Parts

Best composite part

The composite part pRAM_ProgRAM-recording-tape2.0 (Part:BBa_K5102073) is designed for the ProgRAM molecular recording system and features a recording tape composed of a series of START codons in the context of Kozak consensus arranged in three forward open reading frames (ORFs). In the composite part, the tape is in state 0, indicating that no molecular events have been recorded, and all adenosines in the START codons remain unmodified by dPspCas13b-ADAR2DD fusion. Downstream of the tape, a sequence of fluorescent proteins enables visualization of the current recorded state. The design incorporates sequentially modifiable adenosine sites within the RNA tape, creating a dynamic “traffic light” system that allows for precise in vivo monitoring of recording events without disrupting cellular functions. Each adenosine corresponds to a START codon; upon deamination, this modification disrupts the codon, shifting the open reading frame by one base pair and triggering the expression of one of three distinct fluorescent proteins: miRFP670nano3, mScarlet3, or mTagBFP2.

The frameshift-driven translation of multiple fluorescent proteins (XFPs) from a single construct required codon optimization in all three forward open reading frames, eliminating premature STOP codons.

For continuous and reliable translational-level control of total protein expression across our system, we incorporated eUnaG (Truong et al., 2024), a small green fluorescent protein codon-optimized for all three ORFs.To ensure proper protein folding, each fluorescent protein is encoded downstream of the RNA tape and preceded by a 2A peptide, which promotes ribosomal skipping during translation.

During recording tape design part design careful considerations have been taken to ensure high editing rates, as well as specificity of gRNA binding. The molecular recording utilized in the project is based on the REPAIR v2 system developed by Cox et al., 2017. It has previously been shown that both the nucleotides surrounding the modified adenosine, called central base triplet (CBT), as well as location of the modified A within the sequence play an important role in the editing efficiency. For 30 nucleotide gRNA spacer design, 22nd and 28th positions have been shown to be the most efficient. Introduction of a A12G mismatch showed increased binding disruption of gRNA, ensuring highly selectable editing.

While several Cas enzymes require a highly conserved Protospacer adjacent motif (PAM) sequence, PspCas13b does not require it for its activity. However, it still shows a preference for targets with protospacer flanking sites (PFSs).

After applying all of these considerations, we were left with the following minimal tapes design: GCCGUGGNNNGCCGUGGNNNGCCAUGGNNNGCCAUGGNNNGCCAUGGNNNGC. The missing nucleotides were designed in a way that: (i) N could be replaced by any nucleotide but adenosine, (ii) the gRNA complementary to the binding tape must have formed a conserved stem loop structure required by PspCas13b, which binds the ADAR2DD to the target deamination site. To ensure best design, to this end we have employed computational methods (please refer to the Model wiki for more details).

Additionally the composite part contains several elements ensuring high expression and stability of transcript:

• 5’UTR (601–680): 5’ untranslated region. In the current instance, CMV 5’UTR (BBa_K5102068). This region can be substituted with synthetic alternatives, such as (BBa_K5102079 and BBa_K5102080), offering customizable designs for modulation of RNA stability and ribosome recruitment as outlined on the iGEM Munich 2024 model page.
• 3’UTR (4241–4284): 3’ untranslated region. In the current instance, human beta-globin 3’UTR (BBa_K5102053).
• WPRE (4382–4979): woodchuck hepatitis virus posttranscriptional regulatory element (BBa_K5102069) for increasing transgene expression by minimizing readthrough transcription and improving termination.

The rest of the features of the composite part include:

• Mammalian promoter: promoter for plasmid expression of ProgRAM in a mammalian cell line. In the current instance, a CMV enhancer (BBa_K5102067) and a CMV promotor (BBa_K2217006). Alternative mammalian promoters driving the expression are possible, for instance, BBa_J433025, BBa_J433001, or BBa_J433002.
• T7 promoter (681–698): phage T7 promoter (BBa_K3633015) for in vitro expression of the ProgRAM.
• Aptamer (4295-4317): an RNA aptamer acting as an anchor, enabling tape pulldown or localization. In the current instance, PP7 phage aptamer (BBa_K5102054).
• T7 terminator (4334–4381): phage T7 transcriptional terminator (BBa_K73172) for in vitro expression of the ProgRAM.
• polyA (4984–5105): a polyadenylation site for mammalian transcription termination and RNA polyadenylation. In the current instance, SV40 polyA (BBa_K2217005). Alternative polyA sites could be used.

