title: Flexibility of single-stranded DNA measured by single-molecule FRET.
abstract: The mechanical flexibility of ssDNA is crucial for understanding the biological machinery but its characterization has been difficult due to the lack of an experimental tool that measures the structure of ssDNA in the nanometer scale. Here, we demonstrate that single-molecule FRET can be used to probe the structures of a flexible ssDNA. We designed a dsDNA with various lengths of single-stranded overhang and determined the flexibility of the single-stranded segment by measuring the FRET value. We found that three of our ssDNAs with lengths shorter than the persistence length are indeed long enough to undergo folding. Since metal ions present in solution can affect the flexibility of DNA, we employed Na(+) and Mg(2+) at different concentrations. We found that there is no significant effect of charge screening by metal ion when the ssDNA is less than 9 bases in length but it becomes appreciable for longer ssDNAs.
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
authors.forename: Jooyoun
authors.initials: J
authors.lastname: Kang
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea.
authors.forename: Jiwon
authors.initials: J
authors.lastname: Jung
authors.affiliation: Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea; Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-747, Republic of Korea. Electronic address: seongkim@snu.ac.kr.
authors.forename: Seong Keun
authors.initials: SK
authors.lastname: Kim
mesh_terms: D001483:Base Sequence; D002232:Carbocyanines / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer; D007477:Ions / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D012964:Sodium / Q000737:chemistry
chemical_list: D002232:Carbocyanines; D004277:DNA, Single-Stranded; D007477:Ions; C089187:cyanine dye 3; D012964:Sodium; D008274:Magnesium
keywords: Alternating laser excitation (ALEX); FRET; Flexibility; Ion concentration; Overhang DNA; Single-molecule fluorescence resonance energy transfer (smFRET)