Solution structure, mechanism of replication, and optimization of an unnatural base pair

Abstract

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge-on interactions, are replicated by means of a unique intercalative mechanism. Here, we report the synthesis and characterization of three novel derivatives of the nucleotide analogue dMMO2, which forms an unnatural base pair with the nucleotide analogue d5SICS. Replacing the para-methyl substituent of dMMO2 with an annulated furan ring (yielding dFMO) has a dramatically negative effect on replication, while replacing it with a methoxy (dDMO) or with a thiomethyl group (dTMO) improves replication in both steady-state assays and during PCR amplification. Thus, dTMO-d5SICS, and especially dDMO-d5SICS, represent significant progress toward the expansion of the genetic alphabet. To elucidate the structure-activity relationships governing unnatural base pair replication, we determined the solution structure of duplex DNA containing the parental dMMO2-d5SICS pair, and also used this structure to generate models of the derivative base pairs. The results strongly support the intercalative mechanism of replication, reveal a surprisingly high level of specificity that may be achieved by optimizing packing interactions, and should prove invaluable for the further optimization of the unnatural base pair.

Figure 1

Unnatural nucleotides used in current study. Only nucleobases are shown; sugars and phosphates have been omitted for clarity.

Figure 2

Intercalative model for unnatural base pair replication.^[9] The unnatural nucleobase in the template is shown in white and the natural or unnatural nucleobase of the incoming dNTP is shown in black.

Figure 3

a) Sequence of the duplex characterized by NMR and structure of d5SICS-dMMO2 with atoms labeled. b) Family of structures and c) average structure generated from the NMR data.

Figure 4

Structure of unnatural base pairs viewed along helix axis (left, with sugar hydrogens omitted for clarity) or from the major groove (right). a) The NMR structure of the dMMO2-d5SICS base pair, and b – d) the models generated from the parental base pair for dDMO-d5SICS, dTMO-d5SICS, and dFMO-d5SICS, respectively. A color version is provided in Supporting Information.