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2023

61. Shiu, S. C., Kinghorn, A. B., Guo, W., Slaughter, L. S., Ji, D., Mo, X., Wang, L., Tran, N. C., Kwok, C. K., Shum, A. H. C., Tse, E. C. M., Tanner, J. A. Aptamers as Functional Modules for DNA Nanostructures. Methods Mol Biol. 2639, 301-337 (2023). https://doi.org/10.1007/978-1-0716-3028-0_17

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60. Guo, W., Ji, D., Kinghorn, A. B., Chen, F., Pan, Y., Li, X., Li, Q., Huck, W. T. S., Kwok, C.K, Shum, H. C. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condesates. JACS. 145, 2375-2385 (2023). http://doi.org/10.1021/jacs.2c11362

2022

59. Lam, S.Y., Lau, H.L., Kwok, C.K. Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application. Biosensors. 12(12), 1142 (2022). https://doi.org/10.3390/bios12121142


58. Lyu, K, Chen, S.B., Chow, E.Y., Zhao, H., Yuan, J.H., Cai, M., Shi, J., Chan, T.F., Tan, J.H., Kwok, C.K. An RNA G-Quadruplex Structure within the ADAR 5'UTR Interacts with DHX36 Helicase to Regulate Translation. Angewandte Chemie. 61, e20203553 (2022). https://doi.org/10.1002/anie.202203553


57. Zhao, J., Chow, E.U., Yeung P.Y., Zhang, Q.C., Chan, T.F., Kwok, C.K. Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0. BMC Biology. 20, 257 (2022). https://doi.org/10.1186/s12915-022-01448-3


56. Yang, X., Yu, H., Duncan, S., Zhang, Y., Cheema, J., Liu, H., Miller, J.B., Zhang, J., Kwok, C.K., Zhang, H., Ding, Y. RNA G-quadruplex structure contributes to cold adaptation in plants. Nat Commun. 13, 6224 (2022). https://doi.org/10.1038/s41467-022-34040-y


55. Dumetz, F., Enright, A.J., Zhao, J., Kwok, C.K., Merrick, C.J. The in vivo RNA structuromone of the malaria parasite Plasmodium falciparum, a protozoan with an A/U-rich transcriptome. Plos One. 17(9), e0270863 (2022). https://doi.org/10.1371/journal.pone.0270863 


54. Zhang, Y., Juhas, M., Kwok, C. K. Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19. Trends in Biotechnology. 41, 528 - 544 (2022). https://doi.org/10.1016/j.tibtech.2022.07.012


53. Zhao, H., Wong, H.Y., Ji, D., Lyu, K. & Kwok, C.K. Novel L-RNA Aptamer Controls APP Gene Expression in Cells by Targeting RNA G-Quadruplex Structure. ACS Appl. Mater. Interfaces. 14, 30582 - 30594 (2022).https://doi.org/10.1021/acsami.2c06390


52. Chen, X., Xue, G., Zhao, J., Zhang, Y., Zhang, Z., Wang, W., Li, Y., Yuan, J., He, J., Chan, C.Y., Liu, Y., Chen, W., Zhao, Y., Hu, P., Sun, H., Kwok, C.K. & Wang, H. Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5′ UTR rG4 unwinding and Anp32e translation. Cell Rep. 39, 110927 (2022). https://doi.org/10.1016/j.celrep.2022.110927


51. Georgakopoulos-Soares, I., Parada, G.E., Wong, H.Y., Medhi, R., Furlan, G., Munita, R., Miska, E.A., Kwok, C.K. & Hemberg, M. Alternative splicing modulation by G-quadruplexes. Nat Commun. 13, 2404 (2022). https://doi.org/10.1038/s41467-022-30071-7


50. Xu, B., Zhu, Y., Cao, C., Chen, H., Jin, Q., Li, G., Ma, J., Zhao, J., Zhu, J., Ding, Y., Fang, X., JIN, Y., Kwok, C.K., Ren, A., Wan, Y., Wang, Z., Xue, Y., Zhang, H., Zhang, Q. & Zhou,Y. Recent advances in RNA structurome. SCIENCE CHINA Life Sciences. 65, 1285- 1324 (2022). https://doi.org/10.1007/s11427-021-2116-2


​49. Umar, M.I., Chan, CY. & Kwok, C.K. Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX. Nat Protoc. 17, 1385-1414 (2022). https://doi.org/10.1038/s41596-022-00679-6


48. Georgakopoulos-Soares, I., Victorino, J., Parada, G.E., Agarwal, V., Zhao, J., Wong, H.Y., Umar, M,I., Elor, O., Muhwezi, A., An, J., Sanders, S.J., Kwok, C.K., Inoue, F., Hemberg, M. & Ahituv, N. High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genomics. 2, 100111 (2022). https://doi.org/10.1016/j.xgen.2022.100111


47. Feng, H, & Kwok, C.K. Spectroscopic analysis reveals the effect of hairpin loop formation on G-quadruplex structures. RSC Chem. Biol. 3, 431- 435 (2022). https://doi.org/10.1039/d2cb00045h


46. Piao, M., Li, P., Zeng, X., Wang, X., Kang, L., Zhang, J., Wei, Y., Zhang, S., Tang, L., Zhu, J., Kwok, C.K., Hu, X. & Zhang, Q.F.C. An ultra low-input method for global RNA structure probing uncovers Regnase-1-mediated regulation in macrophages. Fundamental Research. 2, 2-13 (2022). https://doi.org/10.1016/j.fmre.2021.12.007

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45. Mou, X., Liew, S. W. & Kwok, C.K. Identification and targeting of G-quadruplex structures in MALAT1 long non-coding RNA. Nucleic Acids Res. 50, 397- 410 (2022). https://doi.org/10.1093/nar/gkab1208

2021

44. Dumetz, F., Chow, E.Y.C., Harris, L.M., Liew, S.W., Jensen, A., Umar, M.I., Chung, B., Chan, T.F., Merrick, C.J. & Kwok, C.K. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res. 49, 12486–12501 (2021). https://doi.org/10.1093/nar/gkab1095

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43. Chen, X., Yuan, J., Xue, G., Campanario, S., Wang, D., Wang, W., Mou, X., Liew, S.W., Umar, M.I., Isern, J., Zhao, Y., He, L., Li, Y., Mann, C.J., Yu, X., Wang, L., Perdiguero, E., Chen, W., Xue, Y., Nagamine, Y., Kwok, C.K., Sun, H., