偶氮苯修饰的DNA对引物延伸的光调控

doi:10.7523/j.issn.2095-6134.2019.01.007

中国科学院大学学报 ›› 2019, Vol. 36 ›› Issue (1): 38-47.DOI: 10.7523/j.issn.2095-6134.2019.01.007

偶氮苯修饰的DNA对引物延伸的光调控

季禾茗¹, 孔德佳³, 莫蒙武², 雷华军³, 陈露¹, 赵瑞琪², 王威², 何裕建², 封禄田¹, 吴丽²

1. 沈阳化工大学应用化学学院, 沈阳 11014;
2. 中国科学院大学化学科学学院, 北京 100049;
3. 江西科技师范大学药学院, 南昌 330013

收稿日期:2017-11-17 修回日期:2018-03-06 发布日期:2019-01-15
通讯作者: 封禄田,E-mail:fenglutian@126.com;吴丽,E-mail:wuli@ucas.ac.cn
基金资助:
国家自然科学基金（21778054，51772289）、国家重点研究发展计划（2016YFF0203703）、校部青年教师科研启动基金（Y55103HY00）、中国科学院大学大学生创新实践训练计划（118900EA12）、北京大学天然药物及仿生药物国家重点实验室开放课题（K20150204）资助

Photoregulating primer extension using azobenzene linked DNA template

JI Heming¹, KONG Dejia³, MO Mengwu², LEI Huajun³, CHEN Lu¹, ZHAO Ruiqi², WANG Wei², HE Yujian², FENG Lutian¹, WU Li²

1. College of Applied Chemistry, Shenyang University of Chemical Technology, Shenyang 11014;
2. College of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
3. College of Pharmacy, Jiangxi Science and Technology Normal University, Nanchang 330013, China

Received:2017-11-17 Revised:2018-03-06 Published:2019-01-15

摘要/Abstract

摘要： 研究偶氮苯单元修饰在核酸上控制引物延伸的行为。系统地筛选5、6、7和8个碱基的保护链通过4，4'-二羟甲基偶氮苯连接的25 mer DNA模板，并研究其在紫外光照前后调控的引物延伸效率。结果表明，具有7个保护碱基的C3对Pri.15和6个碱基短链的C2对Pri.17都具有较好的光调控延伸效果。其中C3，在Vent酶作用下紫外光照后引物延伸效率增加1倍以上。而C2，尽管紫外光照前增加了引物延伸的背景，在Vent酶催化下紫外光照射后的延伸产率达到91.4%，比紫外光照前增加84%。本工作为分子水平上研究基因功能、基因表达网络以及疾病的发生和发展提供了一种新的策略和研究手段。

关键词: 核酸, 偶氮苯, 光调控, 引物延伸

Abstract: It has been a hot topic in recent years to carry out a series of life activities by artificial reversible manipulation of specific gene expression. In this work, the photocontrol of primer extension directed by azobenzene modified DNA templates was investigated. DNA templates attached by protective ODNs with 5, 6, 7, and 8 complementary bases through 4,4'-bis(hydroxymethyl) azobenzene were systematically evaluated in photoregulation of the primer extension without or with UV irradiation. The results showed high efficiencies of C3 with 7 protected bases and C2 with 6-base short chains for photoregulating Pri.15 and Pri.17, respectively. Especially, for C3, when catalyzed by Vent DNA polymerase, primer extension efficiency had one-fold increase upon UV irradiation. Similarly, for C2, the extension efficiency reached 91.4% with UV irradiation and achived 84% increase, compared to that without UV irradiation, although the background of primer extension in the dark was a little high. This work provides a new strategy or means for studying the gene function and gene expression network and for exploring the occurrence and development of disease at the molecular level.

Key words: nucleic acid, azobenzene, photoregulation, primer extension

中图分类号:

季禾茗, 孔德佳, 莫蒙武, 雷华军, 陈露, 赵瑞琪, 王威, 何裕建, 封禄田, 吴丽. 偶氮苯修饰的DNA对引物延伸的光调控[J]. 中国科学院大学学报, 2019, 36(1): 38-47.

JI Heming, KONG Dejia, MO Mengwu, LEI Huajun, CHEN Lu, ZHAO Ruiqi, WANG Wei, HE Yujian, FENG Lutian, WU Li. Photoregulating primer extension using azobenzene linked DNA template[J]. , 2019, 36(1): 38-47.

参考文献

[1] Wang R W, Jin C, Zhu X Y, et al. Artificial base zT as functional "element" for constructing photoresponsive DNA nanomolecules[J]. Journal of the American Chemical Society, 2017, 139(27):9104-9107.
[2] Gorbea C, Mosbruger T, Cazalla D. A viral Sm-class RNA base-pairs with mRNAs and recruits microRNAs to inhibit apoptosis[J]. Nature, 2017, 550(7675):275-279.
[3] Gomez-Santacana X, Pittolo S, Rovira X, et al. Illuminating phenylazopyridines to photoswitch metabotropic glutamate receptors:from the flask to the animals[J]. ACS Central Science, 2017, 3(1):81-91.
[4] Adedeji A O, Singh K, Calcaterra N E, et al. Severe acute respiratory syndrome coronavirus replication inhibitor that interferes with the nucleic acid unwinding of the viral helicase[J]. Antimicrobial Agents and Chemotherapy, 2012, 56(9):4718-4728.
[5] Velema W A, Szymanski W, Feringa B L. Photopharmacology:beyond proof of principle[J]. Journal of the American Chemical Society, 2014, 136(6):2178-2191.
[6] Wu L, Pei F, Zhang J H, et al. Synthesis of site-specifically phosphate-caged siRNAs and evaluation of their RNAi activity and stability[J]. Chemistry-A European Journal, 2014, 20(38):12114-12122.
[7] Hemphill J, Govan J, Uprety R, et al. Site-specific promoter caging enables optochemical gene activation in cells and animals[J]. Journal of the American Chemical Society, 2014, 136(19):7152-7158.
[8] Wu L, Wang Y, Wu J Z, et al. Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells[J]. Nucleic Acids Research, 2013, 41(1):677-686.
[9] Wang Y, Wu L, Wang P F, et al. Manipulation of gene expression in zebrafish using caged circular morpholino oligomers[J]. Nucleic Acids Research, 2012, 40(21):11155-11162.
[10] Szymanski W, Beierle J M, Kistemaker H A, et al. Reversible photocontrol of biological systems by the incorporation of molecular photoswitches[J]. Chemical Reviews, 2013, 113(8):6114-6178.
[11] Beharry A A, Woolley G A. Azobenzene photoswitches for biomolecules[J]. Chemical Society Reviews, 2011, 40(8):4422-4437.
[12] Liu Z F, Hashimoto K, Fujishima A. Photoelectrochemical information-storage using an azobenzene derivative[J]. Nature, 1990, 347(6294):658-660.
[13] Kumar G S, Neckers D C. Photochemistry of azobenzene-containing polymers[J]. Chemical Reviews, 1989, 89(8):1915-1925.
[14] Zimmerman G, Chow L Y, Paik U J. The photochemical isomerization of azobenzene[J]. Journal of the American Chemical Society, 1958, 80(14):3528-3531.
[15] Yang Y Y, Endo M, Hidaka K, et al. Photo-controllable DNA origami nanostructures assembling into predesigned multiorientational patterns[J]. Journal of the American Chemical Society, 2012, 134(51):20645-20653.
[16] Yan Y Q, Chen J I, Ginger D S. Photoswitchable oligonucleotide-modified gold nanoparticles:controlling hybridization stringency with photon dose[J]. Nano Letters, 2012, 12(5):2530-2536.
[17] Lohmann F, Ackermann D, Famulok M. Reversible light switch for macrocycle mobility in a DNA rotaxane[J]. Journal of the American Chemical Society, 2012, 134(29):11884-11887.
[18] Tunitskaya V L, Kochetkov S N. Structural-functional analysis of bacteriophage T7 RNA polymerase[J]. Biochemistry-Moscow, 2002, 67(10):1124-1135.
[19] Nakasone Y, Ooi H, Kamiya Y, et al. Dynamics of inter-DNA chain interaction of photoresponsive dNA[J]. Journal of the American Chemical Society, 2016, 138(29):9001-9004.
[20] Kingsland A, Samai S, Yan Y Q, et al. Local density fluctuations predict photoisomerization quantum yield of azobenzene-modified DNA[J]. The Journal of Physical Chemistry Letters, 2016, 7(15):3027-3031.
[21] Yan Y Q, Wang X, Chen J L, et al. Photoisomerization quantum yield of azobenzene-modified DNA depends on local sequence[J]. Journal of the American Chemical Society, 2013, 135(22):8382-8387.
