Researchers develop tools to sharpen 3D view of large RNA molecules
New technique breaks through a technology roadblock that limited RNA
imaging for 50 years

Date:
October 7, 2020
Source:
University of Maryland
Summary:
Scientists developed a method for generating high resolution 3D
images of RNA, overcoming challenges limiting 3D analysis and
imaging of RNA to only small molecules and pieces of RNA for the
past 50 years. The new method, which expands the scope of nuclear
magnetic resonance (NMR) spectroscopy, will enable researchers to
understand the shape and structure of RNA molecules and learn how
they interact with other molecules.



FULL STORY ========================================================================== University of Maryland scientists have developed a method to determine
the structures of large RNA molecules at high resolution. The method
overcomes a challenge that has limited 3D analysis and imaging of RNA
to only small molecules and pieces of RNA for the past 50 years.


==========================================================================
The new method, which expands the scope of nuclear magnetic resonance
(NMR) spectroscopy, will enable researchers to understand the shape
and structure of RNA molecules and learn how they interact with other molecules. The insights provided by this technology could lead to targeted
RNA therapeutic treatments for disease. The research paper on this work
was published in the journal Science Advances on October 7, 2020.

"The field of nuclear magnetic resonance spectroscopy has been stuck
looking at things that are small, say 35 RNA building blocks or
nucleotides. But most of the interesting things that are biologically
and medically relevant are much bigger, 100 nucleotides or more," said
Kwaku Dayie, a professor of chemistry and biochemistry at UMD and senior
author of the paper. "So, being able to break down the log jam and look
at things that are big is very exciting. It will allow us to peek into
these molecules and see what is going on in a way we haven't been able
to do before." In NMR spectroscopy, scientists direct radio waves
at a molecule, exciting the atoms and "lighting up" the molecule. By
measuring changes in the magnetic field around the excited atoms -- the
nuclear magnetic resonance -- scientists can reconstruct characteristics
such as the shape, structure and motion of the molecule. The data this
produces can then be used to generate images, much like MRI images seen
in medicine.

Ordinarily, NMR signals from the many atoms in a biological molecule such
as RNA overlap with each other, making analysis very difficult. However,
in the 1970s, scientists learned to biochemically engineer RNA molecules
to work better with NMR by replacing the hydrogen atoms with magnetically active fluorine atoms. In relatively small molecules of RNA consisting
of 35 or fewer nucleotides, the fluorine atoms light up readily when
hit with radio waves and remain excited long enough for high-resolution analysis. But as RNA molecules get larger, the fluorine atoms light
up only briefly, then quickly lose their signal. This has prevented high-resolution 3D analysis of larger RNA molecules.

Previous work by others had shown that fluorine continued to produce a
strong signal when it was next to a carbon atom containing six protons
and seven neutrons (C-13). So, Dayie and his team developed a relatively
easy method to change the naturally occurring C-12 in RNA (which has
6 protons and 6 neutrons) to C-13 and install a fluorine atom (F-19)
directly next to it.

Dayie and his team first demonstrated that their method could produce data
and images equal to current methods by applying it to pieces of RNA from
HIV containing 30 nucleotides, which had been previously imaged. They
then applied their method to pieces of Hepatitis B RNA containing 61 nucleotides -- nearly double the size of previous NMR spectroscopy
possible for RNA.

Their method enabled the researchers to identify sites on the hepatitis B
RNA where small molecules bind and interact with the RNA. That could be
useful for understanding the effect of potential therapeutic drugs. The
next step for the researchers is to analyze even larger RNA molecules.

"This work allows us to expand what can be brought into focus,"
Dayie said.

"Our calculations tell us that, in theory, we can look at really big
things, like a part of the ribosome, which is the molecular machine
that synthesizes proteins inside cells." By understanding the shape and structure of a molecule, scientists can better understand its function
and how it interacts with its environment. What's more, this technology
will enable scientists to see the 3D structure as it changes, because
RNA molecules in particular change shape frequently. This knowledge is
key to developing therapeutics that narrowly target disease-specific
molecules without affecting healthy cell functions.

"The hope is that if researchers know the nooks and crannies in a molecule
that is dysfunctional, then they can design drugs that fill the nooks
and crannies to take it out of commission," Dayie said. "And if we can
follow these molecules as they change shape and structure, then their
response to potential drugs will be a little bit more predictable,
and designing drugs that are effective can be more efficient."

========================================================================== Story Source: Materials provided by University_of_Maryland. Note:
Content may be edited for style and length.


========================================================================== Journal Reference:
1. Owen B. Becette, Guanghui Zong, Bin Chen, Kehinde M. Taiwo, David A.

Case, T. Kwaku Dayie. Solution NMR readily reveals distinct
structural folds and interactions in doubly 13C- and
19F-labeled RNAs. Science Advances, 2020; 6 (41): eabc6572 DOI:
10.1126/sciadv.abc6572 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201007145424.htm

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