Selection for Thermodynamically Stable DNA Tetraloops Using Temperature Gradient Gel Electrophoresis Reveals Four Motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc)

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• 作者：Mariko Nakano ; Ellen M. Moody ; Jing Liang ; and Philip C. Bevilacqua
• 刊名：Biochemistry
• 出版年：2002
• 出版时间：December 3, 2002
• 年：2002
• 卷：41
• 期：48
• 页码：14281 - 14292
• 全文大小：217K
• 年卷期：v.41,no.48(December 3, 2002)
• ISSN：1520-4995

文摘

Hairpins play important roles in the function of DNA, forming cruciforms and affectingprocesses such as replication and recombination. Temperature gradient gel electrophoresis (TGGE) andin vitro selection have been used to isolate thermodynamically stable DNA hairpins from a six-nucleotiderandom library. The TGGE-selection process was optimized such that known stable DNA tetraloopswere recovered, and the selection appears to be exhaustive. In the selection, four families of exceptionallystable DNA loops were identified: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc). (Lowercasedenotes the closing base pair; N = A, C, G, or T; and B = C, G, or T.) It appears that the known stabled(cGNAg) triloop motif can be embedded into a tetraloop, with the extra nucleotide inserted into eitherthe middle of the loop, d(cGNNAg), or at the 3'-end of the loop, d(cGNABg). For d(cGNNAg) andd(cGNABg), a CG closing base pair was strongly preferred over a GC, with G₃₇ 2 kcal/mol.Members of the two families, d(cCNNGg) and d(gCNNGc), are similar in stability. The loop sequencesand closing base pairs identified for exceptionally stable DNA tetraloops show many similarities to thoseknown for exceptionally stable RNA tetraloops. These data provide an expanded set of thermodynamicrules for the formation of tetraloops in DNA.