Saturday, February 21, 2009

Charge Migration in DNA

From the last few days, I have been studying the charge migration in DNA. My request to the biologists is that please don’t hate me for trespassing in your field. My curiosity is in understanding the DNA structure from the electronic point of view. Over the years in the scientific literature, there have been reports of DNA acting as quantum molecular wires for transmitting charge, the DNA nano-devices and what not! I guess, all these announcements by my fellow researchers are interesting enough for me to get excited over this new field. However, the reason for my curiosity in DNA Charge Migration is something else. Recently, I was chatting with the mysterious girl, oh yeah, she is talking with me now. We talked about some biotechnology stuff related to genetics, the recent discoveries etc. I know, you must be thinking, what sort of jerk Abu is. Did he do friendship with mysterious girl for discussing genetics? Guys, I have rule in my life, everything that I shall do, should be related to science. I can’t waste time on ordinary stuff. I feel the mysterious girl indirectly took me into a new world of Genetics. There is so much to discover, so much to think and so much to contribute to the humanity in the field of genetics. Well, I can talk about all other non-sense with her, do some good time pass and call it as “attitude”. But somehow I can’t digest it, there are millions of people wasting time in doing time-pass, I am not one among those millions. Anyhow, let me explain you now about charge migration in DNA.

For my traditional electronics and computer science oriented readers, I would first like to give some basic knowledge about DNA. Deoxyribonucleic Acid (DNA) is a big molecule that stores the genetic information in the cells. The chemistry behind the DNA is that it consists of three major components, a heterocyclic base, a deoxyribose sugar (pentose) and a phosphate (phosphoric acid). The sugar molecules and the phosphate molecules form the backbone of the DNA Structure. I am sure you must have seen the Double helix structure of DNA in many movies, cover pages of bio-related books, etc, if not just type DNA in the Live Search, you shall find it. The heterocyclic base consists of four different types of bases namely, Guanine (G), Adenine (A), Cytosine (C) and Thymine (T), famously referred as AGCT sequence. A and G are purine derivatives and C and T are pyrimidine derivatives. I really don’t know what this purine and pyrimidine derivatives are, my speculation is that they belong to some class of organic chemistry. Now, comes the coolest part of DNA, the framework that connects the different heterocyclic bases is hydrogen bonding. Wow, it’s been a long time since I studied hydrogen bonding, believe me it’s an interesting thing to read. I think I am re-invoking my lost love feelings towards chemistry. To the people who don’t know my connection with chemistry, it’s my favorite subject, the only subject I loved. Oh God, I need to learn how to resist myself from thinking about love, now-a-days I am thinking about lot of philosophical stuff. I think scientists are very romantic at their heart; it’s just that they allow the brain to take the control over their lives. Don’t invoke my feelings baby, I am a die hard lover! … Aaaah! … Let me drag myself back to DNA.

The coolest thing about Hydrogen bonding in DNA is that, it can occur only between G-C and A-T. So, that’s the reason you have DNA sequences like GC, AT, GG, AA, CC, and TT but not AG or TC. Understanding the DNA sequences is again an interesting piece of study. Long back, I did some work on DNA sequences at Pentagram research center under Prof. E. G. Rajan. I was involved in developing a MATLAB program for application of Rapid transforms for DNA sequences. Somehow, the work didn’t turn out to be phenomenal, so I left it. I think Rajan Sir will be very angry with me regarding that work. Well, I hope he will glad to know that I am back to genetics with study of Charge Migration in DNA

Now, coming to actual thing, charge migration in DNA refers to transfer of electric charge along the sequence of DNA i.e. the sequence of A, G, C and T. Due to radioactive radiations or through external charge supplies, a additional charge might get added to the DNA. It is important to study this field from the biological damage point of view. However, the recent studies have reveal possibility of nano-technological devices can be framed using the charge migration concept of DNA. Basing on the type of sequence, a DNA can behave as semiconductor, insulator or conductor. The ionization energies of different heterocyclic bases are different. If you go down at sub-atomic level, the charge migration in DNA can be derived from the framework of quantum mechanics. I guess, I should be dancing now, the reason, yes, the Quantum mechanics. Controlling my excitement, the charge migration occurs through electronic transitions among states near the chemical potential. This charge transfer characteristics can be determined through the properties of highest occupied molecular states (HOMO) and the lowest un-occupied molecular states (LUMO), referring to hole transfer and electron transfer. HOMO and LUMO, got to give credit for the creativity of the scientist who framed these acronyms.

Well, don’t you think this much info is enough for a single blog article? I don’t want to go too deep into the subject because of two reasons. Reason one, I don’t want to scare you and reason two, even I don’t understand further than this. Actually, beyond this is full of quantum mechanics with lots of lovely equations. Long back, I told this phrase to one of my friend; just feel like repeating over here, “the beauty surrounding us is due to the symmetry in the equations, which we often neglect”. Try to think deeply over that phrase about the context it was quoted.

November 28 1:37 AM


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