The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models

Giovanni Pinamonti1, Fabian Paul2, Frank Noé1

  • 1Department for Mathematics and Computer Science, Freie Universität, Berlin, Germany.

Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.6K
Mechanical Ventilation I: Indication and Settings01:29

Mechanical Ventilation I: Indication and Settings

Mechanical ventilation is a life-saving technique for managing acute respiratory failure and other respiratory complications. The process involves using a machine known as a ventilator to supply oxygen to the lungs and assist in removing carbon dioxide. It serves as a bridge to long-term mechanical ventilation or a temporary measure until ventilatory support is discontinued. The ventilator can maintain this function for a prolonged period, providing critical support for patients until they can...
2.7K
The Nucleosome Core Particle02:10

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
14.1K
The Quantum-Mechanical Model of an Atom02:45

The Quantum-Mechanical Model of an Atom

Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing hydrogen spectra.
56.8K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
32.6K
Molecular Orbital Theory II03:51

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams
27.1K