Zoom in

part	type	Registry ID	Description
CMV enhancer	regulatory	BBa_K5102067	5’ untranslated region. In the current instance, CMV 5’UTR (BBa_K5102068). This region can be substituted with synthetic alternatives, such as BBa_K5102065, offering customizable designs for modulation of RNA stability and ribosome recruitment as outlined on the model page.
CMV 5' UTR	regulatory	BBa_K5102068	constitutive mammalian promoter
CMV promoter	regulatory	BBa_K2217006	mammalian constitutive promotwe
T7 promoter	regulatory	BBa_K3633015	phage T7 promoter for in vitro expression of the ProgRAM
ProgRAM recording tape 2.0	RNA	BBa_K5102033	Recording tape, functioning as a deamination target and translation initiation site. In the current instance, a 2.0 tape design (BBa_K5102037). This is a recording tape based on the REPAIR system using gRNAs with 30 nt long spacers.
T2A	coding	BBa_K5102012, BBa_K5102013, BBa_K5102014	ribosomal skip site
P2A	coding	BBa_K5102015 BBa_K5102016 BBa_K5102017	ribosomal skip site
miRFP670nano3	coding	BBa_K5102001	near ir fluorescent protein
mScarlet3	coding	BBa_K5102002	red fluorescent protein
mTagBFP2	coding	BBa_K5102003	blue fluorescent protein
eUnaG	coding	BBa_K5102009, BBa_K5102010, BBa_K5102011	green fluorescent protein
3'UTR	regulatory	BBa_K5102053	Human beta-globin 3’UTR
PP7 aptamer	RNA	BBa_K5102054	a PP7 RNA aptamer acting as an anchor, enabling tape pulldown or localization.
T7 terminator	regulatory	BBa_K73172	phage T7 transcriptional terminator for in vitro expression of the ProgRAM
Woodchuck Posttranscriptional Regulatory Element	regulatory	BBa_K5102069	WPRE increases transgene expression
polyA	polyA	BBa_K2217005	polyA_signal_sequence

