Capacitor like electronic structures of DNA

DNA Electronics

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Abstract

With negative charges in the double helix, a neutral central core with its known ability to transport charges that can drive biochemical processes, allow DNA molecules to be envisaged as capacitors that can store electrical energy on stand alone basis. The envisaged capacitor like internal electronic structures of DNA allows us to attribute all the performing features of a capacitor to DNA. Early molecules like DNA should have readily usable internally stored energy to evolve into a single celled organism via functions such as self assembly, self replication and directed mutations that require energy to be spent.

Introduction

It is generally assumed that all life forms on the Earth might have evolved from a common ancestor, a single celled organism. Construction of even a single celled organism and biological processes within that organism are extremely complex to have appeared instantaneously. These single celled organisms might have evolved from DNA or such similarly ordered molecules. DNA molecules have the capacity 1,2 to self repair, replicate and mutate within the cell environment or an environment simulated, similar to the cell environment. Can DNA perform any function on its own such as constructing its own cell environment? Obviously DNA needs readily usable energy at its disposal to perform such functions.

DNA Structure

Deoxyribonucleic acid simply known as DNA is of double helical structure of polymer chains composed of 2-deoxyribose sugar joined by phosphate residues. Both these chains are joined by four nucleotides, Adenine [A], Thymine [T], Cytosine [C] and Guanine [G]. A on one chain is double bonded with T on the other chain via hydrogen bonds and similarly G on one chain is triple bonded with C via hydrogen bonds. 2-deoxyribose sugar is five carbon pentose sugar and phosphodiesters bonds are formed 3 between the third and fifth carbon atoms of adjacent sugar rings which are asymmetric and thus impart direction to strands of DNA. Sequences of A-T and G-C pairs that join the double helix form the genetic code or the genetic programs that contain all the information/ instructions required to build the organism. The genetic information flows from DNA to ribose nucleic acid [RNA] to proteins.

Intra DNA electronics

It is reported 4 that double helical DNA can serve as a conduit for efficient charge transport reactions over long distances in vitro. The double helical structure adopted by B- form DNA, where a negatively charged sugar – phosphate back bone surrounds a Pi stacked array of heterocyclic aromatic base pairs, allows it to serve as an efficient medium for long range charge transport 5. This chemistry has now been well established 4 as a property of DNA. The transport of charge along DNA can be rapid and may cause 6 chemical changes at a distance of 200 angstroms.

Pi stacking due to A-T and G-C pairs at the core of DNA is non polar 7 which also mean that the central core of the DNA molecule is neutral and hydrophobic. Being hydrophobic the central core may not only repel water molecules but also may induce some sort of structure 8 similar to ice-1 in the nearest neighbour water molecules. Each A-T and G-C also has a dipole [due to London – Van der Waal forces] which may differ slightly with each other due to structural differences. Further in the given situation of DNA, the charges in the dipoles are likely to be influenced by the negative charge in the back bone structure of the double helix in a way similar to the envisaged 9 polarisation of heavy metal ions near zinc sulphide surface.

It is reported 10 that a positive charge [A hole resulting upon the removal of an electron. semi conductor materials with such positive charges are p-type and n-type semi conductors have electrons to carry charge] is more stable on a G-C base pair than on A-T base pair. It is further 11,12 said that G-C rich DNA shows p-type properties while A-T sequences show n-type properties and it is envisaged that combining such DNA molecules could create logic elements that would be more powerful than any silicon-based device.

Discussion

The negatively charged back bone structure of sugar phosphate double helix as outer circular tube and the Pi stacked non polar core as inner circular conductor, we notice that the DNA has the features of a capacitor. We may visualize each A-T and G-C pair as the neutral, non polar conductor and the two five carbon pentose sugar [2-deoxyribise sugar] molecules attached to the nucleotide pairs on each side as the dielectric and the two polymer chains [2-deoxyribose sugar joined by phosphate residues] as outer circular negatively charged conductor with varying diameter along the length. Such visualization gives us an idea that each segment of DNA containing a nucleotide pair has similar electronic structure to that of a capacitor and these capacitors are connected in parallel along the length of the DNA molecule. Symbolic depiction is shown in figure 1.

Capacitors have the following features: [a] ability to stored electrical energy [b] blocking direct current while allowing alternate current [c] sensitivity to surroundings [d] ability to select a particular frequency from signals of multiple frequencies, that is creation of new information from entropy and [e] to store and process the information, etc.

