Parts

Our team contributed a diverse collection of genetic parts designed to advance RNA-based therapeutics, antibody engineering, and synthetic biology research. These parts are available in the iGEM Registry for future teams to build upon.

Basic Parts

Composite Part

Part Collections

Parts Description

GAL10 promoter inducible by galactose - BBa_25TUTX7H

Drives transcription of downstream genes in S. cerevisiae in response to galactose. Expression is tightly repressed in glucose and strongly induced when galactose is the sole carbon source.

GFP (8 first codons yeast-optimized) - BBa_25KK1S7Z

Encodes the green fluorescent protein (GFP) optimized for expression in Saccharomyces cerevisiae. Produces green fluorescence upon blue light excitation, allowing for easy visualization and quantification of gene expression in yeast systems.

Flexible linker - BBa_25ZMWGR0

This part encodes a short, flexible peptide linker designed for in-frame fusion of protein domains. The linker sequence GGTGCTGGGGCAggtacC encodes a glycine/serine-rich motif that provides structural flexibility, reducing steric hindrance between fused protein domains and helping maintain the correct folding and function of each domain.

Auxin-responsive IAA17 degron - BBa_25ML5EUW

This part encodes the Auxin-Inducible Degron (AID) motif derived from the IAA17/AXR3 protein of Arabidopsis thaliana. Proteins fused to this degron undergo rapid degradation upon treatment with the plant hormone auxin, enabling conditional and reversible control of protein levels in eukaryotic cells.

CYC1 Transcriptional Terminator (S. cerevisiae) - BBa_250SRT22

This part encodes the transcriptional terminator of the CYC1 gene from Saccharomyces cerevisiae. The CYC1 terminator is widely used in yeast expression systems to ensure proper transcription termination and polyadenylation of mRNA transcripts.

MALAT1 Antisense Oligonucleotide - BBa_25RYGOTP, BBa_25I1LOKC, BBa_25YRNV63, BBa_25XN9X2G, BBa_2572988U, BBa_25D5J2R8, BBa_25CWZZ88

This antisense oligonucleotide (ASO) is designed to target the long non-coding RNA MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1). The ASO binds to MALAT1 RNA and recruits RNase H, leading to transcript degradation and reduced MALAT1 expression. This sequence is chemically optimized with phosphorothioate (PS) linkages throughout and 2′-MOE modifications at the 5′ and 3′ ends to enhance stability and nuclease resistance.

Full Sequence with modifications described in the part page. We uploaded three ASOs from the first iteration of our computational model and four from the second iteration.

GFP Antisense Oligonucleotide - BBa_25GPTZBQ, BBa_25QOYYSX, BBa_25L38810

This antisense oligonucleotide (ASO) is designed to specifically bind to the GFP mRNA transcript through Watson-Crick base pairing, leading to targeted degradation via RNase H–mediated cleavage. The ASO is chemically modified with 2′-O-methoxyethyl (2′MOE) groups at both 5 nucleotides ends for increased nuclease resistance and phosphorothioate (PS) linkages throughout to enhance stability. When delivered into cells, the ASO reduces GFP expression by lowering transcript abundance, enabling knockdown experiments and validation of ASO delivery and activity.

Full Sequence with modifications described in the part page.

Optimized Cetuximab (Erbitux) Light Chain - BBa_25OL7B19

This part encodes the light chain (κ) of Cetuximab, an EGFR-binding monoclonal antibody.
Intended use: Co-expression with the optimized heavy chain to form a full IgG that binds human EGFR, enabling antibody-mediated delivery to EGFR-positive cells.
Host / system: Optimized for mammalian expression (CHO cells). sequence contains signal peptide secretion.

Optimization pipeline:

• ESO (Evolutionary Stability Optimizer) to reduce mutational hot-spots while preserving sequence (ACS Synth Biol, 2021: https://doi.org/10.1021/acssynbio.1c00426).

MNDL Bio optimization for enhanced recombinant yield.

• https://www.mndl.bio/

Design goals: Stable, high-expression light chain that assembles with the heavy chain, supports high-titer secretion, and preserves Cetuximab EGFR affinity.

