Molpigs

@molpigs.bsky.social

164 Followers 29 Following

We are the MOLecular Programming Interest Group, early-career researchers in the field of molecular programming building our community through podcasts, reading groups and community activities. Links to all podcast feeds and Slack at molpi.gs

The gel showing assembly and disassembly of the cube. The important lane is lane 4, which shows a single, high-weight band corresponding to the assembled and purified cube. Lanes 5-11 are then various restriction enzyme digestions, resulting in either 3, 2 or 1 interlocked DNA circles depending on which sides of the cube are cut by the enzymes.
The gel demonstrating successful ligation of the triple-catenene. Each lane shows many bands containing sub-products, but what's important is the topmost band in each lane, corresponding to the fully-formed triple catenene. Lanes 1 and 3 are the assembled catenene with 10 and 11 base-pairs per side, respectively. Lanes 2 and 4 show the same structures after digestion with an exonuclease which will remove any un-ligated strands. In lane 2, the top band is still present showing successful ligation, while in lane 4, it's gone, showing that for some reason the 11-base loops will not close.
Figure 2 from the paper showing stepwise assembly of the "belt" structure which can be ligated into the cube. Addition of each strand leads to a slightly higher band on the gel, until you ligate two of the 5-strand complexes together, at which point a faint target band appears and a huge aggregate stuck in the well.
Figure 1 from the paper showing how you can add strands in a stepwise manner to create a cube, first creating two opposite faces separately with overhangs which can be ligated to form a "belt", then the belt can be purified into three interlocked rings, reconstituted with its strands, and then those can be ligated again to form a cube.
The circuit diagrams from "design of a biochip". Honestly I have no idea where to even start describing them. Each circuit has 12 input/output connections, split into two halves connected by a metal atom which serves as the 'bit' which can be read/written.
Figure 2 from "Design of a biochip" showing various conducting polymers: linear trans-polyacetyline which could act as a molecular wire and branched ladder polymers polyphenothiazine and polyphenoxazine which could be used as junctions between polyacetyline ladders.
An outline rendering of a DNA holiday junction showing the way the two duplexes cross on top of each other.
Figure 2 from "An immobile nucleic acid junction constructed from oligonucleotides" showing a giant acrylamide gel with extra annotations along the top showing which strands are in wells a-r, respectively. In wells c-f we can see fast-moving bands corresponding to single strands 1-4 of the junction. Wells f-j contain each 3-strand complex, which run much slower than the single strands. Well k contains the 4-strand complex, which again is larger. Wells m-r are all of the 2-strand complexes. The 2-strand complex which bind show similar mobility to the 3-strand complexes, while the two diagonal pairs show single-strands. Wells a, b and l are duplex DNA from restriction digests to show the size of a straight duplex. The 4-strand complex is 64 nucleotides, and there is a 66 nucleotide strand in well a which is much larger.
Figure 1 from "An immobile nucleic acid junction constructed from oligonucleotides" showing the sequence and topology of a 4-way junction with a sequence which is asymmetric, preventing junction migration. In the caption it notes that there is no symmetry at the junction and that it contains no GC sequences longer than 2 to prevent alternate configurations.
Figure 6 from "Nucleic Acid Junctions and Lattices" showing schematically how one could connect the immobile junctions from the previous figures into a 2D lattice via sticky-end cohesion. The caption also points out that "This procedure is not limited in theory to rank-4 junctions nor is it limited to two dimensions."
Figure 3 from "Nucleic Acid Junctions and Lattices" showing a junction without sequence symmetry which would not be able to slide. Notice that at the junction, you would not be able to form neither the C-C + G-G nor the T-T + A-A required for junction migration.
Figure 2 from "Nucleic Acid Junctions and Lattices" showing the sliding of Holliday junctions during genetic recombination. Because of sequence symmetry, the crossover point between the four strands is able to slide as the two halves of the junction exchange base pairs.
MC Escher's "Depth" which shows an endless lattice of fish with 4 fins each reaching out to touch each other in a cubic lattice.