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Lapham, Jon; Rife, Jason P.; Moore, Peter B.; Crothers, Donald M.

doi:10.1023/a:1018310702909

Cited by 117 publications

(75 citation statements)

References 14 publications

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“…Still, the diffusion limit of the system used by Bazemore et al (48) can be crudely estimated to be on the order of 10 7 to 10 8 M Ϫ1 s Ϫ1 , depending on what kind of shape we assume for the diffusing particles (see Ref. 49 for different equations to calculate diffusion constants; we also assumed that only 1% of the collision is productive). Thus, it appears that the DNA synapsis reaction is fundamentally a slow binding reaction.…”

Section: Discussionmentioning

confidence: 99%

No Sliding during Homology Search by RecA Protein

Adzuma

1998

Journal of Biological Chemistry

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The RecA protein of Escherichia coli is a prototype of the RecA/Rad51 family of proteins that exist in virtually all the organisms. In a process called DNA synapsis, RecA first polymerizes onto a single-stranded DNA (ssDNA) molecule; the resulting RecA-ssDNA complex then searches for and binds to a double-stranded DNA (dsDNA) molecule containing the almost identical, or "homologous," sequence. The RecA-ssDNA complex thus can be envisioned as a sequence-specific binding entity. How does the complex search for its target buried within nonspecific sequences? One possible mechanism is the sliding mechanism, in which the complex first binds to a dsDNA molecule nonspecifically and then linearly diffuses, or slides, along the dsDNA. To understand the mechanism of homology search by RecA, this sliding model was tested. A plasmid containing four homologous targets in tandem was constructed and used as the dsDNA substrate in the synapsis reaction. If the sliding is the predominant search mode, the two outermost targets should act as more efficient targets than the inner targets. No such positional preference was observed, indicating that a long range sliding of the RecA-ssDNA complex does not occur. These and other available data can be adequately explained by a simple three-dimensional random collision mechanism.

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Section: Discussionmentioning

confidence: 99%

No Sliding during Homology Search by RecA Protein

Adzuma

1998

Journal of Biological Chemistry

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“…At the high concentrations required for biophysical studies, RNA has the potential to form dimeric structures. The presence of the stem-loop structure was unambiguously established from the very favorable linewidth and relaxation properties of the NMR resonances and from diffusion measurements that directly monitor the molecular mass of the sample (27). The RNA concentrations for the UV melting experiments were 1-2 M. They were 0.8-1.5 mM for the NMR experiments.…”

Section: Methodsmentioning

confidence: 99%

Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17

Varani

Hasegawa

Spillantini

et al. 1999

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

232

195

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Coding region and intronic mutations in the tau gene cause frontotemporal dementia and parkinsonism linked to chromosome 17. Intronic mutations and some missense mutations increase splicing in of exon 10, leading to an increased ratio of four-repeat to three-repeat tau isoforms. Secondary structure predictions have led to the proposal that intronic mutations and one missense mutation destabilize a putative RNA stem-loop structure located close to the splicedonor site of the intron after exon 10. We have determined the three-dimensional structure of this tau exon 10 splicing regulatory element RNA by NMR spectroscopy. We show that it forms a stable, folded stem-loop structure whose thermodynamic stability is reduced by frontotemporal dementia and parkinsonism linked to chromosome 17 mutations and increased by compensatory mutations. By exon trapping, the reduction in thermodynamic stability is correlated with increased splicing in of exon 10.

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“…where λ = D(∆-δ/3), g(λ) is the diffusion dimension, G(q 2 ) is the PGSE based decay function and the exponential term is the right hand side of Equation (6). The inverse Laplace transform of G(q 2 ) results in g(λ), the "spectrum" of diffusion constants.…”

Section: Uses In Counterfeit Medicationmentioning

confidence: 99%

“…The applications of these measurements include the determination of the aggregation state of proteins [1][2][3], the calculations of self-association constants of peptides [4], proteins, [5] and DNA [6], the degree of ligand binding to protein substrates [7], the quantification of protein hydration [8,9] and the characterization of protein folding [10]. Self-diffusion coefficient measurements are also becoming an integral part of high throughput drug discovery in pharmaceutical research [11].…”

Section: Introductionmentioning

confidence: 99%

NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications

Heisel¹,

Goto²,

Krishnan³

2012

AJAC

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Nuclear magnetic resonance (NMR) spectroscopy is an excellent analytical tool for precise structural characterization of organic and bio-molecules. Though NMR is often used to characterize a single compound in solution, emerging experimental methods using pulsed-field-gradients (PFGs) allow structural dynamic characterization of several compounds, simultaneously in the same solution. NMR as a chromatography tool is often an overlooked application by analytical chemists. Therefore, in this article we introduce the concept of NMR based diffusion measurements, basic operational methods and novel applications. We expect this article to increase the overall use and appreciation of NMR-based diffusion measurements in general and in particular, in analytical chemistry applications.

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Untitled

Cited by 117 publications

References 14 publications

No Sliding during Homology Search by RecA Protein

No Sliding during Homology Search by RecA Protein

Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17

NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications

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