Brent Znosko
Saint Louis University, MO·Biochemistry
RNA molecules fold into shapes that determine what they do, but for most known RNA sequences the shape has never been measured. Lab methods such as NMR (nuclear magnetic resonance) and X-ray crystallography can solve 3D structures, but they are slow and labor-intensive.
- Fields
Biochemistry
Chemistry
Biophysics
- Topics
RNA secondary structure
RNA tertiary structure
RNA structure prediction
- Grants
- 1 known grant, through Jun 2028
What they work on
- Derive improved nearest neighbor parameters, energy values that prediction programs use, from optical melting experiments on RNA secondary structure motifs to better predict RNA stability and folding from sequence.
- Identify recurring structural patterns of secondary structure motifs in previously solved RNA 3D structures to improve prediction of RNA tertiary structure.
- Develop online tools that annotate and compare RNA 3D structures, supporting in-depth analysis of the structural features of common motifs.
More about the research
Millions of RNA sequences are now available. Computer programs can predict how an RNA folds from its sequence. Those predictions are limited, however, by missing experimental data for irregular regions, by the inability to handle modified nucleotides, and by little knowledge of how conditions inside cells affect stability. The lab's long-term goal is to improve prediction of RNA secondary structure (the 2D pattern of base pairs) and tertiary structure (the 3D shape) from sequence.
Why it matters
Accurate RNA structure prediction helps any researcher who studies how RNA works or how it interacts with other molecules. It especially matters to those designing drugs that target RNA or using RNA itself as a therapy. Better predictions could speed research on human, bacterial and viral RNAs related to the causes, diagnosis and treatment of disease.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Yousuf Khan
Stanford University, CA·Biophysics
Assemble RNAmass, a large RNA sequence database including viral and non-coding RNAs. Use it to train RNA-FLM1, a foundation language model, first on all sequences and then on evolutionarily conserved ones.
Christopher Hartley
Miami University-Oxford, OH·Chemistry
Determine how chains that combine attractive and repulsive interactions within a single molecule fold, programming structure by inserting pyrazine-2,3-diyl units, nitrogen-containing aromatic rings, into ortho-phenylene sequences.
Zhengqing Ouyang
University of Massachusetts, MA·Biochemistry
Develop statistical and computational methods to infer in vivo RNA 3D structures from proximity-ligation sequencing data, which records which RNA segments are physically close in living cells.
The school
Saint Louis University: 5 labs on PI Pages, $96M a year on research, 251 research doctorates a year.
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