DNA在溶液和染色质中每圈有多少碱基对？一些理论计算。
How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations.
作者信息
Levitt M
出版信息
Proc Natl Acad Sci U S A. 1978 Feb;75(2):640-4. doi: 10.1073/pnas.75.2.640.
Abstract
Calculations on a 20-base pair segment of DNA double helix using empirical energy functions show that DNA can be bent smoothly and uniformly into a superhelix with a small enough radius (45 A) to fit the dimensions of chromatin. The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn. This result, which has a simple physical interpretation, explains the pattern of nuclease cuts and the linkage number changes observed for DNA arranged in chromatin.
摘要
使用经验能量函数对一段20个碱基对的DNA双螺旋片段进行计算表明，DNA能够平滑且均匀地弯曲成半径足够小（45埃）的超螺旋，以适应染色质的尺寸。能量随碱基对围绕螺旋轴扭转的变化表明，溶液中自由的直链DNA每圈约有10.5个碱基对时最稳定，而不是像在固态中观察到的那样为10个碱基对，而染色质中的超螺旋DNA每圈约有10个碱基对时最稳定。这一结果具有简单的物理解释，解释了染色质中DNA的核酸酶切割模式和观察到的连接数变化。
相似文献
1
How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations.DNA在溶液和染色质中每圈有多少碱基对？一些理论计算。
Proc Natl Acad Sci U S A. 1978 Feb;75(2):640-4. doi: 10.1073/pnas.75.2.640.
2
How many base-pairs per turn does DNA have in solution and in chromatin? An answer from wide-angle X-ray scattering.在溶液和染色质中，DNA每圈有多少碱基对？来自广角X射线散射的答案。
Biomed Biochim Acta. 1983;42(6):697-703.
3
The helical periodicity of DNA on the nucleosome.核小体上DNA的螺旋周期性。
Nucleic Acids Res. 1981 Sep 11;9(17):4267-83. doi: 10.1093/nar/9.17.4267.
4
Fluctuations in superhelical DNA.超螺旋DNA的波动
Nucleic Acids Res. 1979 Mar;6(3):967-82. doi: 10.1093/nar/6.3.967.
5
Superhelicity of nucleosomal DNA changes its double-helical repeat.核小体DNA的超螺旋性改变了其双螺旋重复序列。
Cell Biophys. 1983 Dec;5(4):281-3. doi: 10.1007/BF02788626.
6
The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.三角十聚体C-G-A-T-C-G-6meA-T-C-G的晶体结构：一种每圈含10.6个碱基对的B-DNA螺旋结构。
J Mol Biol. 1993 Jun 5;231(3):768-84. doi: 10.1006/jmbi.1993.1325.
7
The effect of the superhelicity on the double helix twist angle in DNA.超螺旋对DNA双螺旋扭转角的影响。
Nucleic Acids Res. 1979 Mar;6(3):983-92. doi: 10.1093/nar/6.3.983.
8
Possibility of nonkinked packing of DNA in chromatin.染色质中DNA非扭结堆积的可能性。
Proc Natl Acad Sci U S A. 1978 Jan;75(1):103-7. doi: 10.1073/pnas.75.1.103.
9
Nucleosomes arrangement in chromatin.染色质中的核小体排列
Nucleic Acids Res. 1978 Nov;5(11):4431-49. doi: 10.1093/nar/5.11.4431.
10
Structure of the nucleosome core particle at 8 A resolution.8埃分辨率下核小体核心颗粒的结构。
J Biomol Struct Dyn. 1989 Aug;7(1):1-18. doi: 10.1080/07391102.1989.10507747.
引用本文的文献
1
Evolutionary dynamics of predicted G-quadruplexes in human and other great apes.人类及其他类人猿中预测的G-四链体的进化动力学
Genome Biol. 2025 Jun 11;26(1):161. doi: 10.1186/s13059-025-03635-1.
2
Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.用于大规模获取膜蛋白纳米级组织的邻近激活DNA扫描编码测序。
Proc Natl Acad Sci U S A. 2025 Apr 15;122(15):e2425000122. doi: 10.1073/pnas.2425000122. Epub 2025 Apr 10.
3
Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography.DNA 连接子与核小体核心颗粒之间的角度通过单颗粒冷冻电镜断层成像揭示了其对阵列紧缩的调控。
Nat Commun. 2024 May 23;15(1):4395. doi: 10.1038/s41467-024-48305-1.