The physical shape of the DNA molecule such as the width of the minor, major grooves and even the very helical structure might be the result of the mechanical stresses due to electrical repulsions/ attractions within DNA between the electrons in the helix and the dipoles in the central core. It is recently reported that the shape of DNA plays a role in protein –DNA recognition 13.

It must be noted 14, “At physiological pH, it [DNA] will therefore be negatively charged in solution. This charge is partially neutralized by counter ions, such as sodium [Na+], potassium [K+], and magnesium [Mg+]”. Thus under in vivo conditions only a part of the negative charge in the double helix might be available for charging the capacitors inside the DNA molecule and that charge might be the sensory input of the ionic environment adjacent to DNA molecule.

The suggestion that DNA has the features of a capacitor makes it eligible to use its stored electrical energy independent of Adenosine Di Phosphate/ Tri Phosphate chemistry, to perform basic functions such as self repair, replication and directed mutations that is evolution. This coupled with other electronic features 10-12 of DNA might enable it to act as an information processing device too. Such ability is necessary to DNA [or its precursor similar to it] to evolve from a self assembling/ self replicating molecules to a single celled organism.

Closing Remarks

[1] The capacitor like structure at each nucleotide pair might act as a probe that can sense the environment of counter ions of genome just adjacent to the DNA in vivo.

[2] The capacitor like electronic structure of DNA plus G-C rich regions having p-type and A-T rich regions having n-type electronic properties might qualify DNA as an information processing system. Such features are indeed necessary on stand alone basis for DNA [or early molecules similar them] to evolve from molecules to single celled organism with particular reference to the ability required to store/ process the information and the energy to be spent while constructing the cell body with all its physiological functions/ features by executing the genomic programmes.

Acknowledgements

The author is thankful to Dr. D. Ravindranath and Dr. Frantisek Baluska for providing reprints of many of the articles cited here. Special thanks are due to Er. John Britto for his help in preparing the manuscript and the figure 1.

References:

1. George Wald, The origin of life, Molecules to living cells, W.H. Freeman and Company, San Francisco. 1980.
2. Philip C Hanawalt, “Protein Structure and Function: Assembly of Viruses and Ribosomes”, ibid, 1980.
3. http://en.wikipedia.org/wiki/DNA
4. Edward J Merino, Amie K Boal and Jacqueline K Barton, “Biological contexts for DNA charge transport chemistry”, Current Opinion in Chemical Biology, 2008, 12: 229-237.
5. O’ Neill MA, Barton JK: “Sequence-dependant DNA dynamics: the regulator of DNA – mediated charge transport” in charge transfer in DNA: from Mechanism to application. Ed. Wagenknecht HA, Wiley-VHC; 27-75, 2005, Cf [4].
6. Nunez ME, Hall DB, Barton, JK, “Long range oxidative damage to DNA: effects of distance and sequence”. Chem. Biol, 1999, 6: 85-97.
7. Stuart Hameroff, “That’s life! The geometry of Pi electron resonance clouds”, 2007. http://www.quantumconsciousness.org/documents/Hameroff_received-1-05-07.pdf
8. Ernest Grunwald, , “Thermodynamic properties of non polar solutes in water and structure of hydrophobic hydration shells”, J.A.M.Chem.Soc., 1986,Vol.108, No. 19.
9. Sekhar, DMR and Rama Shanker, “Products of Activation and the Floatability of Sphalerite – An Alternate View”, Mineral Processing and Extractive Metallurgy Review, 1990, Vol.7, 19-22.
10. Cees Dekker and Mark Ratner, “Electronic properties of DNA”, Physics World, http://physicsworld.com/cws/article/print/60
11. Vijayender Bhalla, Ram P, Bajpai and Lalit M, Bharadwaj, “DNA electronics”, EMBO reports, 2003, 4, 5, 442-445
12. Lee, H.Y, et al, “Control of electrical conduction in DNA using oxygen hole doping” Appl. Phys. Lett, 2002, 80, 1670-1672.
13. Remo Rohs, et al, “The role of DNA shape in protein – DNA recognition”, nature, 2009, Vol. 461
14. Massimiliano Di Ventra and Michel Zwolak, “DNA Electronics”, Encyclopedia of Nanoscience and Nanotechnology, 2004, Vol. X, 1-19

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