Quantum mechanics and DNA and RNA

[eehiram]

Since nucleotides are molecules, how does quantum mechanics pertain to DNA and RNA? I have heard there is the study of stability of the DNA and RNA molecules, for instance. What does DNA and RNA actually look like -- as opposed to textbook drawings which illustrate spherical balls attached to a double helix?

o| Hiram

 

[Revenged]

RNA is normally single stranded btw... and there are many types - e.g. mRNA, tRNA and rRNA...

 

[eehiram]

Thanks for the response, Revenged

Yes, RNA is usually single-stranded, and mRNA carries protein building instructions; rRNA is a major component of ribosomes; and tRNA delivers amino acids one by one to a ribosome in the order specified by mRNA.

Can anyone suggest a good image of what it looks like? Is this a good model: http://sbchem.sunysb.edu/msl/DNA.html" ?

o| Hiram

 

[Moridin]

Well, if you are looking for the actual chemical structure of DNA and RNA, http://www.blc.arizona.edu/Molecular_Graphics/DNA_Structure/DNA_Tutorial.HTML could provide some level of understanding.

 

[siddharth]

Since nucleotides are molecules, how does quantum mechanics pertain to DNA and RNA? I have heard there is the study of stability of the DNA and RNA molecules, for instance.

Quantum mechanics determines the structure and shape of all molecules, including DNA and RNA. You might find these set of articles on http://www.britannica.com/nobelprize/article-43417" useful.

What does DNA and RNA actually look like -- as opposed to textbook drawings which illustrate spherical balls attached to a double helix?

http://img333.imageshack.us/my.php?image=dnaex6.jpg - DNA through an electron microscope (From Wasserman, Dungan, and Cozzarelli, 1985)

EDIT: Link fixed

 

[eehiram]

thanks for the links siddharth

However, the second link, which is what I meant, was blocked. "Sorry we don't allow offsite image links."

 

[limarodessa]

Bieberich Erhard. Probing quantum coherence in a biological system by means of DNA amplification. // Biosystems.- 2000. – Volume 57, Issue 2. – pp. 109-124.

Cooper W. Grant. Necessity of Quantum Coherence to Account for the Spectrum of Time-Dependent Mutations Exhibited by Bacteriophage T4. - http://www.springerlink.com/content/k548422512457312/

Dipankar Home and Rajagopal Chattopadhyaya DNA Molecular Cousin of Schrödinger's Cat: A Curious Example of Quantum Measurement http://prl.aps.org/abstract/PRL/v76/i16/p2836_1

Dipankar Home and Rajagopal Chattopadhyaya Determination of When an Outcome is Actualised in a Quantum Measurement using DNA - Photolyase System
http://arxiv.org/abs/quant-ph/9903036

Karafyllidis Ioannis G. Quantum Mechanical Model for InformationTransfer from DNA to Protein. - http://arxiv.org/ftp/arxiv/papers/0801/0801.2882.pdf

Mayburov S. Quantum Effects and Genetic Code: Dynamics and Information Transfer in DNA Replication. - http://arxiv.org/ftp/q-bio/papers/0611/0611009.pdf

McFadden Johnjoe. A quantum mechanical model of adaptive mutation./ Johnjoe McFadden and Jim Al-Khalili.// Biosystems. – 1999. – Volume 50, Issue 3, June. – Pages 203-211.

Mirzaee, M.; Chian, M.F. DNA and quantum theory. // Quantum, Nano, and Micro Technologies. – 2007. - Volume , Issue , 2-6. - Page(s):4 – 4.

