Drawing RNA Secondary Structure

Alexander Batelaan Author

08/04/2020 Added

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This research project focused on improving the rna_draw python program to draw RNA secondary structures by using matplotlib.

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[00:00:01.476]Hello, my name is Alexander Batelaan
[00:00:04.436]and I will be presenting the research
[00:00:06.446]that I have been working on this
[00:00:07.630]summer which is “Drawing RNA
[00:00:09.398]Secondary Structures”
[00:00:13.530]RNA is a very essential molecule in
[00:00:15.440]cell biology. It transports genetic
[00:00:17.390]instructions stored in DNA to
[00:00:20.680]the cytoplasm to generate proteins.
[00:00:23.290]RNA can fold into complex structures
[00:00:25.700]which have the potential
[00:00:27.140]to be used for nanomedicine.
[00:00:30.060]In our research we wanted to
[00:00:31.790]improve a program that can draw
[00:00:33.130]the secondary structure of RNA.
[00:00:35.310]The program, called rna_draw, used
[00:00:37.300]a cairosvg library to generate images.
[00:00:41.020]But, cairosvg is not a part of the
[00:00:43.110]standard python package. So, we
[00:00:44.990]decided to replace the cairosvg functions
[00:00:47.577]with matplotlib functions which are part
[00:00:49.943]of the standard python package.
[00:00:52.450]It would be helpful to efficiently
[00:00:54.180]draw the structure of RNA because
[00:00:56.020]RNA is biologically important.
[00:00:58.500]This image shows how RNA is
[00:01:00.120]part of the process of decoding
[00:01:01.800]genetic information to build proteins.
[00:01:05.800]RNA folding is essential for its
[00:01:07.610]biological functions. RNA can fold
[00:01:10.850]according to primary, secondary,
[00:01:13.400]and tertiary structure. Primary
[00:01:16.150]structure is the sequence of the
[00:01:17.730]RNA nucleotides, secondary
[00:01:19.890]structure is how the sequence
[00:01:21.190]forms base pairs in a 2D space,
[00:01:24.430]and tertiary structure is how the
[00:01:26.120]2D structure folds in on itself to
[00:01:28.300]make a 3D shape. There are programs
[00:01:31.580]that can draw RNA secondary
[00:01:33.500]structures. The rna_draw python
[00:01:36.030]files developed by the Yesselman
[00:01:37.850]Research group is an example of a
[00:01:39.580]program that can draw
[00:01:40.810]RNA secondary structures.
[00:01:44.646]The rna_draw program works
[00:01:46.236]by translating structure and
[00:01:47.806]sequence inputs into an image
[00:01:49.286]of the RNA secondary structure.
[00:01:52.146]The secondary structure of RNA
[00:01:53.936]can be represented by
[00:01:55.256]dot-bracket notation. In
[00:01:57.486]dot-bracket notation the brackets
[00:01:59.296]represent paired nucleotides and
[00:02:01.666]dots represent unpaired nucleotides.
[00:02:05.086]If you look at the image of the
[00:02:06.636]dot bracket notation, you can see
[00:02:08.396]that the arrows show which of
[00:02:09.986]the brackets are connected to
[00:02:11.516]each other. For example, the first
[00:02:14.036]open bracket is paired with the
[00:02:15.636]last closing bracket. This shows
[00:02:17.606]that the first G in the sequence is
[00:02:19.676]paired with the last C in the sequence.
[00:02:22.206]The rna_draw program reads the
[00:02:24.636]dot-bracket notation and produces
[00:02:26.786]a pairmap. Then, the pairmap produces
[00:02:29.406]a tree. The tree is used to find the
[00:02:31.746]coordinates for each nucleotide.
[00:02:34.106]After the coordinates of the
[00:02:35.826]nucleotide are found, the picture
[00:02:38.326]of the RNA secondary structure is drawn.
[00:02:44.403]My research focused on changing
[00:02:46.523]how the RNA secondary structure
[00:02:48.333]image was drawn. I replaced cairosvg
[00:02:51.463]functions with matplotlib functions.
[00:02:54.403]One of the problems that I ran into
[00:02:55.983]was determining the correct figure
[00:02:57.653]size. I solved this problem by testing
[00:03:00.063]RNA structures with a range of
[00:03:01.773]different sizes. I printed out the
[00:03:04.303]area covered by the RNA structures
[00:03:06.083]according to the coordinates and
[00:03:07.863]defined a figure size variable which
[00:03:09.763]I set at a correct figure size for
[00:03:11.583]each test structure. I plotted
[00:03:14.333]Area versus the Figure Size Variable
[00:03:16.303]and fit the curve. I then used the
[00:03:18.923]curve fit equation to define the
[00:03:21.493]figure size for all RNA structure sizes.
[00:03:24.733]The four RNA structures that I tested
[00:03:26.953]were the hairpin loop, t-RNA,
[00:03:29.703]corona virus 5’ untranslated region,
[00:03:33.173]and the 50S-ribosome. I tested from
[00:03:35.863]one of the smallest RNA structures,
[00:03:37.883]the hairpin loop, all the way up to
[00:03:39.373]the 50S-Ribosome which is the
[00:03:41.123]largest RNA structure known.
[00:03:43.583]This gives rna_draw the capability
[00:03:45.873]to plot any size of RNA structure.
[00:03:49.534]In conclusion, the curve fit that
[00:03:51.294]I used to control the figure size
[00:03:52.884]worked well. It successfully drew
[00:03:54.944]RNA structures with a large
[00:03:56.624]range of different sizes. The
[00:03:58.564]quality of the fit was determined
[00:04:00.364]visually by comparing the resulting
[00:04:02.074]images. I was also successful
[00:04:05.324]in modifying rna_draw to use
[00:04:07.324]matplotlib instead of cairosvg.
[00:04:10.364]This makes rna_draw a more
[00:04:11.894]useful tool for RNA chemistry
[00:04:13.544]research groups. It allows rna_draw
[00:04:16.404]to be used on Jupyter notebook
[00:04:17.874]for Mac and Windows computers.
[00:04:20.024]Here is an example of how to use
[00:04:21.784]rna_draw. First, we define a secondary
[00:04:32.084]structure, then we define a sequence, then we define a color
[00:04:39.580]scheme. Then we run all, and we get
[00:04:48.860]the resulting image.
[00:04:55.250]In the future we are planning to
[00:04:57.080]improve the secondary structure
[00:04:58.700]images generated by rna_draw
[00:05:00.670]even further. Currently, some of the
[00:05:03.080]larger RNA structures are drawn
[00:05:05.160]with overlapping regions. We are
[00:05:07.640]planning to reorganize the coordinates
[00:05:09.950]of the nucleotides into a python class
[00:05:12.690]to make it easier to manipulate
[00:05:14.170]and solve this problem.
[00:05:16.242]Here are my references and I
[00:05:18.172]would like to thank UCARE for
[00:05:19.832]sponsoring this research. I would
[00:05:21.762]also like to thank Dr. Yesselman
[00:05:23.632]and Chris Jurich for mentoring me
[00:05:25.512]and helping me so much with
[00:05:26.632]learning all of the python programming.
[00:05:29.302]Thank you for listening
[00:05:30.522]to my presentation.

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Drawing RNA Secondary Structure

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