title: Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications.
abstract: The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.
authors.affiliation: Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
authors.forename: Nahid
authors.initials: N
authors.lastname: Farkhari
authors.affiliation: Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran; School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
authors.forename: Sara
authors.initials: S
authors.lastname: Abbasian
authors.affiliation: Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran; School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran. Electronic address: moshaii@modares.ac.ir.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Moshaii
authors.affiliation: Department of Nanobiotechnology, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
authors.forename: Maryam
authors.initials: M
authors.lastname: Nikkhah
mesh_terms: D000327:Adsorption; D001483:Base Sequence; D015374:Biosensing Techniques / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006046:Gold / Q000737:chemistry*; D053768:Metal Nanoparticles / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry; D012834:Silver / Q000737:chemistry*; D013059:Spectrum Analysis, Raman; D020349:Surface Plasmon Resonance; D013941:Thymine / Q000737:chemistry
chemical_list: D004277:DNA, Single-Stranded; D009841:Oligonucleotides; D012834:Silver; D006046:Gold; D004247:DNA; D013941:Thymine
keywords: Aggregation sensors; DNA bases; Gold nanoparticles; Localized surface plasmon resonance; Silver nanoparticles