Quantum Computing in DNA

Stuart Hameroff

Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.

I. The "pi stack"

Looking “down” the long axis of the DNA molecule (in cross section):

Illustrations from Introduction to DNA StructureA Molecular Graphics companion to an Introductory Course in Biology or Biochemistry. Copyright 1995, Richard B. Hallick. The University of Arizona

The "pi stack" is the internal core (blue) of the DNA molecule made up of base pair purine and pyrimidine rings. Such polarizable ring structure are known for delocalizable ("pi") electrons, and Barton et al have shown extremely high conductance along the length of DNA, suggestive of superconductivity in the pi stack.

II. Base pairs

The pi stack is comprised of the purine and pyrimidine ring structures of the base pairs which are always either Adenine (purine) and Thymine (pyrimidine, “A-T”), or Guanine (purine) and Cytosine (pyrimidine, “G-C”). Purines have a double ring structure, with a 6 member ring fused to a 5 member ring, whereas pyrimidines have a single 6 member ring. (The complementary base pairs are held together by hydrogen bonds— 2 between A and T, and 3 between G and C.) Thus each base pair always consists of one 6/5 purine ring and one 6 pyrimidine ring.

III. Base pair dipoles

Each A-T and G-C base pair also has a dipole—a type of van der Waals London force due to mutually induced polarizations between electron clouds of the purine and pyrimidine rings. At any particular time an electron negative charge may be shifted either toward the purine ring, or toward the pyrimidine ring (with corresponding conformational shifts).

For the A-T base pair we can have negative charge more localized toward the adenine purine ring, e.g. AT, or more toward the thymine pyrimidine ring AT

For the base pair G-C we can similarly have

GC, or GC

But as these dipole couplings are quantum mechanical they can exist in superposition of both possibilities. So quantum mechanically we can have:

Both AT and AT which eventually collapse to either AT or AT

As well as

Both GC and GC which eventually collapse to either GC or GC

Using quantum nomenclature we can refer to the quantum superpositions of both possible states | AT > + | AT >

And similarly

| GC > + | GC >

Such superpositions are used in quantum computing as "qubits", bit states which can exist in quantum superposition of, e.g. Both 1 AND 0. DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared

Consider a string of three base pairs:

A-T

G-C

G-C

A-T can be either AT or AT, or quantum superposition of both | AT > + | AT >

G-C can be either GC or GC, or quantum superposition of both | GC > + | GC>

As each pair may be in two possible dipole states mediated by quantum mechanical interactions, the 3 base pairs may be seen as a quantum superposition of 8 possible dipole states:

AT  AT    AT    AT

GC    GC    GC    GC

GC    GC    GC    GC

AT   AT    AT    AT

GC    GC    GC    GC

GC    GC    GC    GC

As each dipole differs slightly due to structural differences, so for example

AT and GC have slightly different dipoles though pointing in the same general direction whereas AT and GC have more or less opposite dipoles. The slight differences will introduce irregularities in the pi stack quantum dynamics, and couple to mechanical/conformational movements of the DNA strand. Net and complex dipoles within the pi stack may show emergent phenomena. Particular dipoles corresponding to loops, hairpins, dyads etc. may have specific properties. Superconductive DNA loops, for example, could function in a way analogous to SQUIDs (superconductive quantum interference devices). Squids have a superconductive ring with one segment of lower conductance; current through the ring is highly sensitive to dipoles. DNA loops may serve as quantum antenna, with nonlocal communication with other DNA, and perhaps cell machinery.

We can then consider DNA as a chain of qubits (with helical twist).

Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement.