Unlimited increase in the resolution of DNA ladders

The reactivity of dicoordinated Sn(0) compounds, stannylones, is probed using density functional theory (DFT)-based reactivity indices and compared with the reactivity of dicoordinated Sn(II) compounds, stannylenes. For the former compounds, the influence of different types of electron-donating ligands, such as cyclic and acyclic carbenes, stannylenes and phosphines, on the reactivity of the central Sn atom is analyzed in detail. Sn(0) compounds are found to be relatively soft systems with a high nucleophilicity, and the plots of the Fukui function f(-) for an electrophilic attack consistently predict the highest reactivity on the Sn atom. Next, complexes of dicoordinated Sn compounds with different Lewis acids of variable hardness are computed. In a first part, the double-base character of stannylones is demonstrated in interactions with the hardest Lewis acid H(+). Both the first and second proton affinities (PAs) are high and are well correlated with the atomic charge on the Sn atom, probing its local hardness. These observations are also in line with electrostatic potential plots that demonstrate that the tin atom in Sn(0) compounds bears a higher negative charge in comparison to Sn(II) compounds. Stannylones and stannylenes can be distinguished from each other by the partial charges at Sn and by various reactivity indices. It also becomes clear that there is a smooth transition between the two classes of compounds. We furthermore demonstrate both from DFT-based reactivity indices and from energy decomposition analysis, combined with natural orbitals for chemical valence (EDA-NOCV), that the monocomplexed stannylones are still nucleophilic and as reactive towards a second Lewis acid as towards the first one. The dominating interaction is a strong σ-type interaction from the Sn atom towards the Lewis acid. The interaction energy is higher for complexes with the cation Ag(+) than with the non-charged electrophiles BH(3), BF(3), and AlCl(3).

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“…Alternatively, it could allow the user to separate the two particles using a smaller size system. This is the virtual gel concept 19.…”

Section: Adding Randomness To Fige‐like Pulse Sequencesmentioning

confidence: 99%

Reactivity of Dicoordinated Stannylones (Sn⁰) versus Stannylenes (Sn^II): An Investigation Using DFT‐Based Reactivity Indices

et al. 2013

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“…This analysis yields a characteristic timescale of 0.1 ms, an order of magnitude smaller than the period of the applied electric field. Our method is also distinct form zero‐integrated field approaches where the electric field strength and duration are simultaneously varied but the period is not tuned to match a system timescale . It is worthwhile to point out that there is a rich history of exploration of forward/reverse electric field actuation mechanisms to enhance size‐dependent electrophoretic transport and trapping.…”

Section: Resultsmentioning

confidence: 99%

Noise‐enhanced gel electrophoresis

Shi

Ugaz

2014

Electrophoresis

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Macromolecules confined within a nanoporous matrix experience entropic trapping when their dimensions approach the average pore size, leading to emergence of anomalous transport behavior that can be beneficial in separation applications. But the ability to exploit these effects in practical settings (e.g., electrophoretic separation of DNA) has been hindered by additional dispersion introduced as a consequence of the uncorrelated process by which the embedded macromolecules discretely hop from pore to pore. Here, we show how both the source and solution to these difficulties are intimately linked to the inherent dynamics of the underlying activated transport mechanism. By modulating the applied electric field at a frequency tuned to the characteristic activation timescale, a resonance condition can be established that synergistically combines accelerated mobility and reduced diffusion. This resonance effect can be precisely manipulated by adjusting the magnitude and period of the driving electric field, enabling enhanced separation performance and bi-directional transport of different-sized species to be achieved. Notably, these phenomena are readily accessible in ordinary hydrogels (as opposed to idealized nanomachined topologies) suggesting broad potential to apply them in a host of useful settings.

