title: Changes in Spectra and Conformation of Hairpin DNA-Stabilized Silver Nanoclusters Induced by Stem Sequence Perturbations.
abstract: It is well-known that even small perturbations of the DNA sequence can drastically and unpredictably disrupt or alter the fluorescence of DNA-stabilized silver nanoclusters (DNA-AgNCs). Understanding how the structure of DNA affects the nanocluster that it stabilizes is the key to rationalizing such effects. We approach this challenge by strategically modifying the stem sequence of a hairpin DNA that hosts a spectrally pure, red-emitting nanocluster. Most of our modifications (base composition, sequence orientation, and loop location) reduce AgNC fluorescence in purity and shift it in wavelength, but one modification (appending poly(thymidine) to the 3' end of the stem) is inert with respect to fluorescence. Microfluidic capillary electrophoresis reveals that all of the modifications induce conformational changes of the DNA and that the original, spectrally pure nanocluster exists in two structurally distinct conformations. Interestingly, appending five or more thymidines, despite having no effect on fluorescence, eliminates this structural degeneracy. To explain this result, we propose that the original spectrally pure cluster is stabilized by a pair of hairpins whose stems can arrange in either a cis or trans orientation. Finally, we quantify the extent to which thymidine appendages of different lengths can be used to fine-tune the electrophoretic mobility of DNA-AgNC.
authors.affiliation: Department of Mechanical Engineering, ‡Department of Physics, and §Program in Biomolecular Science & Engineering, University of California , Santa Barbara 93106, United States.
authors.forename: Jackson Travis
authors.initials: JT
authors.lastname: Del Bonis-O'Donnell
authors.affiliation: Department of Mechanical Engineering, ‡Department of Physics, and §Program in Biomolecular Science & Engineering, University of California , Santa Barbara 93106, United States.
authors.forename: Sumita
authors.initials: S
authors.lastname: Pennathur
authors.affiliation: Department of Mechanical Engineering, ‡Department of Physics, and §Program in Biomolecular Science & Engineering, University of California , Santa Barbara 93106, United States.
authors.forename: Deborah K
authors.initials: DK
authors.lastname: Fygenson
mesh_terms: D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D019075:Electrophoresis, Capillary; D005453:Fluorescence; D055029:Inverted Repeat Sequences; D056656:Lab-On-A-Chip Devices; D053768:Metal Nanoparticles / Q000737:chemistry*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011071:Poly T / Q000737:chemistry*; D012834:Silver / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D011071:Poly T; D012834:Silver; D004247:DNA