Nelayev Vladislav V., Dovzhik Krishna N., Lyskouski Viacheslav. Quantum Effects in Biomolecular Structures. - http://www.ipme.ru/e-journals/RAMS/no_12009/nelayev.pdf

Ogryzko Vasily V. A quantum-theoretical approach the phenomenon of directed mutations in bacteria. - http://arxiv.org/ftp/q-bio/papers/0701/0701050.pdf

Ogryzko Vasily V. Erwin Schroedinger, Francis Crick and epigenetic stability. - http://www.biology-direct.com/content/3/1/15

Ogryzko Vasily V. On two quantum approaches to adaptive mutations in bacteria. - http://arxiv.org/ftp/arxiv/papers/0805/0805.4316.pdf

Ogryzko Vasily V. Origin of adaptive mutants: a quantum measurement ? - http://arxiv.org/ftp/arxiv/papers/0704/0704.0034.pdf

Ogryzko Vasily V. Quantum approach to adaptive mutations. Didactic introduction. - http://arxiv.org/ftp/arxiv/papers/0802/0802.2271.pdf

Ogryzko Vasily V. Quantum information processing at the cellular level. Euclidean approach. - http://arxiv.org/abs/0906.4279

Patel Apoorva. Quantum Algorithms and the Genetic Code. - http://xxx.lanl.gov/abs/quant-ph/0002037

Patel Apoorva. Testing quantum dynamics in genetic information processing. - http://xxx.lanl.gov/PS_cache/quant-ph/pdf/0102/0102034v2.pdf

Patel Apoorva. Why genetic information processing could have a quantum basis. - http://xxx.lanl.gov/PS_cache/quant-ph/pdf/0105/0105001v2.pdf

Sugawara Hirotaka. Quantum Theory of DNA. - http://ptp.ipap.jp/link?PTPS/164/17/

York D. M., Lee, T. S. and Yang W. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronics structuremethods. // Physical Review – 1998. – vol. 80. – pp. 5011-5014.

York Darrin M., Khandogin Jana. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. - http://cat.inist.fr/?aModele=afficheN&cpsidt=16006968




An algorithm for the study of DNA sequence evolution based on the genetic code
Biosystems
Volume 77, Issues 1-3, November 2004, Pages 11-23
G. Ch. Sirakoulis, I. Karafyllidis, R. Sandaltzopoulos, Ph. Tsalides and A. Thanailakis

Comment on Book Review of `Quantum Evolution' (Johnjoe McFadden) by Mathew J. Donald
Authors: Johnjoe McFadden, Jim Al-Khalili
http://arxiv.org/abs/quant-ph/0110083

 

[sylas]

That's a very interesting collection of links, limarodessa.

The whole association of quantum mechanics with biology is tricky, because the quality of the published work is so variable. On the one hand, quantum mechanics is fundamental to chemistry of all kinds, and the chemistry involved in biology can get very complicated. On the other hand, there is a tendency in some quarters to use poorly understood quantum mechanics to support rather speculative ideas with little real scientific merit, especially with reference to living processes.

To put my own biases front and center... I think the most useful work relating quantum mechanics and biology is hard physics, working out the details of reactions and interactions. There is an important role for quantum mechanics here. But I think the people who appeal to quantum mechanics to explain consciousness or evolution or life vs non-life are mostly kidding themselves.

I've tried to have a quick look through this list of references to try and sort out what kinds of ideas are being presented here. This response is not authoritative! I have not read the references in detail and I am not previously familiar with them. But I'm curious to see what they entail and so I did look them up and tried to have a really quick estimate of what they are about. I'd be very interested to hear of more comment from any biologists in the house, especially if they have heard of any of this work.

The references seem to be a rather mixed bag, some of which set of all kinds of red flags for me, and others of which seem quite sensible. I've quoted your references, but have rearranged two of them to keep related articles together. I've noted the two moves in my own comments. Here we go...

Bieberich Erhard. Probing quantum coherence in a biological system by means of DNA amplification. // Biosystems.- 2000. – Volume 57, Issue 2. – pp. 109-124.

This looks to be an interesting consequence of quantum mechanical effects in the chemistry of DNA amplification by polymerase chain reaction, resulting in measurable changes in thermodynamics and binding energies.

Cooper W. Grant. Necessity of Quantum Coherence to Account for the Spectrum of Time-Dependent Mutations Exhibited by Bacteriophage T4. - http://www.springerlink.com/content/k548422512457312/

This one might be a bit more controversial. There's a report at thescientist.com, where various biologists express guarded interested and some skepticism. See http://www.the-scientist.com/blog/display/56267/. The paper first appeared online only a couple of months ago.

