Difference between revisions of "Exponential drop in yield"
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Given that the success ratios at each steps on average and in general not exceedingly high, <br> | Given that the success ratios at each steps on average and in general not exceedingly high, <br> | ||
the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br> | the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero. <br> | ||
| − | For a large number of identical chains molecules synthesized together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed. | + | For a large number of identical chains molecules synthesized simultaneously together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed. |
= Ways to avert this yield-drop in the synthesis of chain molecules (polymers, [[foldamers]]) = | = Ways to avert this yield-drop in the synthesis of chain molecules (polymers, [[foldamers]]) = | ||
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= Related = | = Related = | ||
| − | * [[ | + | * [[Chemical synthesis]] |
| − | * [[ | + | * [[Foldamer]]s, [[Spiroligomer]]s, peptidomimentics |
* [[Iterated one pot binding site finding]] | * [[Iterated one pot binding site finding]] | ||
| + | ---- | ||
| + | * [[Structural DNA nanotechnology]] | ||
| + | * [[De-novo protein engineering]] | ||
Latest revision as of 12:04, 19 November 2024
Synthesizing linear chain molecules (polymers, oldamers) iteratively in vivo the failure likelihood (success rate smaller than factor one) at each addition reaction multiplies.
Given that the success ratios at each steps on average and in general not exceedingly high,
the overall success ratio for an individual chain molecule strand to be synthesized to full lengths as desired with no errors quickly drop down to near zero.
For a large number of identical chains molecules synthesized simultaneously together (as it is the case in such synthetic chemistry) that translates to a low yield and high impurity with incomplete and or faulty chain moleculed.
Contents
Ways to avert this yield-drop in the synthesis of chain molecules (polymers, foldamers)
Near term
Employing natural synthesis mechanisms
- Hijacking the cells machinery (ribosomes & more) for making proteins according to artificial plan
- There are even chaperone proteins that helping along in post synthesis correct folding
Still expensive experimental stuff:
- Artificial amino acid tweaks (?)
- Artificial codon tweaks
Far term
Piezochemical machanosynthesis has low enough error rates for this to not be a problem and even error corrention can be implemented.
Ways to avert this yield-drop in thermally driven selfassembly of blocks
Self assembly via iterative binding site finding suffers from the exact same problem as iterative syntesis of polymers in synthetic chemistry. The same exponential drop in yield with chain length is prestent.
Self assembly via one pot binding site finding of 2D or even 3D structures
hugely averts the problem in that assembly can just move around sites of faulty assembly.
For a complete breakdown of all further assembly all paths need to be blocked simultaneously which can get exceedingly unlikely.
One pot binding site finding comes with other downsides though. Including steric kinetic traps.
Best may be an intermediate approach: iterated one pot binding site finding
(TODO: Work out the math for the assembly of a stiff rod that is a bundle of several rods where selfassembly can move redundantly arrond faulty assembly sites)
Related
- Chemical synthesis
- Foldamers, Spiroligomers, peptidomimentics
- Iterated one pot binding site finding
