Three initial CFPS designs: submitted compositions

Ketiga desain telah disimpan di Coopetition pada 5 Oktober 2026. Catatan ini menghubungkan keputusan dengan sumber, perhitungan, dan bukti simpan. Semua desain masih berupa hipotesis biologis; hasil eksperimen belum tersedia.

Date: October 5, 2026

Parent journal: HTBAA 2026 — Jurnal Homework 3: Desain Reaksi Cell-Free

Status: SUBMITTED — three platform save confirmations and one composition under each target in My Compositions were read back on 5 October 2026 (WIB). Local volume checks passed. Each design differs from its reference preset. No exhaustive community-wide duplicate audit or experimental success is claimed.

Local checks and target correction

All three reagent lists total exactly 20,000 nL. Every volume is a multiple of 25 nL. Each contains fixed base buffer 2000 nL, lysate 5000 nL, and exactly one target-matched DNA template 2000 nL; additives plus water total 11,000 nL. PETase/TfCut2 uses template_petase; Reteplase uses template_reteplase. The local JSON target keys were corrected to match the official specification.

Interface pitfall: loading a preset does not automatically switch the DNA/protein target. Check both the selected protein target and the exported template_* key before submission. A PETase or Reteplase preset can otherwise retain the previously selected sfGFP template. Matching fixed volume alone cannot detect this error.

Concentration basis

Stock labels for variable reagents come from the visible public DOM snapshot captured on 5 October 2026. DNA and base-buffer stock values come from the official specification. Nominal final concentration = stock concentration × reagent volume / 20,000 nL, plus any defined base-buffer contribution. The fixed buffer contributes HEPES 30 mM, potassium glutamate 200 mM, magnesium glutamate 2.6 mM, amino-acid mix 1 mM, and cysteine 1 mM. Tyrosine is represented within the base-buffer amino-acid contribution; the platform displays 1 mM tyrosine with no separate addition in these recipes. Listed amino-acid-mix levels are nominal mixture/per-component levels, not a sum across all amino acids. Base-buffer contributions are already included in affected table rows and must not be added twice. Unknown endogenous lysate contributions and free-ion concentrations are not determined by this calculation; potassium-glutamate concentration is not total potassium concentration. Folinic acid stays in mg/mL because that is the verified stock unit.

Recorded UI costs

The costs below are UI estimates for the reaction as mixed, recorded during draft preparation, not a full procurement or project budget. They do not represent a bottle purchase, minimum order, shipping, labor, capital, or complete downstream workflow. USD per 20 µL reaction is calculated as the displayed USD/mL × 0.020 mL; source values are rounded. These same rounded costs were visible immediately after the respective save confirmations. A later load of the saved PETase additive mix displayed $306.69/mL ($6.1338/reaction), while retaining the designer's then-current Reteplase template. The cause of this display difference has not been established. Loading a composition does not by itself verify its saved DNA target or a definitive cost. The break-even values below are conditional on the original paired UI snapshots, not verified procurement costs or measured cost improvements.

1. sfGFP: one-step magnesium screen

Reference: sfGFP Ribose (sfGFP_R2PC_054).

Submitted sample ID: naufal_tsabitul_azmi_2026-10-05_sfgfp_mg76_v1. Published composition ID: 14sqepz2b15y1o0.

Change: Supplemental magnesium glutamate: 225 → 200 nL; water: 175 → 200 nL. Nominal final magnesium glutamate: 8.225 → 7.600 mM, including the fixed base-buffer contribution.

Hypothesis: A one-droplet reduction in supplemental magnesium may preserve or improve folded sfGFP production by changing the ionic environment of the ribose/NMP formulation. Magnesium is sensitive to formulation context, so the direction of any effect remains unknown. The direct salt saving is small; the primary test is functional output relative to reaction cost.

Risk: A small volume step can still move the reaction away from its magnesium optimum. Nominal magnesium concentration does not measure free Mg²⁺, and the optimum from another energy system or lysate cannot be assumed here.