Dipankar Home and Rajagopal Chattopadhyaya DNA Molecular Cousin of Schrödinger's Cat: A Curious Example of Quantum Measurement http://prl.aps.org/abstract/PRL/v76/i16/p2836_1
Dipankar Home and Rajagopal Chattopadhyaya Determination of When an Outcome is Actualised in a Quantum Measurement using DNA - Photolyase System http://arxiv.org/abs/quant-ph/9903036

The first is a much older paper, from 1998, in Phys. Rev. Lett. 76, 2836–2839. I'm skeptical of this one: it attracted two critical comments in reply. Here's one: http://www.lebedev.ru/intranet/publications/journals/prl/prl_v80/pdfs/vol_80/iss_6/1348_1.pdf by Philip Pearle and Euan Squires, in Phys. Rev. Lett. 80(6), page 1348.

The second loops pretty similar, and apparently not formally published that I can see. My initial reaction to these two is strong skepticism, particularly given the critical published comments.

Karafyllidis Ioannis G. Quantum Mechanical Model for InformationTransfer from DNA to Protein. - http://arxiv.org/ftp/arxiv/papers/0801/0801.2882.pdf
[...]
An algorithm for the study of DNA sequence evolution based on the genetic code
Biosystems
Volume 77, Issues 1-3, November 2004, Pages 11-23
G. Ch. Sirakoulis, I. Karafyllidis, R. Sandaltzopoulos, Ph. Tsalides and A. Thanailakis

I've brought these two together, as they are close related. Work by electrical engineers with an interest in biology, looking at some interesting and sensible possibilities for how quantum effects may impact the likelihood of different mutations.

Mayburov S. Quantum Effects and Genetic Code: Dynamics and Information Transfer in DNA Replication. - http://arxiv.org/ftp/q-bio/papers/0611/0611009.pdf

This is marked as having been submitted to J. Theor. Biology; but it does not seem to have been accepted, as far as I can tell.

Mirzaee, M.; Chian, M.F. DNA and quantum theory. // Quantum, Nano, and Micro Technologies. – 2007. - Volume , Issue , 2-6. - Page(s):4 – 4.

Can't find out much about this conference paper.

Nelayev Vladislav V., Dovzhik Krishna N., Lyskouski Viacheslav. Quantum Effects in Biomolecular Structures. - http://www.ipme.ru/e-journals/RAMS/no_12009/nelayev.pdf

I can't access the website at present.

Ogryzko Vasily V. A quantum-theoretical approach the phenomenon of directed mutations in bacteria. - http://arxiv.org/ftp/q-bio/papers/0701/0701050.pdf
Ogryzko Vasily V. Erwin Schroedinger, Francis Crick and epigenetic stability. - http://www.biology-direct.com/content/3/1/15
Ogryzko Vasily V. On two quantum approaches to adaptive mutations in bacteria. - http://arxiv.org/ftp/arxiv/papers/0805/0805.4316.pdf
Ogryzko Vasily V. Origin of adaptive mutants: a quantum measurement ? - http://arxiv.org/ftp/arxiv/papers/0704/0704.0034.pdf
Ogryzko Vasily V. Quantum approach to adaptive mutations. Didactic introduction. - http://arxiv.org/ftp/arxiv/papers/0802/0802.2271.pdf
Ogryzko Vasily V. Quantum information processing at the cellular level. Euclidean approach. - http://arxiv.org/abs/0906.4279

The first looks like fairly extreme fringe. The paper is apparently not formally published, and is explicitly marked "hypothesis".
The second is published and open access: a short and fairly high level general essay about possible roles for quantum effects. I'm skeptical.
The third looks far fetched. For example, it seems to propose that a "starving bacterium" is in a particular state understood in quantum mechanical terms. Not published, I think.
The rest are more apparently unpublished papers? In any case, this group sets all kinds of alarm bells ringing for me. I don't know anything about the author. Is anyone else here familiar with this?

