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Using R2D2 to Understand RNA Folding

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If you love learning more about biology at a fundamental level, I have a great video for you! It simulates the 3D folding of RNA. RNA is a single stranded molecule, but it is still capable of forming internal loops that can be stabilized by base pairing, just like its famously double-stranded parent, DNA. Understanding more about RNA folding may be valuable in many different areas of biomedical research, including developing ways to help people with RNA-related diseases, such as certain cancers and neuromuscular disorders, and designing better mRNA vaccines against infectious disease threats (like COVID-19).

Because RNA folding starts even while an RNA is still being made in the cell, the process has proven hugely challenging to follow closely. An innovative solution, shown in this video, comes from the labs of NIH grantees Julius Lucks, Northwestern University, Evanston, IL, and Alan Chen, State University of New York at Albany. The team, led by graduate student Angela Yu and including several diehard Star Wars fans, realized that to visualize RNA folding they needed a technology platform that, like a Star Wars droid, is able to “see” things that others can’t. So, they created R2D2, which is short for Reconstructing RNA Dynamics from Data.

What’s so groundbreaking about the R2D2 approach, which was published recently in Molecular Cell, is that it combines experimental data on RNA folding at the nucleotide level with predictive algorithms at the atomic level to simulate RNA folding in ultra-slow motion [1]. While other computer simulations have been available for decades, they have lacked much-needed experimental data of this complex folding process to confirm their mathematical modeling.

As a gene is transcribed into RNA one building block, or nucleotide, at a time, the elongating RNA strand folds immediately before the whole molecule is fully assembled. But such folding can create a problem: the new strand can tie itself up into a knot-like structure that’s incompatible with the shape it needs to function in a cell.

To slip this knot, the cell has evolved immediate corrective pathways, or countermoves. In this R2D2 video, you can see one countermove called a toehold-mediated strand displacement. In this example, the maneuver is performed by an ancient molecule called a single recognition particle (SRP) RNA. Though SRP RNAs are found in all forms of life, this one comes from the bacterium Escherichia coli and is made up of 114 nucleotides.

The colors in this video highlight different domains of the RNA molecule, all at different stages in the folding process. Some (orange, turquoise) have already folded properly, while another domain (dark purple) is temporarily knotted. For this knotted domain to slip its knot, about 5 seconds into the video, another newly forming region (fuchsia) wiggles down to gain a “toehold.” About 9 seconds in, the temporarily knotted domain untangles and unwinds, and, finally, at about 23 seconds, the strand starts to get reconfigured into the shape it needs to do its job in the cell.

Why would evolution favor such a seemingly inefficient folding process? Well, it might not be inefficient as it first appears. In fact, as Chen noted, some nanotechnologists previously invented toehold displacement as a design principle for generating synthetic DNA and RNA circuits. Little did they know that nature may have scooped them many millennia ago!

Reference:

[1] Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-naïve folding intermediates. Yu AM, Gasper PM Cheng L, Chen AA, Lucks JB, et. al. Molecular Cell 8, 1-14. 18 February 2021.

Links:

Ribonucleic Acid (RNA) (National Human Genome Research Institute/NIH)

Chen Lab (State University of New York at Albany)

Lucks Laboratory (Northwestern University, Evanston IL)

NIH Support: National Institute of General Medical Sciences; Common Fund

6 Comments

  • Ronald Henderson says:

    The sad thing is that we drift farther away from a solution when we think our models involve an ‘ancient’ (think evolution) entity which might be due to past evolutionary processes. We waste time and means running up the wrong path! If we think ‘perfect’ ‘God made,’ we immediately have intelligence to work with. Intelligence breathes intelligent deductions.

    • Andrew Goldstein says:

      Sad? “Past evolutionary processes” inform science about future outcomes just as understanding ‘ancient’ cosmological processes enlighten us about the future of the universe we inhabit.

  • Andrew Goldstein says:

    I would like to request a follow-up blog post with a basic description of the “rules” that the RNA (or should I say the computer program) follows as it goes through its folding and untangling process. I imagine things like molecular bonding forces and the matrix in which the RNA folding takes place play key roles in driving “toehold displacement?” It would make the simulation more meaningful. Thanks.

  • Jack says:

    All resulting from nuclei mass effect correlated to distance with ultra micro distance variations and attenuated by electron energy levels and quantity. Basically a filtered electromechanical ultra micro patterning and sequencing of motion defined by ultra micro interaction of Newton’s big G=mM/r2 (skewed deflationary) and Einstein’s E=mc2 with inflationary correction on an ultra micro level with extremely small relatively static yet fluid interactive graduations. The “Morris code” of a self structuring fluid 3d existence. The extenuated “dots and dashes” being incremental energy and or energetic particle structural entity levels (self structuring-subatomic, atomic, molecular, etc.) designated as photons, quarks, qualms, electrons, protons, neutrons, etc. Extremely simple, just extensive structural-pattern and actions-sequential inter and intra molecular movement identity.

  • Tony T. says:

    This video clearly describes how RNA takes its shape in the cell. DNA and RNA-related experiments have been going on for a long time … RNA plays a major role for different features of human life.

  • Tom George III says:

    Great article in Time magazine. You are still my hero. Blessings from Wilmington NC. Father of Sandra Hall.

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