(O)H, —NHC(O)—OH, —NHOH, —OCF3, —OCCl3, —OCBr3, —OCI3, —OCHF2, —OCHCl2, —OCHBr2, —OCHI2, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
• R1B, R1C, R2B, R2C, R3B and R1C substituents bonded to the same nitrogen atom may optionally be joined to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
• and
• X1.1, X2.1 and X3.1 are independently —Cl, —Br, —I or —F.