Patel Apoorva. Quantum Algorithms and the Genetic Code. - http://xxx.lanl.gov/abs/quant-ph/0002037
Patel Apoorva. Testing quantum dynamics in genetic information processing. - http://xxx.lanl.gov/PS_cache/quant-ph/pdf/0102/0102034v2.pdf
Patel Apoorva. Why genetic information processing could have a quantum basis. - http://xxx.lanl.gov/PS_cache/quant-ph/pdf/0105/0105001v2.pdf

These three papers all look a bit more interesting to me; they seem to look at associations between quantum physics and genetics as information processing. I haven't looked at it closely.

Sugawara Hirotaka. Quantum Theory of DNA. - http://ptp.ipap.jp/link?PTPS/164/17/[/URL]
York D. M., Lee, T. S. and Yang W. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronics structuremethods. // Physical Review – 1998. – vol. 80. – pp. 5011-5014.
York Darrin M., Khandogin Jana. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. - [url=http://cat.inist.fr/?aModele=afficheN&cpsidt=16006968]http://cat.inist.fr/?aModele=afficheN&cpsidt=16006968[/url][/QUOTE]
These three look like conventional hard physics papers, applying quantum mechanics to details of the physical processes with DNA molecules.

[QUOTE]McFadden Johnjoe. A quantum mechanical model of adaptive mutation./ Johnjoe McFadden and Jim Al-Khalili.// Biosystems. – 1999. – Volume 50, Issue 3, June. – Pages 203-211.
[...]
Comment on Book Review of `Quantum Evolution' (Johnjoe McFadden) by Mathew J. Donald
Authors: Johnjoe McFadden, Jim Al-Khalili
[url=http://arxiv.org/abs/quant-ph/0110083]http://arxiv.org/abs/quant-ph/0110083[/url][/QUOTE]
I've moved these two together. This looks very dubious indeed. The choice of citation in the second case is a bit odd. The first is a paper, which is not well regarded by most biologists as far as I can see. But in any case, since that paper McFadden has also written a book about his ideas on quantum evolution. The book was reviewed, and rather than cite the book, or the review, the second reference is for a response to a very critical review of the book.

Better references might be:
[list][*]http://www.surrey.ac.uk/qe/quantumevolution.htm, by Johnjoe McFadden, (HarperCollins, 2000) (Link to the author's site for the book.)
[*][url=http://arxiv.org/abs/quant-ph/0101019]A review of Johnjoe McFadden's book "Quantum Evolution''[/url], by Matthew J. Donald. (Link to arXiv:quant-ph/0101019v1).
[*][url=http://arxiv.org/abs/quant-ph/0110083]Comment on the review[/url] by Johnjoe McFadden. (Link to arXiv:quant-ph/0110083v1, as given in previous post)
[*][PLAIN]http://www.bss.phy.cam.ac.uk/~mjd1014/qevrevr.html[/URL] by Matthew Donald, at his own home page at the Univ of Cambridge, UK.[/list]
I don't know the standing of Matthew Donald either, frankly. But since you cite a response to his review, I thought I'd give the whole exchange.

There is also a very negative review [url=http://www.nature.com/hdy/journal/v85/n2/full/6887651a.html]book review by Arthur Wallace[/url], published in Heredity (2000) 85, page 199.

Cheers -- sylas

 

[ThomasEdison]

To the OP:
Are you looking for evidence that the bizarre nature of quantum chaos might spur a DNA's mutation or miscopy independant of outside environmental factors?

For example:
Quantum particles popping into and out of existence, or tunnelling and other weird behavior and if this can effect a copy error in the DNA code during cell division?

Or put another way if I make no sense above:
Along the same lines that solar radiation is considered a trigger for mutation and evolutionary change, that perhaps what happens at the quantum level (independant of outside factors) that the chaos there can cause mutation also.
So no outside factor is required for a cells mutation because enough random change to a DNA's structure will happen because of the crazy quantum weirdness that all matter undergoes everywhere?

If you mean that then it is something I find interesting and it would be great if this question has been addressed in biology or physics of biology or whichever cross disciplinary field it is within.

