Wednesday, May 6, 2009

PhD pages on DNA base-stacking interactions

I was recently approached by Dr. Victor Zhurkin, a well-known computational biologist at the NIH, asking for some details about the sigma/pi charges used in my JMB publication on DNA base-stacking interactions. It was a paper based on my PhD thesis with Dr. Chris Hunter at Sheffield University. Ever since its publication a decade ago, this is the first time I have been asked questions about it (Dr. Hunter was the corresponding author).

This request was both a nice surprise, and at the same time, a challenge since I do not have the original files at hand. Over the years, I have never been a (big) fan of energy calculations. So unlike my SCHNAaP/SCHNArP papers for which I do keep the original source code and data files to reproduce the results published back-to-back in JMB, I do not have direct access to the original files for del Re (sigma) and Huckel (pi) charges used in my base-stacking interactions paper. I did find the HP 60 meter Data Cartridge I took from Sheffield which should contain all the details of my PhD work, but it is hard these days to find a machine to read it. At the meantime, I found a hard copy of my PhD thesis, which contains further details. So I used my digital camera, took pictures of 11 pages that are relevant, and made it available online in a tarball file.

The key feature of my DNA-stacking interaction work is the distributed charge model for the aromatic bases. This charge model was based on the seminal work of "The Nature of Pi-Pi Interactions" by Hunter and Sanders published in JACS in 1990. This simple distributed charge model catches the aromaticity concept nicely, making it easily understandable to bench chemists and biologist. As I have just checked it out, this 1990 JACS paper has been cited 2280+ times, according to Web of Science. My 1997 JMB DNA-stacking interaction paper has received 78 citations -- certainly not comparable to the JACS paper, but overall not bad at all. (Google Scholar gives much smaller citation numbers, for unknown reasons).

Looking back, the DNA base-stacking project was the main theme of my PhD work. It was the close collaboration with El Hassan in Dr. Chris Calladine's group at Cambridge University that introduced me to the elegant CEHS scheme, and based on which I created the SCHNAaP/SCHNArP software programs. The mathematical rigor of the CEHS scheme, i.e., its complete reversibility with the analysis/rebuilding of dinucleotides, put my theoretical energy calculation on a solid basis for comparison with oligonucleotide X-ray crystal structures. The "detour" to SCHNAaP/SCHNArP reflected my personal interest, and was the starting point that later led to the resolution of the long-standing discrepancies among nucleic acid conformational analyses, the establishment of standard base reference frame, and the creation of the now popular 3DNA software package.


  1. I have been visiting various blogs for my term papers writing research. I have found your blog to be quite useful. Keep updating your blog with valuable information... Regards

  2. Thank you for your encouragement! I am glad that you have found my blog posts useful to your "term papers writing research". Recently, I've been thinking about writing a post on my one year of blogging (time is really flying), and your comment provides me another incentive to keep blogging!

    Keep visiting back and make comments -- as with 3DNA questions (or even more so), I will strive to be responsive.


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