4
Single-chain models illustrate the 3D RNA folding shape during translation.单链模型展示了翻译过程中RNA的三维折叠形状。
Biophys Rep (N Y). 2022 Aug 5;2(3):100065. doi: 10.1016/j.bpr.2022.100065. eCollection 2022 Sep 14.
5
In-gel fluorescence detection by DNA polymerase elongation.通过DNA聚合酶延伸进行凝胶内荧光检测。
APL Bioeng. 2020 Nov 20;4(4):046104. doi: 10.1063/5.0021149. eCollection 2020 Dec.
6
V(DD)J recombination is an important and evolutionarily conserved mechanism for generating antibodies with unusually long CDR3s.V(D)J 重组是一种产生具有异常长 CDR3 的抗体的重要且进化上保守的机制。
Genome Res. 2020 Nov;30(11):1547-1558. doi: 10.1101/gr.259598.119. Epub 2020 Sep 18.
7
A Membrane-Bound Transcription Factor is Proteolytically Regulated by the AAA+ Protease FtsH in Staphylococcus aureus.一种膜结合转录因子被金黄色葡萄球菌中的 AAA+ 蛋白酶 FtsH 进行蛋白水解调节。
J Bacteriol. 2020 Apr 9;202(9). doi: 10.1128/JB.00019-20.
8
Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.染色质高级折叠：以连接 DNA 角度看问题。
Biophys J. 2018 May 22;114(10):2290-2297. doi: 10.1016/j.bpj.2018.03.009. Epub 2018 Apr 6.
9
Nucleosomal arrangement affects single-molecule transcription dynamics.核小体排列影响单分子转录动力学。
Proc Natl Acad Sci U S A. 2016 Nov 8;113(45):12733-12738. doi: 10.1073/pnas.1602764113. Epub 2016 Oct 24.
10
A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases.共转录RNA聚合酶协同行为的机制模型
PLoS Comput Biol. 2016 Aug 12;12(8):e1005069. doi: 10.1371/journal.pcbi.1005069. eCollection 2016 Aug.
本文引用的文献
1
Refinement of protein conformations using a macromolecular energy minimization procedure.使用大分子能量最小化程序优化蛋白质构象。
J Mol Biol. 1969 Dec 14;46(2):269-79. doi: 10.1016/0022-2836(69)90421-5.
2
The secondary structure of DNA in solution and in nucleohistone.溶液中和核组蛋白中的DNA二级结构。
J Mol Biol. 1971 May 28;58(1):277-88. doi: 10.1016/0022-2836(71)90246-4.
3
Structure of crystalline -chymotrypsin. V. The atomic structure of tosyl- -chymotrypsin at 2 A resolution.结晶胰凝乳蛋白酶的结构。V. 对甲苯磺酰基-胰凝乳蛋白酶在2埃分辨率下的原子结构
J Mol Biol. 1972 Jul 21;68(2):187-240. doi: 10.1016/0022-2836(72)90210-0.
4
Optimised parameters for A-DNA and B-DNA.A-DNA和B-DNA的优化参数。
Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9. doi: 10.1016/0006-291X(72)90243-4.
5
Energy refinement of hen egg-white lysozyme.鸡蛋清溶菌酶的能量优化
J Mol Biol. 1974 Jan 25;82(3):393-420. doi: 10.1016/0022-2836(74)90599-3.
6
Chromatin structure: a repeating unit of histones and DNA.染色质结构：组蛋白与DNA的重复单元。
Science. 1974 May 24;184(4139):868-71. doi: 10.1126/science.184.4139.868.
7
Flexibility of DNA.DNA的柔韧性
Biopolymers. 1974 Jan;13(1):217-26. doi: 10.1002/bip.1974.360130115.
8
Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers.B-DNA结构的优化及其对生物聚合物纤维X射线衍射数据分析的启示
J Mol Biol. 1973 Dec 5;81(2):93-105. doi: 10.1016/0022-2836(73)90182-4.
9
The dimensions and shapes of the furanose rings in nucleic acids.核酸中呋喃糖环的尺寸和形状。
Biochem J. 1972 Nov;130(2):453-65. doi: 10.1042/bj1300453.
10
Subunit structure of chromatin.染色质的亚基结构。
Nature. 1974 Sep 20;251(5472):249-51. doi: 10.1038/251249a0.
Zotero 插件