Single-molecule analysis of chirality in a multicomponent reaction network

Abstract

Single-molecule approaches to chemical reaction analysis can provide information that is not accessible by studying ensemble systems. Changes in the molecular structures of compounds tethered to the inner wall of a protein pore are known to affect the current carried through the pore by aqueous ions under a fixed applied potential. Here, we use this approach to study the substitution reactions of arsenic(III) compounds with thiols, stretching the limits of the protein pore technology to track the interconversion of seven reaction components in a network that comprises interconnected Walden cycles. Single-molecule pathway analysis of 'allowed' and 'forbidden' reactions reveals that sulfur-sulfur substitution occurs with stereochemical inversion at the arsenic centre. Hence, we demonstrate that the nanoreactor approach can be a valuable technique for the analysis of dynamic reaction systems of relevance to biology.

Nanopore Sequencing: From Imagination to Reality

“…1E), e.g., photodeprotection and photoisomerization, thiol-disulfide chemistry, polymer chain growth, organoarsenic chemistry, metal chelation, a kinetic isotope effect, and S-nitrosothiol chemistry. In recent work, a complex reaction network involving seven states was analyzed (13). Many analytes of physiological relevance are chemically reactive, ranging from chemical warfare agents to components of garlic and onion, and we have demonstrated detection based on covalent chemistry (14).…”

Semisynthetic protein nanoreactor for single-molecule chemistry

“…By contrast with WT 7 , the addition of Cu(I) to both compartments in the presence of 2 mM APB400 or APB700 (trans) eventually led to an irreversible partial blockade of the WT 6 SM 1 pore, suggesting that Cu(I) triggered a reaction between the substrate and the alkyne within the pore. 7 , and most of the SM polypeptide is undigested. Fragment a is generated after cleavage near the N terminus in the prepore form of SM 7 (∼32 kDa) (41).…”

“…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.…”

Recent advances of DNA sequencing via nanopore-based technologies

“…After nearly 20 years' rapid development, nanopore-based sensing technology has become one type of important method for detecting various analytes such as metal ions [1,2], organic small molecules [3,4], biomacromolecules including oligonucleotides [5], peptides [6], and so on [7,8]. Among all of those research efforts, DNA sequencing has drawn the most attention [9].…”