July 4, 2010
A recent paper by Rieper, Anders and Vedral
(arxiv.org/abs/1006.4053: The Relevance Of Continuous Variable Entanglement In DNA) suggests
that quantum entanglement among base pairs in the DNA double helix stabilizes the molecule.
A summary of their paper is reported in MIT Technology Review
(http://www.technologyreview.com/blog/arxiv/25375/) is below
Rieper et al ascribe the entangling connections to van der Waals interactions among the pi electron clouds
of base pairs in the DNA double helix. Base pairs are composed of purines and pyrimadines, aromatic carbon
and nitrogen rings with several mobile pi electrons.
In single aromatic ring structures (purines, pyrimadines, but also amino acids tryptophan, phenylalanine,
tyrosine), pi electrons may 1) localize and occupy specific sites, or 2) remain fully delocalized above and
beneath the ring in an electron resonance cloud,i.e. in quantum superposition of possible locations.
However when two or more rings with pi electron clouds are precisely adjacent (near the van der Waals radius),
a third possibility ensues, involving a particular type of van der Waals force, the London force.
London forces arise when mobile electrons in one cloud repel electrons in the neighboring cloud, inducing
an electron cloud dipole which in turn induces a dipole in the first cloud. A pair of coupled dipoles (like tiny bar magnets) results, with a slight attractive force between them.If the clouds get pushed together closer than the van der Waals radius, a repulsive force comes into play, 100 time stronger than the attractive force, perhaps enabling nonlinear phonon couplings to conformational, or mechanical vibrations. (These types of effects apparently occur in certain proteins in which groups of aromatic amino acids (e.g. tryptophan, phenlyalanine) form non-polar pockets in which London forces couple to conformational states.Anesthetic gas molecules, binding by their own London forces, act in such pockets).
Reiper et al describe such interactions between adjacent base pairs (purines, pyrimadines)
along the vertical axis of the DNA double helix.
Figure 1. Rieper et al - van der Waals coupling between electron clouds of
adjacent base pairs in DNA.
However we should also consider sideways, or lateral interactions
between the two members of each base pair.
(Following drawings from R Hallick, University of Arizona)
Figure 2. DNA double helix, as in Figure 1.
The base pairs are always either Adenine (purine) and Thymine (pyrimidine, “A-T”),
or Guanine (purine) and Cytosine (pyrimidine, “G-C”).
Elecxtron resonance regions are shown in blue. Purines have a double ring structure,
with a 6 member ring fused to a 5 member ring, and 4 mobile pi electrons whereas pyrimidines
have a single 6 member ring with one pi electron.Both have mobile pi electrons (e.g. blue in
Figure 2). 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
with 4 pi electrons and one 6 pyrimidine ring with one pi electron.
Figure 3. Base pairs linked by hydrogen bonds (yellow) may also form
London force couplings due to pi electrons (blue).
If we assume the complementary base pair members are near the van der Waals
radius they will form van der Waals London force couplings
(in addition to hydrogen bonds) each A-T and G-C base pair also has van der Waals
couplings and dipoles which are 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.
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 >
| GC > + | GC >
Such superpositions may be 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 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:
1 2 3 4
AT AT AT AT
GC GC GC GC
GC GC GC GC
5 6 7 8
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.
If we consider the longitudinal quantum couplings as described by Rieper et al, the quantum states at each
level may be nonlocally entangtled with many other base pairs, perhaps all of them.
To what end? If we think of DNA as purely a repository of information, there is no need for
quantum computation. However gene expression is regulated by various external factors, both
directly and indirectly. These could include entanglement between a signalling factor with a particular
base pair, or group, as well as mechanical/conformational phonons of the DNA strand.
Net and complex dipoles within the pi stack may show emergent phenomena, in some cases
corresponding to loops, hairpins, dyads etc, each having specific properties. Superconductive DNA loops,
for example, could function in a way analogous to SQUIDs (superconductive quantum interference devices).
or serve as quantum antenna.
Perhaps gene expression involves a reduction of base pair dipole superpostion to particular dipole states.
For each base pair, the two possible altenatiive dipole states could correspond with ON or OFF, in terms of gene expression. The nornal state may be in superposition of both, till an interaction, or combination of interactions causes quantum state reduction - collapse of the wave function to one dipole state or the other, the proper one resulting in expression of that particular base pair genetic information.
(See Appendix 2 in chapter: Thats life! The geometry of pi electron resonance clouds
in Abbott, Davies, Patil, World Scientific, 2007
Also see see
From MIT Tech Review
There was a time, not so long ago, when biologists swore black and blue that quantum mechanics could play no role in the hot, wet systems of life. Since then, the discipline of quantum biology has emerged as one of the most exciting new fields in science. It's beginning to look as if quantum effects are crucial in a number of biological processes, such as photosynthesis and avian navigation which we've looked at here and here.
Now a group of physicists say that the weird laws of quantum mechanics may be more important for life than biologists could ever have imagined. Their new idea is that DNA is held together by quantum entanglement.
That's worth picking apart in more detail. Entanglement is the weird quantum process in which a single wavefunction describes two separate objects. When this happens, these objects effectively share the same existence, no matter how far apart they might be.
The question that Elisabeth Rieper at the National University of Singapore and a couple of buddies have asked is what role might entanglement play in DNA. To find out, they've constructed a simplified theoretical model of DNA in which each nucleotide consists of a cloud of electrons around a central positive nucleus. This negative cloud can move relative to the nucleus, creating a dipole. And the movement of the cloud back and forth is a harmonic oscillator.
When the nucleotides bond to form a base, these clouds must oscillate in opposite directions to ensure the stability of the structure.
Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix. Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled, just like other quantum objects. To start with, Rieper and co imagine the helix without any effect from outside heat. "Clearly the chain of coupled harmonic oscillators is entangled at zero temperature," they say. They then go on to show that the entanglement can also exist at room temperature.
That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.
That would be of little significance if it had no overall effect on the helix. But the model developed by Rieper and co suggests that the effect is profound.
Although each nucleotide in a base pair is oscillating in opposite directions, this occurs as a superposition of states, so that the overall movement of the helix is zero. In a purely classical model, however, this cannot happen, in which case the helix would vibrate and shake itself apart.
So in this sense, these quantum effects are responsible for holding DNA together.
The question of course is how to prove this. They say that one line of evidence is that a purely classical analysis of the energy required to hold DNA together does not add up. However, their quantum model plugs the gap. That's interesting but they'll need to come up with something experimentally convincing to persuade biologists of these ideas.
One tantalising suggestion at the end of their paper is that the entanglement may have an influence on the way that information is read off a strand of DNA and that it may be possible to exploit this experimentally. Just how, they don't say.
Speculative but potentially explosive work.
Ref: arxiv.org/abs/1006.4053: The Relevance Of Continuous Variable Entanglement In DNA