Structure of B-DNA with Cations Tethered in the Major Groove

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• 作者：Tinoush Moulaei ; Tatsuya Maehigashi ; George T. Lountos ; Seiji Komeda ; Derrick Watkins ; Michael P. Stone ; Luis A. Marky ; Jian-sen Li ; Barry Gold ; and Loren Dean Williams
• 刊名：Biochemistry
• 出版年：2005
• 出版时间：May 24, 2005
• 年：2005
• 卷：44
• 期：20
• 页码：7458 - 7468
• 全文大小：1712K
• 年卷期：v.44,no.20(May 24, 2005)
• ISSN：1520-4995

文摘

Here, we describe the 1.6-Å X-ray structure of the DDD (Dickerson-Drew dodecamer), whichhas been covalently modified by the tethering of four cationic charges. This modified version of theDDD, called here the DDD⁴⁺, is composed of [d(CGCGAAXXCGCG)]₂, where X is effectively a thymineresidue linked at the 5 position to an n-propyl-amine. The structure was determined from crystals soakedwith thallium(I), which has been broadly used as a mimic of K⁺ in X-ray diffraction experiments aimedat determining positions of cations adjacent to nucleic acids. Three of the tethered cations are directedradially out from the DNA. The radially directed tethered cations do not appear to induce structural changesor to displace counterions. One of the tethered cations is directed in the 3' direction, toward a phosphategroup near one end of the duplex. This tethered cation appears to interact electrostatically with the DNA.This interaction is accompanied by changes in helical parameters rise, roll, and twist and by a displacementof the backbone relative to a control oligonucleotide. In addition, these interactions appear to be associatedwith displacement of counterions from the major groove of the DNA.