Also: Since it was addressed earlier in the thread what RNA is (single stranded). I thought that not only is RNA the primitive ancestor of DNA but it currently plays an important role in the process of folding and unfolding the actual substance of DNA into proteins. Am I probably completely offbase here? This is only an uneducated guess so I could be completely wrong.

 

[x12179x]

Since nucleotides are molecules, how does quantum mechanics pertain to DNA and RNA?

I once did a report on QM and molecular biology, which I can't find now...

Here are a few topics I remember discussing:
*Electron delocalization
*Quantum Tunneling
*Enol-Keto Tautomers
*DNA mutation caused by UV Radiation About how QM specifically relates to the structure/stability of DNA:

Image 1: 2 of the bases that make up DNA (G/T) can switch from enol to keto forms, which affects the shape of the molecule.

Image 2: This influences if it can base pair with C/A respectively, since G/T can only base pair with C/A in its keto form - when the Hydrogen in G/T is bonded to the Nitrogen and available for N-H bonding with C/A.

Image 3: UV radiation can add energy to bases in DNA...maybe making conversions in the G/T base to the enol tautomer so it no longer base pairs with C/A.

Links I quickly found, which may or may not be relevant, since I merely skimmed them to find images to use here:
DNA Nucleotides and Tautomeric Form:
http://www.accessexcellence.org/RC/AB/WYW/wkbooks/SFTS/activity1.php"

What effect can ionizing radiation have on DNA?:
http://www.hss.energy.gov/healthsafety/OHRE/roadmap/achre/intro_9_5.html"

UV Radiation:
http://earthobservatory.nasa.gov/Features/UVB/"

DNA Mutation Puzzle Has Roots in Quantum Physics Weirdness:
http://www.rochester.edu/news/show.php?id=2229"and yes ThomasEdison I find this stuff interesting too! I remember it being difficult finding information when I was writing my report (like physical explanation of tautomers. What exactly is happening to the electrons/hydrogen? QM explanations...) ...or at least it was difficult to find info at a laymen's level, and as Sylas mentioned, you have to weed out those who

use poorly understood quantum mechanics to support rather speculative ideas with little real scientific merit, especially with reference to living processes...the people who appeal to quantum mechanics to explain consciousness or evolution or life vs non-life.

which I ran into when searching for QM relation to biology.

 

[limarodessa]

http://www.nature.com/nature/journal/v463/n7281/abs/nature08811.html

Nature 463, 644-647 (4 February 2010) | doi:10.1038/nature08811; Received 14 July 2009; Accepted 17 December 2009


Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature
Elisabetta Collini1,3,4, Cathy Y. Wong1,3, Krystyna E. Wilk2, Paul M. G. Curmi2, Paul Brumer1 & Gregory D. Scholes1

1.Department of Chemistry, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St George Street, Toronto, Ontario, M5S 3H6 Canada
2.School of Physics and Centre for Applied Medical Research, St Vincent’s Hospital, The University of New South Wales, Sydney, New South Wales 2052, Australia
3.These authors contributed equally to this work.
4.Present address: Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35100, Padova, Italy.
Correspondence to: Gregory D. Scholes1 Correspondence and requests for materials should be addressed to G.D.S. (Email: gscholes@chem.utoronto.ca).


Top of pagePhotosynthesis makes use of sunlight to convert carbon dioxide into useful biomass and is vital for life on Earth. Crucial components for the photosynthetic process are antenna proteins, which absorb light and transmit the resultant excitation energy between molecules to a reaction centre. The efficiency of these electronic energy transfers has inspired much work on antenna proteins isolated from photosynthetic organisms to uncover the basic mechanisms at play1, 2, 3, 4, 5. Intriguingly, recent work has documented6, 7, 8 that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws9 at temperatures up to 180 K. This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures. Here we present two-dimensional photon echo spectroscopy10, 11, 12, 13 measurements on two evolutionarily related light-harvesting proteins isolated from marine cryptophyte algae, which reveal exceptionally long-lasting excitation oscillations with distinct correlations and anti-correlations even at ambient temperature. These observations provide compelling evidence for quantum-coherent sharing of electronic excitation across the 5-nm-wide proteins under biologically relevant conditions, suggesting that distant molecules within the photosynthetic proteins are ‘wired’ together by quantum coherence for more efficient light-harvesting in cryptophyte marine algae.

