Effect of G-Tract Length on the Topology and Stability of Intramolecular DNA Quadruplexes

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• 作者：Phillip A. Rachwal ; Tom Brown ; Keith R. Fox
• 刊名：Biochemistry
• 出版年：2007
• 出版时间：March 20, 2007
• 年：2007
• 卷：46
• 期：11
• 页码：3036 - 3044
• 全文大小：248K
• 年卷期：v.46,no.11(March 20, 2007)
• ISSN：1520-4995

文摘

G-Rich sequences are known to form four-stranded structures that are based on stacks ofG-quartets, and sequences with the potential to adopt these structures are common in eukaryotic genomes.However, there are few rules for predicting the relative stability of folded complexes that are adopted bysequences with different-length G-tracts or variable-length linkers between them. We have used thermalmelting, circular dichroism, and gel electrophoresis to examine the topology and stability of intramolecularG-quadruplexes that are formed by sequences of the type d(G_nT)₄ and d(G_nT₂)₄ (n = 3-7) in the presenceof varying concentrations of sodium and potassium. In the presence of potassium or sodium, d(G_nT)₄sequences form intramolecular parallel complexes with the following order of stability: n = 3 > n = 7> n = 6 > n = 5 > n = 4. d(G₃T)₄ is anomalously stable. In contrast, the stability of d(G_nT₂)₄ increaseswith the length of the G-tract (n = 7 > n = 6 > n = 5 > n = 4 > n = 3). The CD spectra for d(G_nT)₄in the presence of potassium exhibit positive peaks around 260 nm, consistent with the formation ofparallel topologies. These peaks are retained in sodium-containing buffers, but when n = 4, 5, or 6, CDmaxima are observed around 290 nm, suggesting that these sequences [especially d(G₅T)₄] have someantiparallel characteristics. d(G₃T₂)₄ adopts a parallel conformation in the presence of both sodium andpotassium, while all the other d(G_nT₂)₄ complexes exhibit predominantly antiparallel features. The propertiesof these complexes are also affected by the rate of annealing, and faster rates favor parallel complexes.