Movies

Movie 16. Duke University Press release on our 2018 Nature paper studying the roles of Watson-Crick-like mismatches in genetic mutations. See Press Release and Nature Paper


Movie 15. The N1-methyl adenine is a post-transcriptional modification in RNA and form of alkylation damage in both DNA and RNA. The modification (residue in grey) induces melting of A-form RNA duplexes whereas it is stably accommodated as Hoogsteen base pairs in B-form DNA. More information.

Movie 14. An RNA Excited State Folding Intermediate
This movie shows base reshuffling leading to a short-lived RNA excited state as an intermediate during P5abc tertiary folding. More information.

 

Movie 13. Duke University Press release featuring graduate student Isaac Kimsey and his 2015 Nature paper on rare tautomeric and anionic bases and their potential role in genetic mutation. See Press Release and Nature Paper

Movie 12. The movie shows transitions between a ground state structure for the ribosomal A-site and a higher energy transient conformation that has a population of ~3% and lifetime of 250 microseconds. The transient conformations are visualized by combining NMR relaxation dispersion experiments with mutagenesis and computer modeling. More information.

Movie 11. The movie shows transitions between a ground state structure for the HIV-1 TAR RNA apical loop and a higher energy transient conformation that has a population of ~13% and lifetime of ~45 microseconds.
The transient conformation is visualized by combining NMR relaxation dispersion experiments with mutagenesis and computer modeling. More information.

Movie 10. HIV-1 TAR ES-2

Lee J., Dethoff E.A., Al-Hashimi H.M.  (2014).  “Invisible RNA State Dynamically Couples Distant Motifs.”  PNAS 111(26):9485-90.

Movie 9. The movie shows transitions between a ground state structure for the HIV-1 stem-loop 1 and two higher energy transient conformations that have populations of ~2% and 9% and lifetimes of 200 and 120 microseconds.
The transient conformations are visualized by combining NMR relaxation dispersion experiments with mutagenesis and computer modeling. More information.

Movie 8. The movie shows a simulated transition from a Watson-Crick to a Hoogsteen G•C base pair (orange) inside a B-DNA duplex generated by the CPR path-sampling method, which features an anti-to-syn rotation of the guanine base around the glycosidic bond as seen above for A•T . Here, the final syn-G conformation does not reach optimal Hoogsteen geometry competent for hydrogen bonding with its C partner due to the lack of C N3 protonation in the simulation, but rather forms an intra-residue hydrogen bond between its amino proton and a backbone oxygen. C1’ and C8 carbon sites that exhibit chemical exchange are shown in green. More information.

Movie 7. The movie shows a simulated transition from a Watson-Crick to a Hoogsteen A•T base pair (orange) inside a B-DNA duplex generated by the CPR path-sampling method, which features an anti-to-syn rotation of the adenine base around the glycosidic bond without significant base opening, and expansion of the B-form helix without loss of base pairing to accommodated the adenine rearrangement into a Hoogsteen geometry with two hydrogen bonds. C1’ and C8 carbon sites that exhibit chemical exchange are shown in green. More information.

Movie 6. This movie is derived from the contact model criteria determined for RNA topology and shows in three dimensions how two helical portions of an RNA molecule bend and twist in a highly concerted manner. The specific RNA molecule shown here is based on a generalized two-bulge RNA motif adjacent to two A-form helices. More information.

Movie 5. This all-atom structural ensemble of HIV-1 TAR is constructed by combining domain-elongated NMR RDC data with molecular dynamics simulations. The movie is constructed by ordering conformers according to ascending inter-helical bend angle. More information.

Movie 4. This all-atom structural ensemble of HIV-2 TAR is constructed by combining domain-elongated NMR RDC data with molecular dynamics simulations. The movie is constructed by ordering conformers according to ascending inter-helical bend angle. More information.

Movie 3.This movie illustrates the spatial resolution with which complex rigid-body motions can be spatially reconstructed using multi-alignment RDCs and a new formalism for interpreting RDCs in terms of continuous motional paths. Shown is an approximate reconstruction (in blue) of a complex inter-helix motional trajectory derived form a 65 ns MD trajectory in (grey) using five independent sets of theoretical RDCs. More information.

Movie 2. This movie is derived based on domain-elongated NMR RDC data only and shows in three dimensions how two helical portions of an RNA molecule bend and twist in a highly concerted manner. The specific RNA molecule shown here, known as TAR, is critical for replication of HIV, making it a key target for anti-HIV drugs. More information.

Movie 1. This movie is derived based on domain-elongated NMR RDC data only shows in gray the various conformations the TAR RNA takes when bound to different small molecules molecules, including ligands designed to combat HIV. The moving green image shows how the RNA molecule bends and twists on its own in the unbound state. The movie shows how the RNA molecule passes through various critical conformations in the process of bending and twisting. More information.