Seeing is understanding as well as believing

As the old saying goes, a picture is worth a thousand words. To help you have a better idea of what 3DNA/DSSR is about, we’ve collected the following pictures; they serve to demonstrate selected features from 3DNA/DSSR’s versatile functionality.

Cartoon-block schematic representations generated with DSSR and PyMOL

yeast phenylalanine tRNA (1ehz) with base blocks yeast phenylalanine tRNA (1ehz) with WC base-pair blocks
1msy: with the minor groove edge (black) of the C-G pair that closes the GUAA tetraloop facing the viewer 27-nt rRNA fragment with GUAA tetraloop (1msy) -- base blocks in outline

Schematic diagram of base-pair parameters

Schematic diagram of rigid body parameters

Influence of Slide and Roll on DNA helical conformation

Influence of Slide and Roll on DNA helical conformation

Roll-introduced DNA bending

Roll-introduced DNA bending

Global bending of DNA associated with selective B → A conformational transformation

Global bending of DNA associated with selective B → A conformational transformation

Canonical fiber models of A-, B-, C- and Z-DNA

Canonical fiber models of A-, B-, C- and Z-DNA

3DNA-generated view of a four-way DNA–RNA junction (1egk)

four-way DNA–RNA junction (1egk)

3DNA-detected pentaplets in the large ribosomal subunit (1jj2)

pentaplets in the large ribosomal subunit (1jj2)

3DNA enabled the discovery of the O2′(G)−O2P(U) H-bond which stabilizes the GpU dinucleotide platform

GpU dinucleotide platform stabilized by the O2′(G)−O2P(U) H-bond

Nucleic-acid-containing structures generated with w3DNA

Nucleic-acid-containing structures generated with w3DNA

Analysis of DNA with a B-Z junction (2acj, left) and detection of hydration patterns (right)

B/Z junction and hydration patterns

Schematics images auto-generated via blocview

2f4u 408d 9ant
complex of the bacterial ribosomal aminoacyl-tRNA site (A- site) with a designer antibiotic (2f4u) drug recognition of A-T and T-A base pairs in the B-DNA minor groove (408d) complex of DNA with the Antennapedia homeodomain (9ant)
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Comment

Interested in chromosome architecture and the role of dsDNA supercoiling as a mechanism for chromosome packaging.

I like to explore 3DNA as a tool for my work,

Jaime Conde · 2015-09-14 02:05 · #

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Commenting is closed for this article.

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