Other Composite Parts

Name	ID	Type	Description
pRAM_ProgRAM-recording-tape2.0	BBa_K5102073	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 2.0. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_ProgRAM-recording-tape2.1	BBa_K5102074	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 2.1. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_ProgRAM-recording-tape3.0	BBa_K5102075	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 3.0. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_ProgRAM-recording-tape3.1	BBa_K5102076	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 3.1. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_ProgRAM-recording-tape4.0	BBa_K5102077	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 4.0. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_ProgRAM-recording-tape5.0	BBa_K5102078	composite	The composite part is designed for the ProgRAM molecular recording system and features a recording tape 5.0. Downstream of the tape, a sequence of fluorescent proteins is preceded by a 2A peptide. Additionally, eUnaG and elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE are being presented.
pRAM_syntheticUTR-ProgRAM-recording-tape2.0	BBa_K5102079	composite	The composite part consists of: CMV enhancer, CMV promotor, 5' synthetic UTR, T7 promoter, recording tape 2.0, T2A, miRFP670nano3, P2A, eUnaG, T2A, mScarlet3, P2A, eUnaG, T2A, mTagBFP2, P2A, eUnaG, human beta-globin 3'UTR, PP7, T7 terminator, WPRE, SV40 polyA.
pRAM_syntheticUTR-ProgRAM-recording-tape3.0	BBa_K5102080	composite	The composite part consists of: CMV enhancer, CMV promotor, 5' synthetic UTR, T7 promoter, recording tape 3.0, T2A, miRFP670nano3, P2A, eUnaG, T2A, mScarlet3, P2A, eUnaG, T2A, mTagBFP2, P2A, eUnaG, human beta-globin 3'UTR, PP7, T7 terminator, WPRE, SV40 polyA.
miRFP670nano3 in fusion with eUnaG	BBa_K5102081	composite	The part contains a CMV enhancer and CMV promoter driving the expression of miRFP670nano3, a near-infrared fluorescent protein, followed by a P2A self-cleaving peptide linking eUnaG, another fluorescent protein.
mScarlet-3 in fusion with eUnaG	BBa_K5102082	composite	The part contains a CMV enhancer and CMV promoter driving the expression of mScarlet-3, a red fluorescent protein, followed by a P2A self-cleaving peptide linking eUnaG, another fluorescent protein.
mTagBFP2in fusion with eUnaG	BBa_K5102083	composite	The part contains a CMV enhancer and CMV promoter driving the expression of mTagBFP2, a blue fluorescent protein, followed by a P2A self-cleaving peptide linking eUnaG, another fluorescent protein.
pU6_gRNA1-ProgRAM_tape1	BBa_K5102086	composite	This construct includes a guide RNA (gRNA1 targeting first adenosine in the ProgRAM recoding tape 1) driven by the U6 promoter.
pU6_gRNA2-ProgRAM_tape1	BBa_K5102087	composite	This construct includes a guide RNA (gRNA2 targeting first adenosine in the ProgRAM recoding tape 1) driven by the U6 promoter.
pU6_gRNA3-ProgRAM_tape1	BBa_K5102088	composite	This construct includes a guide RNA (gRNA3 targeting first adenosine in the ProgRAM recoding tape 1) driven by the U6 promoter.
pU6_gRNA1-ProgRAM_tape2	BBa_K5102089	composite	This construct includes a guide RNA (gRNA1 targeting first adenosine in the ProgRAM recoding tape 2) driven by the U6 promoter.
pU6_gRNA2-ProgRAM_tape2	BBa_K5102090	composite	This construct includes a guide RNA (gRNA2 targeting first adenosine in the ProgRAM recoding tape 2) driven by the U6 promoter.
pU6_gRNA3-ProgRAM_tape2	BBa_K5102091	composite	This construct includes a guide RNA (gRNA3 targeting first adenosine in the ProgRAM recoding tape 2) driven by the U6 promoter.
pU6_gRNA1-ProgRAM_tape3	BBa_K5102092	composite	This construct includes a guide RNA (gRNA1 targeting first adenosine in the ProgRAM recoding tape 3) driven by the U6 promoter.
pU6_gRNA2-ProgRAM_tape3	BBa_K5102093	composite	This construct includes a guide RNA (gRNA2 targeting first adenosine in the ProgRAM recoding tape 3) driven by the U6 promoter.
pU6_gRNA3-ProgRAM_tape3	BBa_K5102094	composite	This construct includes a guide RNA (gRNA3 targeting first adenosine in the ProgRAM recoding tape 3) driven by the U6 promoter.
pU6_gRNA1-ProgRAM_tape4	BBa_K5102095	composite	This construct includes a guide RNA (gRNA1 targeting first adenosine in the ProgRAM recoding tape 4) driven by the U6 promoter.
