Gödel, Escher, Bach An Eternal Golden Braid by Douglas R. Hofstadter

You can perhaps remember this molecular pairing scheme by recalling that

Achilles is paired with the Tortoise, and the Crab with his Genes.

When "copying" a strand, therefore, you don't actually copy it, but you

manufacture its complementary strand. And this one will be written upside

down above the original strand. Let's see this in concrete terms. Let the

previous enzyme act on the following strand (and that enzyme also happens

to like to start at A):

CAAAGAGAATCCTCTITGAT

There are many places it could start. Let's take the second A, for example.

The enzyme binds to it, then executes step 1: Search for the nearest

pyrimidine to the right. Well, this means a C or a T. The first one is a T

somewhere near the middle of the strand, so that's where we go. Now step

2: Copy mode. Well, we just put an upside-down A above our T. But that's

not all, for Copy mode remains in effect until it is shut off-or until the

enzyme is done, whichever comes first. This means that every base which is

passed through by the enzyme while Copy mode is on will get a com-

plementary base put above it. Step 3 says to look for a purine to the right of

our T. That is the G two symbols in from the right-hand end. Now as we

move up to that G, we must "copy"-that is, create a complementary strand.

Here's what that gives:

'v'1J1J'v'1J\f\f\f'J

CAAAGAGAATCCTCTTTGAT

The last step is to cut the strand. This will yield two pieces:

'v'1J1J'v'1J\f\f\f'J

CAAAGAGAATCCTCTTTG

and AT.

And the instruction packet is done. We are left with a double strand,

however. Whenever this happens, we separate the two complementary

strands from each other (general principle); so in fact our end product is a

set of three strands:

AT, CAAAGAGGA, and CAAAGAGAATCCTCTITG.

Notice that the upside-down strand has been turned right side up, and

thereby right and left have been reversed.

Now you have seen most of the typographical operations which can be

carried out on strands. There are two other instructions which should be

mentioned. One shuts off Copy mode; the other switches the enzyme from a

strand to the upside-down strand above it. When this happens, if you keep

the paper right side up, then you must switch "left" and "right" in all the

instructions. Or better, you can keep the wording and just turn the paper

around so the top strand becomes legible. If the "switch" command is

Self-Ref and Self-Rep 507