基于稳健红外技术检测双链DNA中稳定且部分占据的G-C和A-T Hoogsteen碱基对。
Robust IR-based detection of stable and fractionally populated G-C and A-T Hoogsteen base pairs in duplex DNA.
作者信息
Stelling Allison L, Xu Yu, Zhou Huiqing, Choi Seung H, Clay Mary C, Merriman Dawn K, Al-Hashimi Hashim M
机构信息
Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
Department of Chemistry, Duke University, Durham, NC, USA.
出版信息
FEBS Lett. 2017 Jun;591(12):1770-1784. doi: 10.1002/1873-3468.12681. Epub 2017 Jun 19.
Abstract
Noncanonical G-C and A-T Hoogsteen base pairs can form in duplex DNA and play roles in recognition, damage repair, and replication. Identifying Hoogsteen base pairs in DNA duplexes remains challenging due to difficulties in resolving syn versus antipurine bases with X-ray crystallography; and size limitations and line broadening can make them difficult to characterize by NMR spectroscopy. Here, we show how infrared (IR) spectroscopy can identify G-C and A-T Hoogsteen base pairs in duplex DNA across a range of different structural contexts. The utility of IR-based detection of Hoogsteen base pairs is demonstrated by characterizing the first example of adjacent A-T and G-C Hoogsteen base pairs in a DNA duplex where severe broadening complicates detection with NMR.
摘要
非经典的G-C和A-T Hoogsteen碱基对可在双链DNA中形成，并在识别、损伤修复和复制中发挥作用。由于通过X射线晶体学解析顺式与反式嘌呤碱基存在困难，鉴定DNA双链体中的Hoogsteen碱基对仍然具有挑战性；并且尺寸限制和谱线展宽会使它们难以通过核磁共振光谱进行表征。在这里，我们展示了红外（IR）光谱如何能够在一系列不同的结构背景下识别双链DNA中的G-C和A-T Hoogsteen碱基对。通过表征DNA双链体中相邻的A-T和G-C Hoogsteen碱基对的首个实例，证明了基于红外检测Hoogsteen碱基对的实用性，在该实例中，严重的谱线展宽使核磁共振检测变得复杂。
相似文献
1
Robust IR-based detection of stable and fractionally populated G-C and A-T Hoogsteen base pairs in duplex DNA.基于稳健红外技术检测双链DNA中稳定且部分占据的G-C和A-T Hoogsteen碱基对。
FEBS Lett. 2017 Jun;591(12):1770-1784. doi: 10.1002/1873-3468.12681. Epub 2017 Jun 19.
2
Binding of quinomycin antibiotic UK-65,662 to DNA: 1H-n.m.r. studies of drug-induced changes in DNA conformation in complexes with d(ACGT)2 and d(GACGTC)2.喹诺霉素抗生素UK-65,662与DNA的结合：1H-核磁共振研究药物诱导的与d(ACGT)2和d(GACGTC)2形成复合物时DNA构象的变化。
Biochem J. 1994 Dec 15;304 ( Pt 3)(Pt 3):967-79. doi: 10.1042/bj3040967.
3
Direct evidence for (G)O6···H-N4(C) hydrogen bonding in transient G(syn)-C and G(syn)-mC Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R relaxation dispersion measurements.从胞嘧啶氨基氮去共振 R 弛豫弥散测量中，直接证明了 DNA 双链中瞬态 G(syn)-C 和 G(syn)-mC Hoogsteen 碱基对中的 (G)O6···H-N4(C) 氢键。
J Magn Reson. 2019 Nov;308:106589. doi: 10.1016/j.jmr.2019.106589. Epub 2019 Sep 5.
4
NMR investigation of Hoogsteen base pairing in quinoxaline antibiotic--DNA complexes: comparison of 2:1 echinomycin, triostin A and [N-MeCys3,N-MeCys7] TANDEM complexes with DNA oligonucleotides.喹喔啉抗生素-DNA复合物中Hoogsteen碱基配对的核磁共振研究：2:1放线菌素、三孢菌素A和[N-甲基半胱氨酸3，N-甲基半胱氨酸7]串联复合物与DNA寡核苷酸的比较
Nucleic Acids Res. 1994 Dec 11;22(24):5484-91. doi: 10.1093/nar/22.24.5484.
