A primary hydrogen–deuterium isotope effect observed at the single-molecule level

Lu, Siran; Li, Wenwu; Rotem, Dvir; Mikhailova, Ellina; Bayley, Hagan

doi:10.1038/nchem.821

Cited by 71 publications

(72 citation statements)

References 35 publications

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“…With recent technological breakthroughs, such as stochastic sensing [2] and the construction of ionic networks [3–4], the control and understanding of ion-channel attributes at a single-molecule level takes on a new urgency. By being able to tailor molecular features through synthesis, and potentially being accessible in far larger quantity than membrane proteins, de novo channels promise to be useful entities for structure–activity studies as well as practical “ionic components” of more complex systems.…”

Section: Introductionmentioning

confidence: 99%

Planar-bilayer activities of linear oligoester bolaamphiphiles

Chui

Fyles²,

Luong³

2011

Beilstein J. Org. Chem.

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SummaryVoltage-clamp experiments of eight oligoester bolaamphiphiles in two subclasses are described. Syntheses of three new terephthalate-based compounds were achieved in three linear steps. Together with five previously described, related compounds, the ion transport activity was assessed by means of the voltage-clamp technique. All of the compounds show multiple types of conductance behavior in planar bilayers, a subset of which was exponentially voltage-dependent. The varied and irregular activities were summarized with the aid of a recently developed “activity-grid” method.

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Section: Introductionmentioning

confidence: 99%

Planar-bilayer activities of linear oligoester bolaamphiphiles

Chui

Fyles²,

Luong³

2011

Beilstein J. Org. Chem.

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“…Due to the limited size of the constriction of α-HL (∼1.4 nm) (16), the translocation of ssDNA through the channel significantly reduces the electrolyte ion flow, resulting in a deep current blockage, potentially revealing the identity of the nucleotide sequence (17)(18)(19). Recently, this method has also been explored to examine epigenetic markers (20), DNA oxidative damage products (21,22), secondary structures (23), enzymatic activity (24)(25)(26), and chemical reactions (27).…”

Section: Alpha-hemolysin | Crown Ethers | Single-molecule Detection |mentioning

confidence: 99%

Crown ether–electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules

Fleming

White

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

129

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DNA abasic (AP) sites are one of the most frequent lesions in the genome and have a high mutagenic potential if unrepaired. After selective attachment of 2-aminomethyl-18-crown-6 (18c6), individual AP lesions are detected during electrophoretic translocation through the bacterial protein ion channel α-hemolysin (α-HL) embedded in a lipid bilayer. Interactions between 18c6 and Na þ produce characteristic pulse-like current amplitude signatures that allow the identification of individual AP sites in single molecules of homopolymeric or heteropolymeric DNA sequences. The bulky 18c6-cation complexes also dramatically slow the DNA motion to more easily recordable levels. Further, the behaviors of the AP-18c6 adduct are different with respect to the directionalities of DNA entering the protein channel, and they can be precisely manipulated by altering the cation (Li þ , Na þ or K þ ) of the electrolyte. This method permits detection of multiple AP lesions per strand, which is unprecedented in other work. Additionally, insights into the thermodynamics and kinetics of 18c6-cation interactions at a singlemolecule level are provided by the nanopore measurement.alpha-hemolysin | crown ethers | single-molecule detection | DNA damage

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“…Single-molecule chemistry has attracted interest because it provides insights into fundamental chemical processes that cannot be observed at the ensemble scale (6)(7)(8). However, chemistry carried out within the αHL nanoreactor has so far been confined to the reactions of thiolates (i.e., deprotonated Cys side chains) (7)(8)(9)(10)(11)(12) and derivatives of the side chains of Cys residues (13,14). The incorporation of unnatural amino acids into the αHL pore would substantially advance single-molecule chemistry, through the incorporation of a large variety of individual side chains as well as multiple substitutions.…”

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confidence: 99%

Semisynthetic protein nanoreactor for single-molecule chemistry

Lee

Bayley

2015

Proc. Natl. Acad. Sci. U.S.A.

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The covalent chemistry of individual reactants bound within a protein pore can be monitored by observing the ionic current flow through the pore, which acts as a nanoreactor responding to bond-making and bond-breaking events. In the present work, we incorporated an unnatural amino acid into the α-hemolysin (αHL) pore by using solid-phase peptide synthesis to make the central segment of the polypeptide chain, which forms the transmembrane β-barrel of the assembled heptamer. The full-length αHL monomer was obtained by native chemical ligation of the central synthetic peptide to flanking recombinant polypeptides. αHL pores with one semisynthetic subunit were then used as nanoreactors for single-molecule chemistry. By introducing an amino acid with a terminal alkyne group, we were able to visualize click chemistry at the single-molecule level, which revealed a long-lived (4.5-s) reaction intermediate. Additional side chains might be introduced in a similar fashion, thereby greatly expanding the range of single-molecule covalent chemistry that can be investigated by the nanoreactor approach.semisynthesis | alpha-hemolysin | single-molecule chemistry | click chemistry

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A primary hydrogen–deuterium isotope effect observed at the single-molecule level

Cited by 71 publications

References 35 publications

Planar-bilayer activities of linear oligoester bolaamphiphiles

Planar-bilayer activities of linear oligoester bolaamphiphiles

Crown ether–electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules

Semisynthetic protein nanoreactor for single-molecule chemistry

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