RNA droplets

RNA origami design following the designs of Lorenzo Di Michele and Elisa Franco (https://doi.org/10.1038/s41565-024-01726-x, https://doi.org/10.1038/s41467-024-50003-x)

[1]:

import pyfurnace as pf

uracil_connect = pf.Motif.from_structure('.&.', 'U&U')

Droplet A with Malachite Green aptamer

[2]:

kl = pf.KissingLoop(sequence='AUCGCGAAA')

line0 = [kl.copy(),
         pf.Stem(10),
         pf.MalachiteGreenShort(),
         pf.Stem(10),
         uracil_connect.copy(),
         pf.Dovetail(0, up_cross=False),
         pf.Stem(25),
         kl.copy().flip(),
         ]

line1 = [kl.copy(),
         pf.Stem(13),
         pf.start_end_stem(),
         pf.Stem(12),
         pf.Dovetail(0, down_cross=False),
         uracil_connect.copy(),
         pf.Stem(25),
         kl.copy().flip(),
        ]

drop_a = pf.Origami(line0, line1, align='first')

print(drop_a)

                                                                             ╭──────────╮
           ╭NNNKNNNNNNCC───CG─A──CUGNNNNKNNNNNU─────NNNKNNNKNNNNNKNNNNNNKNNNN┼─AUCGCGAAA╯
           │┊┊┊┊┊┊┊┊┊┊┊┊   ┊┊    ┊┊┊┊┊┊┊┊┊┊┊┊┊      ┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊│
╭AAAGCGCUA─┼NNNKNNNNNNGGUAAGCAAUGGACNNNNKNNNNN─U╮╭──NNNKNNNKNNNNNKNNNNNNKNNNN╯
╰──────────╯                                    ││
                                                ││
                                                ↑↓
                                                ││                           ╭──────────╮
               ╭NNNNKNNNNNNNN─3 5─NNNKNNNKNNNN──╯╰U─NNNKNNNNNKNNNNKNNNNKNNNNN┼─AUCGCGAAA╯
               │┊┊┊┊┊┊┊┊┊┊┊┊┊     ┊┊┊┊┊┊┊┊┊┊┊┊      ┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊│
    ╭AAAGCGCUA─┼NNNNKNNNNNNNN─────NNNKNNNKNNNN─────UNNNKNNNNNKNNNNKNNNNKNNNNN╯
    ╰──────────╯

Droplet B with Broccoli aptamer

[3]:

kl_b_seq = 'AGUCGACAA'

drop_b = drop_a.copy()

drop_b[0, 2] = pf.Broccoli()

# insert the sequence of the kissing loop B
for i in (0, -1):
    for j in (0, -1):
        drop_b[i, j].set_sequence(kl_b_seq)

print(drop_b)

                                                                                          ╭──────────╮
           ╭NNNKNNNNNNGGAGAC────GGUCGGG─UC────CAGNNNNKNNNNNU─────NNNKNNNKNNNNNKNNNNNNKNNNN┼─AGUCGACAA╯
           │┊┊┊┊┊┊┊┊┊┊┊┊┊┊ ┊    ┊ ┊┊ ┊  ┊┊    ┊┊┊┊┊┊┊┊┊┊┊┊┊      ┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊│
╭AACAGCUGA─┼NNNKNNNNNNCCUCGG─GUGUGAGAUG─AG─CU─GUCNNNNKNNNNN─U╮╭──NNNKNNNKNNNNNKNNNNNNKNNNN╯
╰──────────╯                                                 ││
                                                             ││
                                                             ↑↓
                                                             ││                           ╭──────────╮
                            ╭NNNNKNNNNNNNN─3 5─NNNKNNNKNNNN──╯╰U─NNNKNNNNNKNNNNKNNNNKNNNNN┼─AGUCGACAA╯
                            │┊┊┊┊┊┊┊┊┊┊┊┊┊     ┊┊┊┊┊┊┊┊┊┊┊┊      ┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊┊│
                 ╭AACAGCUGA─┼NNNNKNNNNNNNN─────NNNKNNNKNNNN─────UNNNKNNNNNKNNNNKNNNNKNNNNN╯
                 ╰──────────╯