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Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.

ABSTRACT: The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides.

SUBMITTER: Clauvelin N

PROVIDER: S-EPMC4004093 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature

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Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.

Clauvelin Nicolas N Olson Wilma K WK Tobias Irwin I

Journal of chemical theory and computation 20120301 3

The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the ...[more]

PMID: 24791158

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Project description:Background: Optical microtraps at the focus of high numerical aperture (high-NA) imaging systems enable efficient collection, trapping, detection and manipulation of individual neutral atoms for quantum technology and studies of optical physics associated with super- and sub-radiant states. The recently developed "Maltese cross" geometry (MCG) atom trap uses four in-vacuum lenses to achieve four-directional high-NA optical coupling to single trapped atoms and small atomic arrays. This article presents the first extensive characterisation of atomic behaviour in a MCG atom trap. Methods: We employ a MCG system optimised for high coupling efficiency and characterise the resulting properties of the trap and trapped atoms. Using current best practices, we measure occupancy, loading rate, lifetime, temperature, fluorescence anti-bunching and trap frequencies. We also use the four-directional access to implement a new method to map the spatial distribution of collection efficiency from high-NA optics: we use the two on-trap-axis lenses to produce a 1D optical lattice, the sites of which are stochastically filled and emptied by the trap loading process. The two off-trap-axis lenses are used for imaging and single-mode collection. Correlations of single-mode and imaging fluorescence signals are then used to map the single-mode collection efficiency. Results: We observe trap characteristics comparable to what has been reported for single-atom traps with one- or two-lens optical systems. The collection efficiency distribution in the axial and transverse directions is directly observed to be in agreement with expected collection efficiency distribution from Gaussian beam optics. Conclusions: The multi-directional high-NA access provided by the Maltese cross geometry enables complex manipulations and measurements not possible in geometries with fewer directions of access, and can be achieved while preserving other trap characteristics such as lifetime, temperature, and trap size.

Dataset Information

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.

Publications

Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.

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