title: Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix.
abstract: The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.
authors.affiliation: Nicholson and MONALISA (MOlecularNAnotechnology for LIfe Science Applications) Laboratories of the Department of Biology, Temple University, 1901 North 13th Street, Philadelphia, PA 19122, USA.
authors.forename: Shiv K
authors.initials: SK
authors.lastname: Redhu
authors.forename: Matteo
authors.initials: M
authors.lastname: Castronovo
authors.forename: Allen W
authors.initials: AW
authors.lastname: Nicholson
mesh_terms: D015374:Biosensing Techniques / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*; D018625:Microscopy, Atomic Force / Q000379:methods*; D054802:Molecular Imprinting / Q000379:methods*; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000648:ultrastructure*; D013499:Surface Properties
chemical_list: D012313:RNA; D004247:DNA