trans-RNA Designer

Programmable mRNA Translation Activator · v3.0

v3.0 — circRNA + Batch + Accessibility

Design trans-RNA Sequences
Programmable mRNA Translation Activation

Input mRNA or circRNA sequences, the system auto-identifies the first AUG, assesses target accessibility, designs optimal trans-RNA pairing regions (front/back-loading), and provides chemical modification recommendations. Supports batch comparison of multiple sequences.

trans-RNA Mechanism

trans-RNA is a short capped RNA (15-50 nt) that delivers an m7G cap to a target mRNA via complementary base pairing, recruiting 43S pre-initiation complexes to initiate translation.

Front-loading

Cap upstream of AUG (< -20 nt), ribosome scans to AUG

Back-loading

Cap downstream of AUG (+2 ~ +80 nt), direct loading at start site

Blind spot (-2 ~ -20 nt)

Scanning ribosome unwinds dsRNA in this zone

circRNA support

Trans-RNA drives circRNA translation (13x in vivo, Fig. 4c)

Batch comparison

Compare designs across multiple sequences simultaneously

trans-RNA Mechanism: Programmable Translation InitiationFront-loading model — Cap upstream of AUG, ribosome scans 5'→3' to reach start codon5' CAPmRNA3'5'→3'AUGTranslation →Complementary Base Pairing3'trans-RNA3' ← 5'5' CAPCap recruits 43S PIC43S scans 5'→3' to AUGRibosome60S (Large)40S (Small)Blind Spot(-2 ~ -20 nt)mRNAtrans-RNAm7G CapBase PairingAUGBlind SpotRibosomeScan

Sequence Input

Single sequence analysis or batch comparison of multiple targets

Linear mRNAcircRNA
SingleBatch
0 nt