5
Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations.通过结合核磁共振弛豫色散、诱变和化学位移计算确定双链DNA中激发态A-T Hoogsteen碱基对的原子结构
J Biomol NMR. 2018 Apr;70(4):229-244. doi: 10.1007/s10858-018-0177-2. Epub 2018 Apr 19.
6
Modulation of Hoogsteen dynamics on DNA recognition.DNA 识别中 Hoogsteen 动力学的调制。
Nat Commun. 2018 Apr 16;9(1):1473. doi: 10.1038/s41467-018-03516-1.
7
Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex.DNA双链体内与放线菌素结合位点相邻的不稳定Hoogsteen碱基对。
Proc Natl Acad Sci U S A. 1989 May;86(9):3006-10. doi: 10.1073/pnas.86.9.3006.
8
Probing Watson-Crick and Hoogsteen base pairing in duplex DNA using dynamic nuclear polarization solid-state NMR spectroscopy.利用固态核磁共振动态极化技术研究双链 DNA 中的 Watson-Crick 和 Hoogsteen 碱基配对。
Proc Natl Acad Sci U S A. 2022 Jul 26;119(30):e2200681119. doi: 10.1073/pnas.2200681119. Epub 2022 Jul 20.
9
Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.鸟嘌呤到次黄嘌呤的替换导致瞬时G·C Hoogsteen碱基对群体大幅增加。
Biochemistry. 2014 Nov 25;53(46):7145-7. doi: 10.1021/bi5011909. Epub 2014 Nov 10.
10
Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.描述在 DNA 双链中的瞬变 G·C Hoogsteen 碱基对中胞嘧啶的质子化状态。
J Am Chem Soc. 2013 May 8;135(18):6766-9. doi: 10.1021/ja400994e. Epub 2013 Apr 29.
引用本文的文献
1
Rapid assessment of Watson-Crick to Hoogsteen exchange in unlabeled DNA duplexes using high-power SELOPE imino H CEST.使用高功率SELOPE亚氨基H CEST快速评估未标记DNA双链体中沃森-克里克到 hoogsteen的交换
Magn Reson (Gott). 2021 Sep 14;2(2):715-731. doi: 10.5194/mr-2-715-2021. eCollection 2021.
2
Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces.核苷酸（dGMP、dCMP、dAMP 和 dTMP）在氧化物颗粒表面的差分表面相互作用和表面模板化。
Langmuir. 2022 Dec 13;38(49):15038-15049. doi: 10.1021/acs.langmuir.2c01604. Epub 2022 Nov 29.
3
Probing the Hydrogen-Bonding Environment of Individual Bases in DNA Duplexes with Isotope-Edited Infrared Spectroscopy.利用同位素编辑红外光谱研究 DNA 双螺旋中单个碱基的氢键环境。
J Phys Chem B. 2021 Jul 22;125(28):7613-7627. doi: 10.1021/acs.jpcb.1c01351. Epub 2021 Jul 8.
4
Modeling the vibrational couplings of nucleobases.核苷酸碱基振动耦合的建模。
J Chem Phys. 2020 Feb 28;152(8):084114. doi: 10.1063/1.5141858.
5
5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex.5-羧基胞嘧啶和胞嘧啶质子化显著改变 DNA 双链的稳定性和去杂交动力学。
J Phys Chem B. 2020 Jan 30;124(4):627-640. doi: 10.1021/acs.jpcb.9b11510. Epub 2020 Jan 14.
6
Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.原子水平上对 DNA 中 Watson-Crick 到 Hoogsteen 转变的动力学途径的深入了解。
Nucleic Acids Res. 2019 Dec 2;47(21):11069-11076. doi: 10.1093/nar/gkz837.
