A versatile photocleavable bifunctional linker for facile synthesis of substrate-DNA conjugates for the selection of nucleic acid catalysts

Covalent photocleavable attachment of small molecules or peptides to oligonucleotides is an integral strategic element in the selection of novel nucleic acid enzymes. Here, we report the synthesis of a multipurpose, photocleavable bifunctional linker (PCBL) suitable for nucleic acid selections and other biotechnology applications. PCBL contains a photocleavable O-nitrobenzyl group flanked on one side by an N-hydroxysuccinimidyl ester (reactive toward primary amines) and on the other side by a sulfhydryl. To demonstrate the utility of PCBL, the linker was used to couple an analog of the antibiotic chloramphenicol (Cam) to the 5' end of an amino-modified 8-mer DNA oligo. Coupling was confirmed by MALDI-TOF spectrophotometry. Decoupling was performed by irradiating the coupled species with near-UV light (approximately 360 nm), regenerating the original amino-modified oligo. Ligation of the Cam-PCBL-DNA conjugate to random-sequence RNA generated a diversity library appropriate for the selection of new ribozymes that catalyze reactions involving the tethered substrate. Coupling and decoupling of the Cam analog from the library was monitored on a trilayered organomercurial polyacrylamide gel. The coupling/decoupling strategy described here is readily generalized to many combinations of macromolecules and small molecules. For example, analogs of this small molecule-DNA conjugate can be generated as synthons for ligation to nucleic acid diversity libraries during each round of novel ribozyme selections, or they can be immobilized onto chips for addresssably reversible microarray analysis.