There are provided, inter alia, methods and reagents for labeling nucleic acids.

Provided herein are, inter alia, compositions and methods for modifying a DNA molecule. The methods include contacting a DNA molecule with a transglycosylase enzyme and a Pre-queuosinel (preQi) analog or derivative, wherein a guanine nucleobase within a hairpin structure in the DNA molecule is exchanged for the preQi analog or derivative.

Provided herein are, inter alia, methods and compositions for linking RNA stem loops. The methods include linking a first RNA stem loop and a second RNA stem loop by way of a preQ1 linking compound.

There are provided, inter alia, methods and reagents for labeling nucleic acids.

Provided herein are, inter alia, methods and compositions for linking RNA stem loops. The methods include linking a first RNA stem loop and a second RNA stem loop by way of a preQ1 linking compound.