Optimized Cetuximab (Erbitux) Heavy Chain - BBa_25E4W9ZP

This part encodes the heavy chain (IgG1) of Cetuximab, an EGFR-binding monoclonal antibody.
Intended use: Co-expression with the optimized light chain to form a full IgG that binds human EGFR, enabling antibody-mediated delivery to EGFR-positive cells.
Host / system: Optimized for mammalian expression (CHO cells). Sequence contains signal peptide secretion.

Optimization pipeline:

• ESO (Evolutionary Stability Optimizer) to reduce mutational hot-spots while preserving sequence (ACS Synth Biol, 2021: https://doi.org/10.1021/acssynbio.1c00426).

MNDL Bio optimization for enhanced recombinant yield.

• MNDL Bio

Design goals: Stable, high-expression heavy chain that assembles with the light chain, supports high-titer secretion, and preserves Cetuximab EGFR affinity.

Cetuximab Light Chain (optimized first 10 codons for CHO expression) - BBa_25IZCSQU

This part contains the first 10 codons of the Cetuximab Light chain variable region (VL) optimized for expression in Chinese Hamster Ovary (CHO) cells using the MNDL Bio codon optimization platform. Cetuximab is a chimeric (human/mouse) IgG1 monoclonal antibody targeting the epidermal growth factor receptor (EGFR), widely used in cancer therapy.

The sequence optimization aimed to enhance translational efficiency and mRNA stability in mammalian expression systems - specifically in CHO cells, which are the standard host for industrial antibody production.

Cetuximab Heavy Chain (optimized first 10 codons for CHO expression)- BBa_25ZW8G2V

This part contains the first 10 codons of the Cetuximab heavy chain variable region (VH) optimized for expression in Chinese Hamster Ovary (CHO) cells using the MNDL Bio codon optimization platform. Cetuximab is a chimeric (human/mouse) IgG1 monoclonal antibody targeting the epidermal growth factor receptor (EGFR), widely used in cancer therapy.

The sequence optimization aimed to enhance translational efficiency and mRNA stability in mammalian expression systems - specifically in CHO cells, which are the standard host for industrial antibody production.

Dual-Reporter Plasmid for Off-Target ASO Evaluation - BBa_25688YXQ

This dual-reporter plasmid is designed to evaluate off-target activity of antisense oligonucleotides (ASOs). It contains: CMV enhancer/promoter → GFP (WT) → Terminator; SV40 enhancer → mCherry → SV40 terminator; CMV enhancer/promoter → GFP (mutated in ASO binding and qPCR primer sites) → Terminator; pUC origin; Ampicillin resistance cassette.

Function and Rationale

GFP (WT) enables measurement of on-target knockdown. GFP (Mutated) mimics an off-target transcript while remaining fluorescent. mCherry serves three roles: (1) breaks repeatability between GFP units to reduce recombination, (2) acts as a transfection control since GFP is expected to decrease under ASO treatment, and (3) functions as a genetic stability marker, disappearing if recombination removes the intervening region. This construct enables simultaneous monitoring of ASO on-target and off-target effects in the same cells with internal controls.

Human MTAP CDS (methylthioadenosine phosphorylase) - BBa_25VQZ2EL

This part is the human MTAP coding sequence (methylthioadenosine phosphorylase), a cytosolic enzyme in the methionine salvage/polyamine pathway. MTAP catalyzes the phosphorolysis of 5′-methylthioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate, thereby supporting adenine/methionine recycling and preventing intracellular MTA accumulation.

We used this CDS to restore MTAP function in MTAP-deleted cancer cell lines in order to test synthetic-lethality hypotheses. Re-expression of MTAP serves as a genetic rescue control: it should reduce MTA levels and attenuate sensitivity to targets that are conditionally essential in the MTAP-loss context (e.g., PRMT5/MAT2A/RIOK1 pathways), compared with vector controls.

• Part type: Coding sequence only (no promoter/UTR/terminator). Clone downstream of a suitable mammalian promoter (e.g., CMV/EF1α) with an appropriate poly(A) signal.

Yeast GFP Expression Cassette - BBa_25RWTF7I

This composite part enables inducible GFP expression in Saccharomyces cerevisiae. The GFP coding sequence is human-optimized with the first 8 codons adjusted for optimal yeast expression. The IAA17 auxin-responsive degron allows regulated protein degradation in the presence of auxin. Integration (to the yeast genome) is achieved via homology arms (not listed here).