title: Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy.
abstract: We introduce herein the use of atomic-force electrochemical microscopy (AFM-SECM) to simultaneously probe locally the conformation and motional dynamics of nanometer-sized single-stranded (ss) and double-stranded (ds) DNA oligonucleotides end-tethered to electrode surfaces. The ss-DNA system studied here consists of a low-density monolayer of (dT)20 oligonucleotides, 5'-thiol end-tethered onto a flat gold surface via a C6 alkyl linker and bearing at their free 3'-end a redox ferrocene label. It is shown that, as a result of the flexibility of the relatively long C6 linker, hinge motion, rather than elastic deformation of the DNA chain, is the major component of the dynamics of both the (dT)20 strand and its post-hybridized (dT-dA)20 duplex. DNA chain elasticity is nevertheless sufficiently contributing to the overall dynamics to result in approximately 4 times slower dynamics for (dT-dA)20 than for (dT)20. Taking advantage of this dissimilar dynamical behavior of ss- and ds-DNA, it is demonstrated that hybridization can be easily locally detected at the scale of approximately 200 molecules by AFM-SECM.
authors.affiliation: Laboratoire d'Electrochimie Moléculaire, Unité Mixte de Recherche Université-CNRS No. 7591, Université de Paris 7--Denis Diderot, Paris Cedex 05, France.
authors.forename: Kang
authors.initials: K
authors.lastname: Wang
authors.forename: Cédric
authors.initials: C
authors.lastname: Goyer
authors.forename: Agnès
authors.initials: A
authors.lastname: Anne
authors.forename: Christophe
authors.initials: C
authors.lastname: Demaille
mesh_terms: D004247:DNA / Q000737:chemistry*; D004563:Electrochemistry; D004566:Electrodes; D005296:Ferrous Compounds / Q000138:chemical synthesis / Q000737:chemistry*; D006046:Gold / Q000737:chemistry; D018625:Microscopy, Atomic Force / Q000379:methods; D015394:Molecular Structure; D009038:Motion; D009841:Oligonucleotides / Q000737:chemistry*; D012680:Sensitivity and Specificity; D013499:Surface Properties
chemical_list: D005296:Ferrous Compounds; D009841:Oligonucleotides; D006046:Gold; D004247:DNA