Sanbonmatsu Team

The Sanbonmatsu team uses computational and experimental approaches to understand the mechanism of a diverse array of non-coding RNA systems, including ribosomes, riboswitches and long non-coding RNAs. Originally focusing on large-scale simulations of the ribosome, we have expanded into joint computational/experimental studies of riboswitches and purely experimental studies of long non-coding RNAs. The ribosome is one of the few large RNA systems that has been studied mechanistically. We are applying our knowledge gained from ribosome studies to long non-coding RNA systems.

Ribosomes

We are performing large-scale molecular simulations of the ribosome to uncover the energy landscape of tRNA selection and translocation. We are using explicit solvent, reduced-model and enhanced sampling methods.

Long non-coding RNA and epigenetics

LncRNAs (typically 1-10 kB) play key roles in development and disease and are often involved in epigenetic mechanism. We are using experimental biochemistry appoaches to probe the structure of long non-coding RNAs (lncRNAs).

Riboswitches

Riboswitches use competing secondary structures to control gene expression. We are using an integrated experiment/computation approach to understand the role of ligand binding, magnesium and the expression platform in controlling riboswitch conformation.

Recent Publications

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

Hawkes, E.J, Hennelly, S.P, Novikova, I.V, Irwin, J.A, Dean, C, and Sanbonmatsu, K.Y. (2016) COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures. Cell Reports, published September 20, 2016. doi:10.1016/j.celrep.2016.08.045. View PDF »

A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

Xue, Z, Hennelly, S.P, Doyle, B, Gulati, A.A, Novikova, I.V, Sanbonmatsu, K.Y, and Boyer, L.A. (2016) A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage. Molecular Cell, published September 8, 2016. doi:10.1016/j.molcel.2016.08.010. View article »

Sanbonmatsu Team

Welcome to the Sanbonmatsu Team

We use experiment and theory to study RNA mechanism.
Interested in a post-doc at a national lab? Let's video chat ASAP!

Supercomputers get faster each year.

We use the state-of-the-art Trinity machine (>900,000 cores) to simulate macromolecular complexes atom-for-atom.

Structural biology is being turned on its head.

Cryo electron microscopy is rapidly becoming the tool of choice. We leverage supercomputers to produce the end-result of this: atomistic models.

Junk DNA is not really junk.

Most of the genome codes for non-coding RNAs, but we don't know what they look like or how they work. We're figuring this out in the wet lab.

The world's most ancient molecular artifact.

The ribosome core is nearly identical in every life form studied to date. It's also a target for cancer and superbug therapeutics. We're investigating its inner workings.

Welcome to the Sanbonmatsu Team

We use experiment and theory to study RNA mechanism.
Interested in a post-doc at a national lab? Let's video chat ASAP!

Supercomputers get faster each year.

We use the state-of-the-art Trinity machine (>900,000 cores) to simulate macromolecular complexes atom-for-atom.

Structural biology is being turned on its head.

Cryo electron microscopy is rapidly becoming the tool of choice. We leverage supercomputers to produce the end-result of this: atomistic models.

Junk DNA is not really junk.

Most of the genome codes for non-coding RNAs, but we don't know what they look like or how they work. We're figuring this out in the wet lab.

The world's most ancient molecular artifact.

The ribosome core is nearly identical in every life form studied to date. It's also a target for cancer and superbug therapeutics. We're investigating its inner workings.

Ribosomes

Long non-coding RNA and epigenetics

Riboswitches

Recent Publications

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

GET IN TOUCH

Sanbonmatsu Team

Welcome to the Sanbonmatsu Team

We use experiment and theory to study RNA mechanism.Interested in a post-doc at a national lab? Let's video chat ASAP!

Supercomputers get faster each year.

We use the state-of-the-art Trinity machine (>900,000 cores) to simulate macromolecular complexes atom-for-atom.

Structural biology is being turned on its head.

Cryo electron microscopy is rapidly becoming the tool of choice. We leverage supercomputers to produce the end-result of this: atomistic models.

Junk DNA is not really junk.

Most of the genome codes for non-coding RNAs, but we don't know what they look like or how they work. We're figuring this out in the wet lab.

The world's most ancient molecular artifact.

The ribosome core is nearly identical in every life form studied to date. It's also a target for cancer and superbug therapeutics. We're investigating its inner workings.

Welcome to the Sanbonmatsu Team

We use experiment and theory to study RNA mechanism.Interested in a post-doc at a national lab? Let's video chat ASAP!

Supercomputers get faster each year.

We use the state-of-the-art Trinity machine (>900,000 cores) to simulate macromolecular complexes atom-for-atom.

Structural biology is being turned on its head.

Cryo electron microscopy is rapidly becoming the tool of choice. We leverage supercomputers to produce the end-result of this: atomistic models.

Junk DNA is not really junk.

Most of the genome codes for non-coding RNAs, but we don't know what they look like or how they work. We're figuring this out in the wet lab.

The world's most ancient molecular artifact.

The ribosome core is nearly identical in every life form studied to date. It's also a target for cancer and superbug therapeutics. We're investigating its inner workings.

Ribosomes

Long non-coding RNA and epigenetics

Riboswitches

Recent Publications

COOLAIR Antisense RNAs Form Evolutionarily Conserved Elaborate Secondary Structures

A G-Rich Motif in the LncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage

GET IN TOUCH

We use experiment and theory to study RNA mechanism.
Interested in a post-doc at a national lab? Let's video chat ASAP!

We use experiment and theory to study RNA mechanism.
Interested in a post-doc at a national lab? Let's video chat ASAP!