pU6_gRNA2-ProgRAM_tape4	BBa_K5102096	composite	This construct includes a guide RNA (gRNA2 targeting first adenosine in the ProgRAM recoding tape 4) driven by the U6 promoter.
pU6_gRNA3-ProgRAM_tape4	BBa_K5102097	composite	This construct includes a guide RNA (gRNA3 targeting first adenosine in the ProgRAM recoding tape 4) driven by the U6 promoter.
pU6_gRNA1-ProgRAM_tape5	BBa_K5102098	composite	This construct includes a guide RNA (gRNA1 targeting first adenosine in the ProgRAM recoding tape 5) driven by the U6 promoter.
pU6_gRNA2-ProgRAM_tape5	BBa_K5102099	composite	This construct includes a guide RNA (gRNA2 targeting first adenosine in the ProgRAM recoding tape 5) driven by the U6 promoter.
pU6_gRNA3-ProgRAM_tape5	BBa_K5102100	composite	This construct includes a guide RNA (gRNA3 targeting first adenosine in the ProgRAM recoding tape 5) driven by the U6 promoter.
pRAM_ProgRAM-recording-tape2.0-4xdOkra	BBa_K5102103	composite	In the composite part, the tape 2 is in state 0 and downstream of the tape, a sequence of fluorescent proteins is being translated. To ensure proper protein folding, each fluorescent protein is encoded downstream of the RNA tape and preceded by a 2A peptide, which promotes ribosomal skipping during translation. To control for part transcription levels, a highly bright and stable green 4xdOkra aptamer is incorporated in the design. The composite part also contains elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE.
pRAM_ProgRAM-recording-tape3.0-4xdOkra	BBa_K5102108	composite	In the composite part, the tape 3 is in state 0 and downstream of the tape, a sequence of fluorescent proteins is being translated. To ensure proper protein folding, each fluorescent protein is encoded downstream of the RNA tape and preceded by a 2A peptide, which promotes ribosomal skipping during translation. To control for part transcription levels, a highly bright and stable green 4xdOkra aptamer is incorporated in the design. The composite part also contains elements to enhance mRNA expression and stability, such as the 5' CMV UTR, human beta-globin 3' UTR, and WPRE.
pcDNA_Zeo_NLuc	BBa_K5102110	composite	The part encodes for NanoLuc luciferase under the control of the CMV promoter, ensuring high-level, constitutive expression in mammalian cells.
pcDNA_Zeo_NLuc_STOP	BBa_K5102111	composite	The part encodes for NanoLuc luciferase under the control of the CMV promoter, ensuring high-level, constitutive expression in mammalian cells. The NanoLuciferase harbors a G35A point mutation introducing a STOP codon in the open reading frame.
023_pU6_PspCas13b-DR-gRNA_NLuc	BBa_K5102112	composite	This construct includes a guide RNA targeting NanoLuciferase STOP codon with a PspCas13b gRNA loop. The expressoion of gRNA is driven by the U6 promoter.
pcDNA_Zeo_NLuc_tape1.0	BBa_K5102114	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 1.0, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape1.1	BBa_K5102115	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 1.1, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape2.0	BBa_K5102116	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 2.0, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape2.1	BBa_K5102117	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 2.1, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape3.0	BBa_K5102118	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 3.0, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape3.1	BBa_K5102119	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 3.1, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape4.0	BBa_K5102120	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 4.0, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape4.1	BBa_K5102121	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 4.1, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape5.0	BBa_K5102122	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 5.0, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pcDNA_Zeo_NLuc_tape5.1	BBa_K5102123	composite	The part consists of a CMV enhancer, CMV promoter, Program recording tape 5.1, T2A, NLuc and bovine growth hormone polyadenylation signal. The RNA recording tape in state zero features a series of start codon.
pRAM	BBa_K5102000	DNA	The minimal synthetic plasmid backbone, pRAM.