7
Infrared Spectroscopic Observation of a G-C Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.溶液条件下 DNA:TATA 框结合蛋白复合物中 G-C Hoogsteen 碱基对的红外光谱观察。
Angew Chem Int Ed Engl. 2019 Aug 26;58(35):12010-12013. doi: 10.1002/anie.201902693. Epub 2019 Jul 25.
8
Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?与 B-DNA 相比，A-RNA 中为什么 Hoogsteen 碱基对在能量上处于不利地位？
Nucleic Acids Res. 2018 Nov 16;46(20):11099-11114. doi: 10.1093/nar/gky885.
9
Modulation of Hoogsteen dynamics on DNA recognition.DNA 识别中 Hoogsteen 动力学的调制。
Nat Commun. 2018 Apr 16;9(1):1473. doi: 10.1038/s41467-018-03516-1.
本文引用的文献
1
m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs.m(1)A和m(1)G通过Hoogsteen碱基对的内在不稳定性破坏A-RNA结构。
Nat Struct Mol Biol. 2016 Sep;23(9):803-10. doi: 10.1038/nsmb.3270. Epub 2016 Aug 1.
2
Structural Basis for p53 Lys120-Acetylation-Dependent DNA-Binding Mode.p53赖氨酸120乙酰化依赖性DNA结合模式的结构基础
J Mol Biol. 2016 Jul 31;428(15):3013-25. doi: 10.1016/j.jmb.2016.06.009. Epub 2016 Jun 23.
3
Excited-State Dynamics of DNA Duplexes with Different H-Bonding Motifs.具有不同氢键模式的DNA双链体的激发态动力学
J Phys Chem Lett. 2016 Mar 17;7(6):950-4. doi: 10.1021/acs.jpclett.6b00074. Epub 2016 Feb 25.
4
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.基于结构的研究对DNA双链体中Hoogsteen碱基对的新见解。
Nucleic Acids Res. 2015 Apr 20;43(7):3420-33. doi: 10.1093/nar/gkv241. Epub 2015 Mar 26.
5
Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.具有Hoogsteen氢键的DNA双链体d(ATTAAT)2的结构
PLoS One. 2015 Mar 17;10(3):e0120241. doi: 10.1371/journal.pone.0120241. eCollection 2015.
6
Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair.鸟嘌呤到次黄嘌呤的替换导致瞬时G·C Hoogsteen碱基对群体大幅增加。
Biochemistry. 2014 Nov 25;53(46):7145-7. doi: 10.1021/bi5011909. Epub 2014 Nov 10.
7
Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids.用于核酸的芳香族[(13)C, (1)H] SOFAST-HMQC核磁共振实验的开发与应用
J Biomol NMR. 2014 Nov;60(2-3):77-83. doi: 10.1007/s10858-014-9856-9. Epub 2014 Sep 4.
8
Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.在具有可变能量学的典型双链DNA中广泛存在的瞬时Hoogsteen碱基对。
Nat Commun. 2014 Sep 4;5:4786. doi: 10.1038/ncomms5786.
9
DFT investigation of the vibrational properties of GC Watson-Crick and Hoogsteen base pairs in the presence of Mg²⁺, Ca²⁺, and Cu²⁺ ions.在存在Mg²⁺、Ca²⁺和Cu²⁺离子的情况下，对GC沃森-克里克碱基对和 hoogsteen 碱基对振动特性的密度泛函理论研究。
J Mol Model. 2014 Apr;20(4):2220. doi: 10.1007/s00894-014-2220-x. Epub 2014 Apr 13.
10
The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine-cytosine base pairs in Watson-Crick and Hoogsteen configurations.非谐性和溶剂效应 对 Watson-Crick 和 Hoogsteen 构型中鸟嘌呤-胞嘧啶碱基对理论振动光谱的影响
J Mol Model. 2014 Mar;20(3):2113. doi: 10.1007/s00894-014-2113-z. Epub 2014 Feb 25.
Zotero 插件