Reactivity-dependent PCR: direct, solution-phase in vitro selection for bond formation

Abstract

In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and DNA-encoded small molecules. Such selections have been widely used to evolve RNA and DNA catalysts and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. While effective, current strategies for selections of bond-forming and bond-cleaving reactivity are generally indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and solid-phase manipulations. In this work we report the successful development and validation of reactivity-dependent PCR (RDPCR), a new method that more directly links bond formation or bond cleavage with the amplification of desired sequences and that obviates the need for solid-phase capture, washing, and elution steps. We show that RDPCR can be used to select for bond formation in the context of reaction discovery and for bond cleavage in the context of protease activity profiling.

Figure 1

Traditional approaches to in vitro selection.

Figure 2

Principles underlying reactivity-dependent PCR (RDPCR). Conditions in (a): 10 nM DNA, 2 mM Mg²⁺, 100 mM NaCl.

Figure 3

Comparison of PCR efficiency of intramolecularly primed versus intermolecularly primed DNA templates. PCR conditions for PAGE samples: 19 fmol of 8 or 19 fmol of 4a+5 in 30 μL, 25 cycles.

Figure 4

Non-natural hairpin linkers support self-priming PCR. R = (CH₂)₆OH.

Figure 5

Selectivity of RDPCR in a library-format mock selection. PCR conditions: 19 fmol of 12 and 13 in 60 μL, 25−35 cycles.

Figure 6

RDPCR-based DNA-encoded reaction discovery selection. PCR conditions for PAGE samples: 1 fmol of 9 in 20 μL, 23 cycles.

Figure 7

RDPCR-based protease-mediated peptide cleavage selection. PCR conditions for PAGE samples: 19 fmol of DNA in 30 μL, 23 cycles (lanes 1−5) or 25 cycles (lanes 6−9). D = DMT-MM; E = EDC + sNHS.