Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis

Long, D. D., Grosse, I., Marx, K. A. (July 2004) Coding and non-coding DNA thermal stability differences in eukaryotes studied by melting simulation, base shuffling and DNA nearest neighbor frequency analysis. Biophysical Chemistry, 110 (1-2). pp. 25-38. ISSN 0301-4622

URL: http://www.sciencedirect.com/science/article/pii/S...
DOI: 10.1016/j.bpc.2004.01.001

Abstract

The melting of the coding and non-coding classes of natural DNA sequences was investigated using a program, MELTSIM, which simulates DNA melting based upon an empirically parameterized nearest neighbor thermodynamic model. We calculated T-m results of 8144 natural sequences from 28 eukaryotic organisms of varying F-GC (mole fraction of G and C) and of 3775 coding and 3297 non-coding sequences derived from those natural sequences. These data demonstrated that the T. vs. F-GC relationships in coding and non-coding DNAs are both linear but have a statistically significant difference (6.6%) in their slopes. These relationships are significantly different from the T-m vs. F-GC relationship embodied in the classical Marmur-Schildkraut-Doty (MSD) equation for the intact long natural sequences. By analyzing the simulation results from various base shufflings of the original DNAs and the average nearest neighbor frequencies of those natural sequences across the F-GC range, we showed that these differences in the T-m vs. F-GC relationships are largely a direct result of systematic F-GC-dependent biases in nearest neighbor frequencies for those two different DNA classes. Those differences in the T. vs. F-GC relationships and biases in nearest neighbor frequencies also appear between the sequences from multicellular and unicellular organisms in the same coding or non-coding classes, albeit of smaller but significant magnitudes. (C) 2004 Elsevier B.V. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: DNA melting simulation Exon-intron sequence shuffling nearest neighbor frequencies melting temperature DEOXYRIBONUCLEIC ACIDS deoxyribonucleic acids SEQUENCE PROPERTIES sequence properties ENZYMATIC SYNTHESIS eyzymatic synthesis DENATURATION denaturation MELTSIM meltsim FAMILIES families PROGRAM program CURVES curves GENOME genome EXONS exons
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > computers > computer software
CSHL Authors:
Depositing User: CSHL Librarian
Date: July 2004
Date Deposited: 31 Jan 2012 21:01
Last Modified: 31 Jan 2012 21:01
URI: http://repository.cshl.edu/id/eprint/22427

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