This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Sandbox1257
From Proteopedia
This sandbox is in use until June 1, 2009 for UMass Chemistry 490a. Others please do not edit this page. Thanks!
DNA:RNA interactions
| |||||||
| 124d, 1 NMR models () | |||||||
|---|---|---|---|---|---|---|---|
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The shown representation is a DNA:RAN hybrid duplex. This is the
in orange and this is the in green. Notice that all hydrogen bonds between the bases are . We can choose to see the base pairs, which show very neatly. First, the G-C pairs: are in blue and are in yellow. Similarly, we can see the in red and the in purple (note that the RNA has U nucleotides instead of T). Furthermore, we can also see the bonding with each other (never with themselves) for a more general view of the bases. In this generic RNA:DNA hybrid all hydrogen bonds between the bases are through the , as shown for the dG-C pair. If we choose to see the in the hybrid, as we'd expect, the whole complex shines: the backbone and the nucleotides are negatively charged.
