Encoding phenotype in bacteria with an alternative genetic set.

An unnatural base-pair architecture with base pairs 2.4 Å larger than the natural DNA-based genetic system (xDNA) is evaluated for its ability to function like DNA, encoding amino acids in the context of living cells. xDNA bases are structurally analogous to natural bases but homologated by the width of a benzene ring, increasing their sizes and resulting in a duplex that is wider than native B-DNA.

Sandwich probes: two simultaneous reactions for templated nucleic acid detection.

Fluorescence-quenched nucleic acid probes with reactive moieties at both the 5' and 3' ends are synthesized and tested for reaction with two adjacent nucleophile-containing DNAs. These probes improve signal to background over singly reactive probes and can discriminate single nucleotide polymorphisms in the target DNA or RNA.

Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore.