title: Complementary and partially complementary DNA duplexes tethered to a functionalized substrate: a molecular dynamics approach to biosensing.
abstract: Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate influence and a series of cooperative events, including recognition, reorientation and reorganization of the bases, could induce the formation of stable duplexes having non-canonical arrangements. Major adjustment of the structures was observed when the mutated base was located in the end region of the chain close to the surface.
authors.affiliation: CNR-ICCOM, Istituto di Chimica dei Composti OrganoMetallici, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy. smonti@iccom.cnr.it
authors.forename: Susanna
authors.initials: S
authors.lastname: Monti
authors.forename: Ivo
authors.initials: I
authors.lastname: Cacelli
authors.forename: Alessandro
authors.initials: A
authors.lastname: Ferretti
authors.forename: Giacomo
authors.initials: G
authors.lastname: Prampolini
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Barone
mesh_terms: D015374:Biosensing Techniques; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012996:Solutions / Q000737:chemistry
chemical_list: D015342:DNA Probes; D012996:Solutions; D004247:DNA