title: Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy.
abstract: BACKGROUND
  DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences.
  
  
  RESULTS
  We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface.
  
  
  CONCLUSIONS
  We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.
authors.affiliation: Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|University of Trieste, Via Valerio 9, Trieste, Italy.
authors.forename: Maryse D Nkoua
authors.initials: MDN
authors.lastname: Ngavouka
authors.affiliation: Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|University of Trieste, Via Valerio 9, Trieste, Italy.
authors.forename: Pietro
authors.initials: P
authors.lastname: Capaldo
authors.affiliation: Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|University of Trieste, Via Valerio 9, Trieste, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Ambrosetti
authors.affiliation: Department of Medical and Biological Sciences, University of Udine, Udine, Italy.
authors.forename: Giacinto
authors.initials: G
authors.lastname: Scoles
authors.affiliation: Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.
authors.forename: Loredana
authors.initials: L
authors.lastname: Casalis
authors.affiliation: Elettra-Sincrotrone Trieste S.C.p.A., s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.|INSTM - ST Unit, s.s. 14 km 163.5 in Area Science Park, Basovizza, Trieste, Italy.
authors.forename: Pietro
authors.initials: P
authors.lastname: Parisse
keywords: DNA monolayers; atomic force microscopy; electrochemical impedance spectroscopy; hybridization; mismatches