[22] Lubbe A S, Szymanski W, Feringa B L. Recent developments in reversible photoregulation of oligonucleotide structure and function[J]. Chemical Society Reviews, 2017, 46(4):1052-1079.
[23] Chen H R, Zhang, H Y, Pan, J, et al. Dynamic and progressive control of DNA origami conformation by modulating DNA helicity with chemical adducts[J]. ACS Nano, 2017, 10(5):4989-4996.
[24] Liu M Z, Asanuma H, Komiyama M. Azobenzene-tethered T7 promoter for efficient photoregulation of transcription[J]. Journal of the American Chemical Society, 2006, 128(3):1009-1015.
[25] Wang X L, Huang J, Zhou Y Y, et al. Conformational switching of G-quadruplex DNA by photoregulation[J]. Angewandte Chemie-International Edition, 2010, 49(31):5305-5309.
[26] Matsunaga D, Asanuma H, Komiyama M. Photoregulation of RNA digestion by RNase H with azobenzene-tethered DNA[J]. Journal of the American Chemical Society, 2004, 126(37):11452-11453.
[27] Liang X G, Asanuma H, Komiyama M. Photoregulation of DNA triplex formation by azobenzene[J]. Journal of the American Chemical Society, 2002, 124(9):1877-1883.
[28] Chaulk S G, MacMillan A M. Caged RNA:photo-control of a ribozyme reaction[J]. Nucleic Acids Research, 1998, 26(13):3173-3178.
[29] Dong M X, Babalhavaeji A, Samanta S, et al. Red-shifting azobenzene photoswitches for in vivo use[J]. Accounts of Chemical Research, 2015, 48(10):2662-2670.
[30] Nishioka H, Liang X G, Asanuma H. Effect of the ortho modification of azobenzene on the photoregulatory efficiency of DNA hybridization and the thermal stability of its cis form[J]. Chemistry-A European Journal, 2010, 16(7):2054-2062.
[31] Wu L, Wu Y, Jin H W, et al. Photoswitching properties of hairpin ODNs with azobenzene derivatives at the loop position[J]. MedChemCommun, 2015, 6(3):461-468.
[32] Wu L, Koumoto K, Sugimoto N. Reversible stability switching of a hairpin DNA via a photo-responsive linker unit[J]. Chem Commun, 2009, 14(14):1915-1917.
[33] Wu L, He Y J, Tang X J. Photoregulating RNA digestion using azobenzene linked dumbbell antisense oligodeoxynucleotides[J]. Bioconjugate Chemistry, 2015, 26(6):1070-1079.
[34] Young D D, Edwards W F, Lusic H, et al. Light-triggered polymerase chain reaction[J]. Chemical Communications, 2008, (4):462-464.
[35] Wang Q, Yi L, Liu L L, et al. A thermostable azo-linker for reversible photoregulation of DNA replication[J]. Tetrahedron Letters, 2008, 49(34):5087-5089.
[36] Yamazawa A, Liang X G, Asanuma H, et al. Photoregulation of the DNA polymerase reaction by oligonucleotides bearing an azobenzene[J]. Angewandte Chemie-International Edition, 2000, 39(13):2356-2357.
[37] Kamiya Y, Takagi T, Ooi H, et al. Synthetic gene involving azobenzene-tethered T7 promoter for the photocontrol of gene expression by visible light[J]. ACS Synthetic Biology, 2015, 4(4):365-370.
[38] Asanuma H, Tamaru D, Yamazawa A, et al. Photoregulation of the transcription reaction of T7 RNA polymerase by tethering an azobenzene to the promoter[J]. Chembiochem, 2002, 3(8):786-789.
[39] Wang X Y, Liang X G. Azobenzene-modified antisense oligonucleotides for site-specific cleavage of RNA with photocontrollable property[J]. RSC Advances, 2016, 6(96):93398-93402.
[40] Tian T, Song Y Y, Wang J Q, et al. Small-molecule-triggered and light-controlled reversible regulation of enzymatic activity[J]. Journal of the American Chemical Society, 2016, 138(3):955-961.

偶氮苯修饰的DNA对引物延伸的光调控

Photoregulating primer extension using azobenzene linked DNA template

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 2

编辑推荐

Metrics

本文评价

访问统计

联系我们

[1]	陈露, 季禾茗, 莫蒙武, 雷华军, 卜新雅, 何裕建, 封禄田, 吴丽. 偶氮苯修饰的发夹DNA对RNA转录的光调控[J]. 中国科学院大学学报, 2020, 37(3): 416-423.
[2]	王光伟, 黄亮, 向开祥, 赵红, 何裕建. 以放射性标记的肽核酸对目标基因的识别与检测[J]. 中国科学院大学学报, 2013, 30(1): 1-5.