Thermodynamic parameters for DNA sequences with dangling ends

碱基对 DNA 复式(建筑) 核糖核酸 生物 核苷酸 遗传学 基因
作者
Salvatore Bommarito,Nicolas Peyret,John SantaLucia
出处
期刊:Nucleic Acids Research [Oxford University Press]
卷期号:28 (9): 1929-1934 被引量:336
标识
DOI:10.1093/nar/28.9.1929
摘要

The thermodynamic contributions to duplex formation of all 32 possible single-nucleotide dangling ends on a Watson–Crick pair are reported. In most instances, dangling ends are stabilizing with free energy contributions ranging from +0.48 () to –0.96 kcal/mol (). In comparison, Watson–Crick nearest-neighbor increments range from –0.58 (TA/AT) to –2.24 (GC/CG) kcal/mol. Hence, in some cases, a dangling end contributes as much to duplex stability as a Watson–Crick A-T base pair. The implications of these results for DNA probe design are discussed. Analysis of the sequence dependence of dangling-end stabilities show that the nature of the closing base pair largely determines the stabilization. For a given closing base pair, however, adenine dangling ends are always more or equally as stable as the other dangling nucleotides. Moreover, 5′ dangling ends are more or equally as stabilizing as their 3′ counterparts. Comparison of DNA with RNA dangling-end motifs shows that DNA motifs with 5′ dangling ends contribute to stability equally or more than their RNA counterparts. Conversely, RNA 3′ dangling ends contribute to stability equally or more than their DNA counterparts. This data set has been incorporated into a DNA secondary structure prediction algorithm (DNA MFOLD) (http://mfold2.wustl.edu/~mfold/dna/form1.cgi ) as well as a DNA hybridization prediction algorithm (HyT her™) (http://jsl1.chem.wayne.edu/Hyther/hythermenu.html ).
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