title: Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity.
abstract: Human telomeric DNA consists of tandem repeats of the sequence 5'-TTAGGG-3' that can fold into various G-quadruplexes, including the hybrid, basket, and propeller folds. In this report, we demonstrate use of the α-hemolysin ion channel to analyze these subtle topological changes at a nanometer scale by providing structure-dependent electrical signatures through DNA-protein interactions. Whereas the dimensions of hybrid and basket folds allowed them to enter the protein vestibule, the propeller fold exceeds the size of the latch region, producing only brief collisions. After attaching a 25-mer poly-2'-deoxyadenosine extension to these structures, unraveling kinetics also were evaluated. Both the locations where the unfolding processes occur and the molecular shapes of the G-quadruplexes play important roles in determining their unfolding profiles. These results provide insights into the application of α-hemolysin as a molecular sieve to differentiate nanostructures as well as the potential technical hurdles DNA secondary structures may present to nanopore technology.
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112.
authors.forename: Na
authors.initials: N
authors.lastname: An
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Fleming
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112.
authors.forename: Eric G
authors.initials: EG
authors.lastname: Middleton
authors.affiliation: Department of Chemistry, University of Utah, Salt Lake City, UT 84112 burrows@chem.utah.edu.
authors.forename: Cynthia J
authors.initials: CJ
authors.lastname: Burrows
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D054856:G-Quadruplexes; D006460:Hemolysin Proteins / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D020080:Tandem Repeat Sequences / Q000235:genetics; D016615:Telomere / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D006460:Hemolysin Proteins; D009841:Oligonucleotides; D011506:Proteins; D004247:DNA
keywords: single-molecule detection; α-hemolysin nanopore