 

[limarodessa]

Full text:


http://pubs.acs.org/doi/full/10.1021/jz900062f

...In accord with the notion that decoherence is a transition from quantum to classical, localization (or at least partial localization) of wave functions is needed if we wish concepts like “moving excitation” to make sense.
The quantum-coherent energy transfer that is the focus of this Perspective occurs in an intermediate regime where there is a balance between interference among electronic resonances to give coherence and coupling to the environment causing decoherence. Phenomena existing within such a balance are fairly widely known and include, for example, band conduction in semiconductors and high Tc superconductivity...


... Are the excitations at different sites in these biological complexes entangled (in the Einstein−Podolsky−Rosen sense), and if so, how can experiment yield direct evidence for that hypothesis? ...

 

[Eclipsen413]

http://psychedelicadventure.blogspot.com/2010/04/bruce-lipton-new-biology-where-mind.html

this guy pretty much explains it all

 

[alxm]

Okay, well I happen to do quantum chemical studies of biochemical systems. So I'm a "quantum biochemist", but I'm loathe to use that term precisely because there's so much nonsense (ranging from pure nonsense to pseudoscience to bad science to real science) going on under that moniker, and most of which is present in this tread as well.

E.g. "Quantum Evolution" is nonsense IMO. I'm very skeptical that Bieberich's model and experiment are accurate enough to measure what he thinks he's measuring. I don't believe it. On the other hand, Weitao Yang (who I've met) is a giant within quantum chemistry and certainly credible (although his research is on the development of linear-scaling DFT methods, which are applicable to large molecules, not DNA per se).

The question "Is QM significant to biochemistry?" is difficult to answer because it's ill-defined.
All of chemistry is fundamentally based on quantum mechanics. Chemical bonding is a quantum-mechanical phenomenon. So in that sense, QM is definitely significant.
However, if you're wondering whether QM has some 'special' significance to biochemistry, as opposed to all other chemistry, then my answer is a strong no. Biochemistry does not differ in any significant way from other chemical systems, it follows the same rules.

For lack of a better word, the worst of the 'quantum-biochemistry' stuff (i.e. pseudoscience/new-age nonsense) is 'neo-vitalist'. I.e. trying to make the claim that biological molecules are somehow fundamentally different from other ones, due to some vague/unlikely/incorrect quantum-mechanical mechanism. The best of it is legitimate research, but shouldn't be interpreted in any way as support for the former.

Now to be specific, quantum mechanics is vital to understanding:
- Reactions
- Chemical bonding
- Electronic structure
- Absorption and emission of light/radiation
- Electron and energy transfer kinetics (i.e. speeds)

So when you're talking about the absorption of light, or the transfer of electrons or energy, it is obviously a quantum-mechanical process. There is simply no classical theory of this whatsoever. And in the case of energy and electron transfer kinetics, this is even outside the realm of traditional chemistry, as these things could not be studied either theoretically or experimentally until quite recently.

But this is the same for the rest of chemistry as well.

Which is why I take issue with this particular statement (emphasized above):

This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures.

This is overstating the case. I don't think anybody ever said that electron and energy transfer couldn't exist in a quantum superposition, even at room temperature. (they provide no reference, either) We know for a fact that they do in many systems. I'd say it's a an expected, although not necessarily common, occurrence.

I wouldn't ever attempt to view electron transfer between molecules or within macromolecules as a classical process (nor do I see how the Feynman paper they cite supports this). In short; they're portraying their discovery (while interesting) as more unexpected than it actually is.

Quantum coherences in biological systems most certainly do exist; but not at chemical timescales. (picoseconds, not femtoseconds), and most certainly not at biological timescales (microseconds). It does not mean that chemically and physically implausible theories such as molecules existing in a structural superposition are any more plausible.