DNA molecules are made of nucleotides, these nucleotides have bases which connect A to T, C to G. These connections are made through hydrogen bonding. But what if instead of that, you have a long rectangular macromolecule that has holes in it, so that you could fit something in there. For example, you could have a many rows, each with 4 possible holes. If the hole is at slot 1, it could code for A, If the hole is at slot 2, it could code for T, and so on. So could this hypothetical system work of microscopic punch cards as a replacement for DNA?

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    $\begingroup$ Bear in mind that "holes" in molecules aren't something through which an object can protrude. Atomic bonds are probabilistic, and molecular structures as represented by molymods or similar things are a convenient lie told to first-year chemistry students. $\endgroup$
    – jdunlop
    Jun 4 at 22:20
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    $\begingroup$ Well, of course it could work if you can invent a suitable mechanism for it to work. I don't understand what the question is asking. You have devised a (rather nebulous) way to encode the 4-symbol alphabet of the the genetic code. (Note that your mechanism can encode a 16-symbol alphabet. But let's assume that the punching machine is defective and can punch only one hole per row.) OK. Now what? You need a mechanism to read the code and command the (equivalent of the) ribosomes to execute it. Are you expecting the community to come up with this for you? $\endgroup$
    – AlexP
    Jun 4 at 22:46
  • $\begingroup$ No I really wanted to know 2 things: A.)Does this mechanism work? and B.) If it does, how big do the holes need to be $\endgroup$
    – KaffeeByte
    Jun 4 at 23:28
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    $\begingroup$ What mechanism? You have not described any mechanism. You have described an encoding. The encoding works. Now, you need to come up with a mechanism to use the encoding. $\endgroup$
    – AlexP
    Jun 5 at 0:24
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    $\begingroup$ While you could use this to code information, you can't copy, translate or store this media with anywhere near enough efficiency. How does a punch card make protein, or copy the information? A big macromolecule is an expensive investment compared to humble DNA. $\endgroup$
    – DWKraus
    Jun 5 at 1:54

2 Answers 2


For one, it lacks the mechanism of double encoding given by the C-G and T-A pairs.

Without this mechanism one cannot reproduce with mithosis by simply splitting the code in half and taking only a single half of the copy as master version. And the double helix folding wouldn't be present, making volume management cumbersome at least.

And I suspect it also doubles the time needed to express a section, since there is only one copy available instead of two.



But lucky you, current DNA in essence is your punching cards, in a sense. I mean it how a punchcard looks like when transferred in microworld, with compliance with rules of microworld.

The problem with holes, which are as big as atoms is they, or rather their surrounding, constantly oscillates, and this hole is more like a probability of a hole, and testing it requires some molecules which are attracted to probabilities or more strictly speaking to probabalistic densities of electron clouds shells. And typical DNA and a transcriptase does exactly that - reacts to probabalistic densities of clouds created by molecule atoms configuration

Flat on those scales does not exists, and your imaginary punch card will try to stick to itself (by bending rolling twisting and do all that in hundreds ways, forming stacks and entangling) and do stick to all other things around, bend twist doing all that.

Current DNA version it creates twisted pair(like ethernet) and insulation for wires(sort of), and it helps it to stick less to some random stuff, the information encoded also affects entanglement of DNA etc.

Drop you punch card, and get back from dark side, we also have cookies. The real DNA is more magical than you think it is, it dwarfs that punch card idea with one finger.

This is electrostatic potencial of benzene molecule, for which you would think there is a hole, but no there is no hole molecule wise


For bigger constructions it becomes harder to distinguish a hole from empty space with a help of a molecule, and bigger holes it starts to wiggle bend and do all kinds of things if one problem is not enough. Atoms in molecules are in constant move, oscillations due to energy which we on our macrolevel call temperature

  • and that tendency to roll itself in a blob, we call it on a macrolevel - surface tension, but on microlevel it that sticking to itself and such. If things aren't done in a rigth way it quite potent energy, it may lower temperature of melting of iron particles to half of its 1.5 tousand degree, as an example, when those particles are small enough.

Rigid structures, detecting aspects which could be rigid on macrolevel is not a good idea on microlevel, and in contrary to rigid properties real molecules they exploit that constant movement existance for them to work.

  • $\begingroup$ Tried to sort-out image formatting, but failed, must be tired. $\endgroup$ Jun 6 at 4:04

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