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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Comparison Between the Simulated Melting and the Average Mutual Information of DNA Sequences

The thermal denaturation (melting) of double-stranded DNA is one of the most fundamental and thoroughly investigated properties of nucleic acids. The DNA melting process is at the core of many techniques in biotechnology. We have established that MELTSIM, a nearest neighbor based statistical thermodynamics program for simulating the melting process of DNAs, can give accurate results when compared to experiments for a number of sequences and even whole genomes under different conditions of ionic strength [1-3].

In the present study we use MELTSIM to calculate the melting curves for a range of eukaryotic DNAs with very different (G+C) contents. In all examined cases, we find that the non-coding regions of the DNA sequences melt earlier than the respective coding regions, and the melting of both sequence types correlates with their (G+C) compositions. In addition, we study if the differences in melting temperature between coding and noncoding DNA are entirely attributable to the different G+C content in coding and noncoding DNA, or if there are additional statistical patterns that influence the melting behavior of coding and noncoding DNA.

As our starting point in the search for such statistical patterns we choose the Average Mutual Information (AMI), which quantifies the degree of non-uniformity of codon usage in DNA sequences, and which has been shown to distinguish coding from non-coding DNA sequences in any given species [4, 5]. We present a systematic comparison of the non-G+C-attributable determinants of the melting temperature and the AMI, and we show how this comparison helps us pinpoint the influences of neighbor base pair effects beyond nearest neighbors on the melting temperature of coding and noncoding DNA.

References and Footnotes
  1. Marx, K.A., et al., J. Biomol. Struct. Dyn., 16 (2), 329-39 (1998)
  2. Blake, R.D., et al., Bioinformatics, 15 (5), 370- 75 (1999)
  3. Bizzaro, J.W., et al., Mat. Res. Soc. Symp. Proc., 489, 73-77 (1998)
  4. Grosse, I., et al., Phys. Rev. E, 61, 5624- 9 (2000)
  5. Grosse, I., et al., Pac. Symp. Biocomput., 614-23 (2000)

Dang D. Long , Kenneth A. Marx *, and Ivo Grosseà.

  Center for Intelligent Biomaterials, Department of Chemistry, University of Massachusetts, Lowell, MA 01854 à Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
phone/fax: 978-934-3658/3013, e-mail: Kenneth_Marx@uml.edu