title: Molecularly resolved label-free sensing of single nucleobase mismatches by interfacial LNA probes.
abstract: So far, there has been no report on molecularly resolved discrimination of single nucleobase mismatches using surface-confined single stranded locked nucleic acid (ssLNA) probes. Herein, it is exemplified using a label-independent force-sensing approach that an optimal coverage of 12-mer ssLNA sensor probes formed onto gold(111) surface allows recognition of ssDNA targets with twice stronger force sensitivity than 12-mer ssDNA sensor probes. The force distributions are reproducible and the molecule-by-molecule force measurements are largely in agreement with ensemble on-surface melting temperature data. Importantly, the molecularly resolved detection is responsive to the presence of single nucleobase mismatches in target sequences. Since the labelling steps can be eliminated from protocol, and each force-based detection event occurs within milliseconds' time scale, the force-sensing assay is potentially capable of rapid detection. The LNA probe performance is indicative of versatility in terms of substrate choice - be it gold (for basic research and array-based applications) or silicon (for 'lab-on-a-chip' type devices). The nucleic acid microarray technologies could therefore be generally benefited by adopting the LNA films, in place of DNA. Since LNA is nuclease-resistant, unlike DNA, and the LNA-based assay is sensitive to single nucleobase mismatches, the possibilities for label-free in vitro rapid diagnostics based on the LNA probes may be explored.
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India.
authors.forename: Sourav
authors.initials: S
authors.lastname: Mishra
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India.
authors.forename: Hiya
authors.initials: H
authors.lastname: Lahiri
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India.
authors.forename: Siddhartha
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India bcrm@iacs.res.in.
authors.forename: Rupa
authors.initials: R
authors.lastname: Mukhopadhyay
mesh_terms: D020137:Base Pair Mismatch; D015374:Biosensing Techniques; D002412:Cations / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D015345:Oligonucleotide Probes / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D012965:Sodium Chloride / Q000737:chemistry
chemical_list: D002412:Cations; D004277:DNA, Single-Stranded; D015345:Oligonucleotide Probes; D009841:Oligonucleotides; C477371:locked nucleic acid; D012965:Sodium Chloride; D004247:DNA