Mass Action at the Single-Molecule Level

Shon, Min Ju; Cohen, Adam E.

doi:10.1021/ja3062425

Cited by 61 publications

(80 citation statements)

References 34 publications

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“…For example, capturing bound molecular complexes from bulk solution into arrays of nanowells enables their stoichiometry and distribution of properties to be determined. Previous nanoreactor approaches using deformable PDMS lids are fundamentally limited in that the cavities exist in either open or closed states and cannot access a continuous range of confinement conditions (18). For example, CLINT can couple molecularly thin chambers to embedded structures, enabling reagent exchange so that continuous reactions can be performed within the well (e.g., local sequencing).…”

Section: Resultsmentioning

confidence: 99%

Convex lens-induced nanoscale templating

Berard

Michaud

Mahshid

et al. 2014

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

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We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.single-molecule manipulation | polymer confinement | genomic mapping | CLIC imaging | nanotechnology N anoconfinement-based manipulation is a powerful approach for controlling the conformation of single DNA molecules on chip. When single polymer chains are squeezed into environments confined at length scales below their diameter of gyration in free solution, the polymer equilibrium conformation will be molded by the surrounding nanoscale geometry. Nanochannel arrays can be used for massively parallel extension of DNA across an optical field, serving as the basis for a highthroughput optical mapping of genomes (1, 2). More varied manipulations can be performed based on the design of the surrounding nanotopology, such as using nanocavities embedded in a nanoslit to trap single DNA molecules (3). Nanoconfinementbased manipulation, compared with competing techniques for single-molecule manipulation such as tweezer technology and surface/hydrodynamic-based stretching, has three key advantages (4): (i) It is highly parallel, providing the high throughput essential for mapping gigabase-scale mammalian genomes (1); (ii) it can be efficiently integrated with microfluidics to rapidly cycle molecules through the channel arrays for upstream/downstream pre-and postprocessing of DNA; and (iii) it does not require applied flow or electric force to maintain the DNA extension.Nanoconfinement-based approaches have, however, a key difficulty inherent to the use of nanoscale dimensions: the need to bridge length scales differing by up to 5 orders...

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Section: Resultsmentioning

confidence: 99%

Convex lens-induced nanoscale templating

Berard

Michaud

Mahshid

et al. 2014

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

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“…This nanoconfi nement entropic effect on chemical equilibrium (NCECE) is universal in a sense that it stems only from the limited amount of molecules in a reaction mixture, resulting in a reduced number of mixed reactant-product microstates in the closed system [1,2]. The effect was predicted for the case of nucleotide dimerization within molecular cages [2] and verifi ed for DNA hybridization [3] that was studied experimentally before [4]. The NCECE is relevant to several advanced routes for the synthesis of encapsulated organic molecules, metallic or inorganic nanoclusters, and other nanoscale structures and applications.…”

Section: Introductionmentioning

confidence: 85%

Prediction of Enhanced Dimerization inside Dilute Alloy Nanoparticles

Polak¹,

Rubinovich²

2017

Int J Nanomater Nanotechnol Nanomed

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According to a unique nano-confi nement effect of entropic origin, predicted by us several years ago for the equilibrium state of chemical reactions, the equilibrium-constant and extent are greatly enhanced depending on the small number of molecules involved, and for many reactions also on the nano-space size. This work explored the validity of this effect in the case of elemental dimerization reactions within dilute alloy nanoparticles with separation tendency, Pd -Ir cuboctahedra in particular. Employing a simple model for the system energetics, computations based on the exact canonical partition-function reveal nano-confi nement induced Ir 2 dimer stabilization within Pd surface segregated nanoparticles, refl ected e.g., by up to ~ 60% increased dimerization extent and by doubling of the 1n K D vs. 1/T slope, as compared to the macroscopic thermodynamic limit. The dual role of the confi gurational entropy, namely mixing of Ir/Ir 2 vs. Pd/Ir is elucidated. Study based on more elaborate energetic models is desirable as the next step of this research.

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“…Bimolecular reactions [3,5,35] between two chemical species S 1 and S 2 to form a third species S 3 ,…”

Section: A Bimolecular Master Equationmentioning

confidence: 99%