RATTLESNAE - another telomerase DNA synthesis scheme

[fenn lipkowitz]

Read Artificial Telomerase Templates for Low Entropy Synthesis of Nucleic Acids by Enzyme

RATTLESNAE

Yet another pie in the sky scheme from the #hplusroadmap goons.

There are probably still errors in the description and example sequences, but I hope this is useful anyway.

Overview

A DNA synthesis or data storage scheme using optogenetically-controlled telomerase RNA component (TERC) template variants to synthesize programmable DNA sequences via telomerase (TERT).

The system encodes 2 bits or one nucleotide base per extension cycle using light-controlled template selection.

This scheme is not complete; I haven't designed a mechanism to select the template strands or protecting groups.

Biological Basis

Background

Telomerase incorporates new nucleotides into a growing DNA strand, complementary to the TERC template CUAACCCUAAC. This template becomes the repeat unit TTAGGG. You can see how telomerase advances one repeat unit along the template:

CUAACCCUAAC
 <- GGGATT

If we splice this sequence we stand a good chance of breaking everything in vivo, even if it's compartmentalized.

TERC Template Mutations Are Viable

• Tumor-derived variants prove template modifications are tolerated:
  • "Mutations in the TERC template sequence can be incorporated into the telomeres of human tumors"
    • https://pmc.ncbi.nlm.nih.gov/articles/PMC9409504/
  • alternative repeat sequence 1: TTGGGG (position 4 template mutation)
  • alternative repeat sequence 2: TTAGTG (position 6 template mutation)
• Constraints on mutation positions:
  • Positions 1-5: require wobble-compatible changes (preserve realignment/processivity)
  • Position 6: freely mutable for encoding (in the copying domain)
    • this means alternative #2 is not that useful since we want to modify that base later
  • Helix P1b structure/linker length defines template boundaries, not sequence
    • many alternative repeat sequences should be possible, and we have an existence proof already
    • longer substring repeat sequences might be possible

The 3-Channel Encoding Scheme

Light Selectors

• Red light: Binary selector bit 0
• Green light: Binary selector bit 1
• Blue light: Deprotection trigger (advances ratchet)

TERC Template Region Variants (TTG-starting repeats)

Using position 6 of the 11-mer template (the X in CCAACXCCAAC):

Light State	Template (5'→3')	DNA Product (5'→3')	Variable Base
R=0, G=0	CCAACCCCAAC	TTGGGG	G (tumor-type)
R=1, G=0	CCAACACCAAC	TTGGTG	T
R=0, G=1	CCAACGCCAAC	TTGGCG	C
R=1, G=1	CCAACUCCAAC	TTGGAG	A

Conversion Logic

DNA repeat (5'→3') → reverse → complement (T→U) → RNA template (5'→3')
Example: TTGGGG → GGGGTT → CCCCAA → substring embedded in CCAACCCCAAC

The Protecting Group Ratchet

Key Constraint

• Only one protecting group exists on the growing DNA strand at any time
• Protecting group gets chewed off by a light driven enzyme, allowing telomerase activity again
• Without it, telomerase would make an endlessly repeating sequence of the template substring

Ratchet Cycle

1. Light selectors (R/G) activate one of four TERC variants
2. TERT extends DNA by one repeat using active template
3. Oligo complement with a protecting group binds to substring and blocks further extension
4. Blue light triggers deprotectase, removes protecting group
5. Next extension cycle begins

Why This Works In Vitro But Not In Vivo

• In vitro: controlled environment, no competing replication machinery
• In vivo: compartmentalization is not perfect in biology, stuff leaks
• Protecting group oligos would bind to genomic DNA and block normal DNA polymerase activity
• It could work with self-triggering deprotectase in the cytoplasm, but would introduce errors

Output: Low-Entropy Spliceable Sequences

The variable bases at position 5 of each repeat create:

• Programmable DNA sequences encoding arbitrary data
• Splice sites for downstream processing
• Information density: 2 bits per ~6 nucleotides per extension cycle

Choose TERC template sequences such that they can be spliced scar-free with enzymes or nanomachines.

If two remaining base pairs are needed for splicing, it's still only 4 bits or 5 separate channels.

Applications

1. DNA data storage: Write arbitrary binary data as telomeric sequences
2. Molecular barcoding: Generate unique identifiers via light programming
3. Gene synthesis: Programmable enzymatic DNA synthesis, the missing tool
4. mRNA synthesis: Real-time control of cell machinery from the internet

other stuff... what is this, a patent? i'm just establishing that i had an idea and putting it out there

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Compiled 2026-01-12 from #hplusroadmap discussion (fenn, MuaddibLLM: mostly GPT-5.2 and Gemini-3-flash) https://gnusha.org/logs/2026-01-11.log (don't actually read this, it's embarrassing)