Other Basic Parts

Name	ID	Type	Description
gRNA2_T1-30bp	BBa_K5102019	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 1 to 2 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA3_T1-30bp	BBa_K5102020	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 2 to 3 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA1_T2-30bp	BBa_K5102021	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA2_T2-30bp	BBa_K5102022	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 1 to 2 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA3_T2-30bp	BBa_K5102023	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 2 to 3 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA1_T3-30bp	BBa_K5102024	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA2_T3-30bp	BBa_K5102025	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 1 to 2 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA3_T3-30bp	BBa_K5102026	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 2 to 3 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA1_T4-30bp	BBa_K5102027	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA2_T4-30bp	BBa_K5102028	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 1 to 2 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA3_T4-30bp	BBa_K5102029	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 2 to 3 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA1_T5-30bp	BBa_K5102030	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA2_T5-30bp	BBa_K5102031	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 1 to 2 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
gRNA3_T5-30bp	BBa_K5102032	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 2 to 3 in the ProgRAM recorder. This gRNA directs a deactivated Cas13b protein from the Prevotella species, which is fused to the ADAR2 deaminase domain. The Cas13b-gRNA complex guides the deaminase to the target sequence, facilitating precise RNA editing for state change.
tape_1.0	BBa_K5102033	RNA	a RNA tape_1 in state zero, designed to record biological events in cells
tape_1.1	BBa_K5102034	RNA	a RNA tape_1 in state one, designed to record biological events in cells
tape_1.2	BBa_K5102035	RNA	a RNA tape_1 in state two, designed to record biological events in cells
tape_1.3	BBa_K5102036	RNA	a RNA tape_1 in state three, designed to record biological events in cells
tape_2.0	BBa_K5102037	RNA	a RNA tape_2 in state zero, designed to record biological events in cells
tape_2.1	BBa_K5102038	RNA	a RNA tape_2 in state one, designed to record biological events in cells
tape_2.2	BBa_K5102039	RNA	a RNA tape_2 in state two, designed to record biological events in cells
tape_2.3	BBa_K5102040	RNA	a RNA tape_2 in state three, designed to record biological events in cells
tape_3.1	BBa_K5102042	RNA	a RNA tape_3 in state one, designed to record biological events in cells
tape_3.2	BBa_K5102043	RNA	a RNA tape_3 in state two, designed to record biological events in cells
tape_3.3	BBa_K5102044	RNA	a RNA tape_3 in state three, designed to record biological events in cells
tape_4.0	BBa_K5102045	RNA	a RNA tape_4 in state zero, designed to record biological events in cells
tape_4.1	BBa_K5102046	RNA	a RNA tape_4 in state one, designed to record biological events in cells
tape_4.2	BBa_K5102047	RNA	a RNA tape_4 in state two, designed to record biological events in cells
tape_4.3	BBa_K5102048	RNA	a RNA tape_4 in state three, designed to record biological events in cells
tape_5.0	BBa_K5102049	RNA	a RNA tape_5 in state zero, designed to record biological events in cells
tape_5.1	BBa_K5102050	RNA	a RNA tape_5 in state one, designed to record biological events in cells
tape_5.2	BBa_K5102051	RNA	a RNA tape_5 in state two, designed to record biological events in cells
tape_5.3	BBa_K5102052	RNA	a RNA tape_5 in state three, designed to record biological events in cells
tdPCP	BBa_K5102055	coding	The tdPCP (tandem dimer PP7 coat protein) is a synthetic protein engineered by fusing two PP7 coat protein (PCP) monomers.
NanoLuciferase	BBa_K5102056	coding	Nanoluciferase is a small, engineered luciferase enzyme, which emits a bright bioluminescent signal when it catalyzes the oxidation of its substrate, furimazine.
NanoLuciferase	BBa_K5102057	coding	Nanoluciferase is a small, engineered luciferase enzyme, which emits a bright bioluminescent signal when it catalyzes the oxidation of its substrate, furimazine.
Nanoluciferase with STOP Codon disrupting expression	BBa_K5102058	coding	Nanoluciferase is a small, engineered luciferase enzyme, which emits a bright bioluminescent signal when it catalyzes the oxidation of its substrate, furimazine. This part harbors a G35A point mutation introducing a STOP codon in the open reading frame.
gRNA_Nlucrestoration	BBa_K5102059	RNA	This part encodes a guide RNA (gRNA) designed to specifically target the G35A point mutation in the NanoLuciferase gene.
REPAIR	BBa_K5102060	coding	fusion protein comprising the deactivated Cas13b enzyme from Prevotella species and the ADAR2DD deaminase domain
mTagBFP2	BBa_K5102061	coding	blue fluorescent protein characterized by an excitation wavelength of 399 nm and an emission wavelength of 454 nm
mScarlet-I	BBa_K5102062	coding	mScarlet-I encodes red fluorescent protein, originating from a synthetic construct. It is characterized by 569 nm excitation and 593 nm emission wavelength
miRFP670nano	BBa_K5102063	coding	miRFPnano part encodes a red fluorescent protein characterized by an excitation wavelength of 645 nm and an emission wavelength of 670 nm
(G4S)3 linker	BBa_K5102064	coding	The (G4S)3 linker is a flexible peptide linker composed of three repeats of the glycine-serine (G4S) motif. It is used to connect two functional protein domains without disrupting their individual activities.
5' synthetic UTR	BBa_K5102065	regulatory	This part encodes for a 5' UTR designed synthetically for high protein expression using the deep learning model developed by Castillo-Hair et al. (2024).
tTa	BBa_K5102066	coding	The tTA (tetracycline-controlled transactivator) is a fusion protein combining the tetracycline repressor (TetR) and a viral transactivation domain (VP16).
4xdOkra	BBa_K5102070	RNA	Okra (Okra505) is a highly bright and stable green aptamer, developed for advanced imaging applications
pU6 promoter	BBa_K5102085	regulatory	Human U6 nuclear promoter for small RNA expression.
gRNA (50bp spacer) for switching state 0 to 1 for ProgRAM (tape I)	BBa_K5102101	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM tape I design.
ProgRAM tape I	BBa_K5102102	RNA	The part encodes an RNA tape designed to record biological events in cells. The tape in state zero features three START codons in subsequent open reading frames (ORFs).
gRNA (50bp spacer) for switching state 0 to 1 for ProgRAM (tape II)	BBa_K5102104	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM tape II design.
gRNA (50bp spacer) for switching state 0 to 1 for ProgRAM (tape III)	BBa_K5102105	RNA	The part encodes a guide RNA (gRNA) that functions to switch the state from 0 to 1 in the ProgRAM tape III design.
ProgRAM tape II	BBa_K5102106	RNA	The part encodes an RNA tape designed to record biological events in cells. The tape in state zero features three START codons in subsequent open reading frames (ORFs).
ProgRAM tape III	BBa_K5102107	RNA	The tape features a series of START codons in Kozak consensus context that are placed in three consecutive forward open reading frames.
CMV promoter	BBa_K5102109	regulatory	The part encodes the CMV promoter, a strong viral promoter that drives high-level, constitutive expression in mammalian cells.
T2A	BBa_K5102113	coding	T2A peptide is a short sequence that causes ribosome skipping during translation, allowing the production of two distinct proteins from one mRNA strand.
Lyn-mCherry-FLAG	BBa_K5102127	coding	mCherry fluorescent protein, N-terminally fused with Lyn, C-terminally with a FLAG tag