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“…FIGE methods are attractive because the electric field remains uniform throughout the gel minimizing the distortion of the shape and spacing of the separated bands, and they are also relatively straightforward to adapt for use in capillary‐based formats. A caveat, however, is that electrophoretic mobility may exhibit a non‐monotonic dependence on fragment length (or even mobility inversions) depending on details associated with the pulsed field profile and experiment conditions 15–18 (these anomalous effects can also be harnessed to provide enhanced separation performance under specific conditions within a particular range of fragment sizes 19–22).…”

Section: Comparison Between Size Dependence Of Dna Mobility Observed mentioning

confidence: 99%

Investigating DNA migration in pulsed fields using a miniaturized FIGE system

Chen

Ugaz

2008

Electrophoresis

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Pulsed field gel electrophoresis (PFGE) is a well-established technique for fractionation of DNA fragments ranging from kilobases to megabases in length. But many of these separations require an undesirable combination of long experiment times (often approaching tens of hours) and application of high voltages (often approaching tens of kV). Here we present a simple miniaturized field inversion gel electrophoresis (FIGE) apparatus capable of separating DNA fragments up to 32.5 kb in length within 3 hours using a modest applied potential of 20 V. The device is small enough to be imaged under a fluorescence microscope, permitting the migrating DNA bands to be observed during the course of the separation run. We use this capability to investigate how separation performance is affected by parameters including the ratio of forward and backward voltage, pulse time, and temperature. We also characterize the dependence of DNA mobility on fragment size N, and observe a scaling in the vicinity of N −0.5 over the size range investigated. The high speed, low power consumption, and simple design of this system may help enable future studies of DNA migration in PFGE to be performed quickly and inexpensively.Keywords pulsed field gel electrophoresis; field inversion gel electrophoresis; DNA As DNA fragment lengths approach tens of kilobases, a point is reached where individual molecules become much larger than the average pore size of the gel matrix. In order to sustain electrophoretic migration in this regime, the DNA molecules must adopt extended conformations preferentially aligned in the electric field direction. But this mode of migration is accompanied by a drastic reduction (and ultimately saturation) in the size dependence of electrophoretic mobility, making separation of long DNA fragments under continuous electric fields extremely challenging if not impossible. One way to overcome these limitations involves introducing a dynamic reorientation process by periodically changing the direction and magnitude of the applied electric field. When the electric field direction is switched, smaller fragments are able to reorient more quickly than larger molecules and thus migrate faster. The size dependent nature of this reorientation process restores the ability to distinguish different sized fragments based on their electrophoretic mobility. These pulsed field gel electrophoresis (PFGE) techniques have greatly extended the range of DNA fragment sizes that can be separated, even up to tens of Mb [1,2]. PFGE methods are important in a variety of applications including analysis of microbial genomes [3][4][5] [7][8][9][10][11]. But despite the instrumental role of PFGE techniques in broadening the range of DNA fragment sizes that can be effectively separated, some important drawbacks remain. First, PFGE can be extremely time consuming, with run times generally ranging in the tens of hours. A major reason for this is that the extent to which the electric field can be increased to drive faster DNA migration is limited by the ...

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Unlimited increase in the resolution of DNA ladders

Cited by 15 publications

References 14 publications

Reactivity of Dicoordinated Stannylones (Sn⁰) versus Stannylenes (Sn^II): An Investigation Using DFT‐Based Reactivity Indices

Reactivity of Dicoordinated Stannylones (Sn⁰) versus Stannylenes (Sn^II): An Investigation Using DFT‐Based Reactivity Indices

Noise‐enhanced gel electrophoresis

Investigating DNA migration in pulsed fields using a miniaturized FIGE system

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Unlimited increase in the resolution of DNA ladders

Cited by 15 publications

References 14 publications

Reactivity of Dicoordinated Stannylones (Sn0) versus Stannylenes (SnII): An Investigation Using DFT‐Based Reactivity Indices

Reactivity of Dicoordinated Stannylones (Sn0) versus Stannylenes (SnII): An Investigation Using DFT‐Based Reactivity Indices

Noise‐enhanced gel electrophoresis

Investigating DNA migration in pulsed fields using a miniaturized FIGE system

Contact Info

Product

Resources

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Reactivity of Dicoordinated Stannylones (Sn⁰) versus Stannylenes (Sn^II): An Investigation Using DFT‐Based Reactivity Indices

Reactivity of Dicoordinated Stannylones (Sn⁰) versus Stannylenes (Sn^II): An Investigation Using DFT‐Based Reactivity Indices