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Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein
Zhou, HJ; Zhang, Y; Ou-Yang, ZC; Lindsay, SM; Feng, XZ; Balagurumoorthy, P; Harrington, RE; Harrington, RE , Arizona State Univ, Dept Microbiol, Tempe, AZ 85287 USA.
2001
发表期刊JOURNAL OF MOLECULAR BIOLOGY
ISSN0022-2836
卷号306期号:2页码:227-238
摘要The tuner-suppressor activity of p53 is closely related to its DNA-binding properties. It binds a number of DNA response-elements and it is likely that these share a common structural feature. Here, we present a new, general method to determine the absolute twist of flexible DNA promoter sequences based on direct imaging of the topology of microcircles containing the sequences. We have used magnetically driven dynamic force microscopy ("MacMode" AFM) to observe, in solution, the conformation of 168 base-pair DNA microcircles, each containing four equally spaced copies of the waf1/cip1/p21 p53 response-element. Analysis of the images showed that the microcircles are markedly puckered with a small excess of negatively writhed molecules. The average measured values of writhe are 0.109 +/- 0.013 (for 60 positively writhed molecules) and -0.098 +/- 0.011 (for 65 negatively writhed molecules). These values lead directly to a difference in Linking number for the positively and negatively writhed molecules prior to ligation, from which we derive a twist mismatch of 178 degrees (overtwist). This is 44.5 degrees for each 42-mer precursor containing a single waf1/cip1/p21 p53 response-element, in good agreement with the range of values deduced by indirect biochemical techniques. The two values of writhe may also be used to determine the ratio of the bending (B) to twisting (C) rigidity, yielding B/C = 0.23. This is about one-third of the value for long, random-sequence DNA, suggesting that the waf1/cip1/p21 p53 response-element is extremely flexible, a result that is also consistent with indirect biochemical experiments. These results support the idea, proposed by us earlier, that torsional stress may play a role in the regulation of p53 binding through modulation of twist at the binding site. (C) 2001 Academic Press.
部门归属Arizona State Univ, Dept Microbiol, Tempe, AZ 85287 USA; Chinese Acad Sci, Inst Theoret Phys, Beijing 100080, Peoples R China; Arizona State Univ, Dept Phys & Astron, Tempe, AZ 85287 USA
关键词Binding Domain Peptides Supercoiled Dna Gel-electrophoresis Torsional Rigidity Crystal-structure Core Domain Curved Dna Sequence Recognition Elasticity
学科领域Physics
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收录类别SCI
WOS记录号WOS:000167192400008
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被引频次:12[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/12811
专题理论物理所1978-2010年知识产出
通讯作者Harrington, RE , Arizona State Univ, Dept Microbiol, Tempe, AZ 85287 USA.
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Zhou, HJ,Zhang, Y,Ou-Yang, ZC,et al. Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein[J]. JOURNAL OF MOLECULAR BIOLOGY,2001,306(2):227-238.
APA Zhou, HJ.,Zhang, Y.,Ou-Yang, ZC.,Lindsay, SM.,Feng, XZ.,...&Harrington, RE , Arizona State Univ, Dept Microbiol, Tempe, AZ 85287 USA..(2001).Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein.JOURNAL OF MOLECULAR BIOLOGY,306(2),227-238.
MLA Zhou, HJ,et al."Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein".JOURNAL OF MOLECULAR BIOLOGY 306.2(2001):227-238.
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