Team:OUC-China/Part Collection

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Overview

This year, OUC-China constructed numerous parts that can perform logical functions. Once the basic components of our design are put together, they can well form logic gates. We hope our parts will make it easier and more efficient for synthetic biologists and future iGEM teams to assemble the logic gates they need. We collect parts for six types of logic gates (OR, AND, NOT, NIMPLY, IMPLY, XOR). Our parts (BBa_K3328000 to BBa_K3328055) were fully documented in the Registry. We present the basic part (BBa_K3328000 to BBa_K3328007, BBa_K3328032 to BBa_K3328055) including RNA switch, logic gate, and compound part (BBa_K3328013 to BBa_K3328028) respectively. In the verification of the logic circuit, the inductors corresponding to the promoter before the switch structure were taken as the inputs, and the expression quantity of fluorescent protein was taken as the output, so as to test the existing logic operations and the logic operations designed by us (NIMPLY2, IMPLY1, IMPLY2, XOR1, and XOR2).

OR

OR gate composed of two switch RNA hairpins. Each switch module has an input RNA recognition site and its own RBS and start codon. Input RNA binding unwinds the corresponding switch stem to activate translation.

Part	Type	Description
BBa_K3328053	RNA	switch of OR
BBa_K3328054	RNA	triggerA of OR
BBa_K3328055	RNA	triggerB of OR
BBa_K3328027	Composite	realize the boolean calculation of OR
BBa_K3328028	Composite	two input trigger of OR logic gate to perform the truth table

AND

AND gate constructed from two input RNAs that bind to yield a complete trigger RNA. When either input RNA is expressed, it is incapable of activating the switch because neither trigger sub-sequence alone can unwind the repressing hairpin. The toehold switch can only be turned on when the two input RNA species hybridize and form a complete trigger sequence.

Part	Type	Description
BBa_K3328044	RNA	switch of AND
BBa_K3328045	RNA	triggerA of AND
BBa_K3328046	RNA	triggerB of AND
BBa_K3328021	Composite	realize the boolean calculation of AND
BBa_K3328022	Composite	two input trigger of AND logic gate to perform the truth table

NOT

NOT gate is made up of 3WJ repressor. Its unstable hairpin was previously demonstrated to be translationally active. When a complementary trigger RNA is expressed, the trigger will bind to the switch RNA, making the originally unstable 3WJ structure stable, and represses translation.

Part	Type	Description
BBa_K3328000	RNA	an OFF-switch to regulate the expression of downstream gene
BBa_K3328001	RNA	an OFF-switch to regulate the expression of downstream gene
BBa_K3328002	RNA	an OFF-switch to regulate the expression of downstream gene
BBa_K3328003	RNA	an OFF-switch to regulate the expression of downstream gene
BBa_K3328004	RNA	binding to 3WJ switch(K3328000) to inhibit the expression of downstream gene
BBa_K3328005	RNA	binding to 3WJ switch(K3328001) to inhibit the expression of downstream gene
BBa_K3328006	RNA	binding to 3WJ switch(K3328002) to inhibit the expression of downstream gene
BBa_K3328007	RNA	binding to 3WJ switch(K3328003) to inhibit the expression of downstream gene4

NIMPLY

In the NIMPLY gate, a deactivating RNA (INPUT A) uses direct hybridization or strand displacement to abolish trigger RNA (input B) activity. So when only the correct trigger RNA is expressed, the switch can be turned on.

Part	Type	Description
BBa_K3328047	RNA	switch of NIMPLY1
BBa_K3328048	RNA	triggerA of NIMPLY1
BBa_K3328049	RNA	triggerB of NIMPLY1
BBa_K3328050	RNA	switch of NIMPLY2
BBa_K3328051	RNA	triggerA of NIMPLY2
BBa_K3328052	RNA	triggerB of NIMPLY2
BBa_K3328023	Composite	realize the boolean calculation of NIMPLY1
BBa_K3328024	Composite	two input trigger of NIMPLY1 logic gate to perform the truth table
BBa_K3328025	Composite	realize the boolean calculation of NIMPLY2
BBa_K3328026	Composite	two input trigger of NIMPLY2 logic gate to perform the truth table

IMPLY

We combined the 3WJ switch and toehold switch to realize the IMPLY Boolean calculation. When no trigger is expressed, this logic gate just likes a 3WJ switch. When trigger A expressed, the trigger will bind to the switch RNA. The binding allows for a branch migration process, exposing AUG and RBS for translation initiation. When trigger B expressed, the trigger will bind to 3WJ switch RNA. The resulting trigger–switch complex has a stable 3WJ structure that effectively sequesters the RBS and the start codon within the loop and stem of the switch RNA, respectively, and strongly represses translation. When both trigger A and B are expressed, the binding of trigger RNA to the toehold sequence allows the ribosome to bind to the former RBS and break open 3WJ stable hairpin.

Part	Type	Description
BBa_K3328038	RNA	switch of IMPLY1
BBa_K3328039	RNA	triggerA of IMPLY1
BBa_K3328004	RNA	triggerB of IMPLY1
BBa_K3328041	RNA	switch of IMPLY2
BBa_K3328042	RNA	triggerA of IMPLY2
BBa_K3328004	RNA	triggerB of IMPLY2
BBa_K3328017	Composite	realize the boolean calculation of IMPLY1
BBa_K3328018	Composite	two input trigger of IMPLY1 logic gate to perform the truth table
BBa_K3328019	Composite	realize the boolean calculation of IMPLY2
BBa_K3328020	Composite	two input trigger of IMPLY2 logic gate to perform the truth table

XOR

The XOR is inspired by the NIMPLY gate, consisting of a toehold switch and two triggers. The trigger’s core sequence is the same and at the triggers’ both ends, there are the nucleotide-binding domains. When input one of these triggers, the switch can turn on. Moreover, when input these two triggers simultaneously, they can pair together and form a ring in the middle. As a result, the switch will still be in the OFF state.

Part	Type	Description
BBa_K3328032	RNA	switch of XOR1
BBa_K3328033	RNA	triggerA of XOR1
BBa_K3328034	RNA	triggerB of XOR1
BBa_K3328035	RNA	switch of XOR2
BBa_K3328036	RNA	triggerA of XOR2
BBa_K3328037	RNA	triggerB of XOR2
BBa_K3328013	Composite	realize the boolean calculation of XOR1
BBa_K3328014	Composite	two input trigger of XOR1 logic gate to perform the truth table
BBa_K3328015	Composite	realize the boolean calculation of XOR2
BBa_K3328016	Composite	two input trigger of XOR2 logic gate to perform the truth table