The Influence of Sequence Context and Length on the Kinetics of DNA Duplex Formation from Complementary Hairpins Possessing (CNG) Repeats

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• 作者：Anthony M. Paiva and Richard D. Sheardy
• 刊名：Journal of the American Chemical Society
• 出版年：2005
• 出版时间：April 20, 2005
• 年：2005
• 卷：127
• 期：15
• 页码：5581 - 5585
• 全文大小：105K
• 年卷期：v.127,no.15(April 20, 2005)
• ISSN：1520-5126

文摘

The formation of unusual structures during DNA replication has been invoked for gene expansionin genomes possessing triplet repeat sequences, CNG, where N = A, C, G, or T. In particular, it has beensuggested that the daughter strand of the leading strand partially dissociates from the parent strand andforms a hairpin. The equilibrium between the fully duplexed parent:daugter species and the parent:hairpinspecies is dependent upon their relative stabilities and the rates of reannealing of the daughter strandback to the parent. These stabilities and rates are ultimately influenced by the sequence context of theDNA and its length. Previous work has demonstrated that longer strands are more stable than shorterstrands and that the identity of N also influences the thermal stability [Paiva, A. M.; Sheardy, R. D.Biochemistry 2004, 43, 14218-14227]. Here, we show that the rate of duplex formation from complementaryhairpins is also sequence context and length dependent. In particular, longer duplexes have higher activationenergies than shorter duplexes of the same sequence context. Further, [(CCG):(GGC)] duplexes havelower activation energies than corresponding [(CAG):(GTC)] duplexes of the same length. Hence, hairpinsformed from long CNG sequences are more thermodynamically stable and have slower kinetics forreannealing to their complement than shorter analogues. Gene expansion can now be explained in termsof thermodynamics and kinetics.