Photoregulating primer extension using azobenzene linked DNA template

doi:10.7523/j.issn.2095-6134.2019.01.007

Abstract

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

CLC Number:

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.

References

[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.