Professor of Chemistry and Biochemistry

Office: Urey Hall 5218
Phone: 858-534-6823
Email: ufmuller@ucsd.edu
Web: https://ribozymes.ucsd.edu/

Group: View group members
Accepting Rotation Students: Yes

2022-25

NASA research award

2021-26

NASA research award

2020-22

Cystic Fibrosis Foundation

2019-22

NASA research award

2018-20

Gilbert Gene Therapy Initiative

2016-19

NASA research award

2013-16

NASA research award

2011-13

Hellman Fellow

2008-11

NSF research award

2004-05

NRSA fellowship from the NIH

2001-04

Postdoctoral award from the German Research Council (DFG)

WE ARE NOW RECRUITING GRADUATE STUDENTS!

The Muller lab is interested in catalytic RNA molecules (ribozymes), with two specific questions:

1 - During the emergence of life, how could catalytic RNAs have mediated self-replication and evolution?

At early stages of life, before the existence of a ribosome (the protein translation machinery), catalytic RNAs (ribozymes) likely catalyzed most, if not all reactions necessary for self-replication and evolution. Support for this idea comes from the findings that the ribosome is a catalytic RNA, that most cofactors are derived from nucleotides, and that lab-generated RNAs are able to catalyze many different chemical reactions. To test how such an early stage of life could have functioned, we are generating novel catalytic RNAs with a technique called in vitro selection.

We have identified ribozymes that can use the prebiotically plausible energy source 'cyclic trimetaphosphate' (cTmp) and generate GTP, one of the four nucleoside triphosphates (NTPs) that are required to polymerase RNA in every known life form. cTmp may have acted as the central energy source of early life forms. This selection was the first selection to directly select a trans-acting ribozyme in emulsion droplets - in fact 10^16 droplets.

In addition, we are selecting ribozymes in different environmental conditions to test what kind of conditions would have been most promising for an RNA world system to arise. For example, we found that ribozymes can not only use the abundant Mg2+ ions but also the less abundant but catalytiucally more potent lanthanide3+ ions. For example we selected ribozymes in the presence of short, prebiotically plausible peptides and found that the peptides alone may not have had a strong benefit for the ribozymes, but peptides coupled to (prebiotically plausible polyarmatic hydrocarbons such as naphtalene and flourene can strongly enhace ribozyme catalysis. By successively building a system of ribozymes that could form a self-replicating system, and by doing that in different chemical environments, we hope to unravel in the future how our distant ancestors - RNA world organisms - could have looked like and functioned.



2 - Can catalytic RNAs be used to treat genetic diseases by repairing the mutations on the RNA level?

Natural group I intron ribozymes are cis-splicing, which means that they remove themselves from the primary transcript in two transesterification reactions. These cis-splicing ribozymes can be transformed into trans-splicing ribozymes. In that new format, the ribozyme can be used to repair genetic mutations on the RNA level. We have re-engineered, and re-evolved the ribozyme to in vitro, and in bacterial cells for increased efficiency and specificity. The long-term goal is to develop a therapeutic ribozyme for mRNA editing, either to repair genetic mutations or to specifically kill cells that indicate a disease status.

Macromolecular Structure
Cellular Biochemistry
Bioorganic

In emulsio selection for a GTP synthase ribozyme. (A) Schematic of the selection system (B) DLS analysis of the emulsion (C) Kinetic Analysis of GTP synthesis..

Coupling of GTP synthesis with RNA polymerization in a minimal metabolic system,

The Muller lab. From left to right: Xu Han, Debolina Sarkar, Tommy Le, Josh Arriola, Uli Müller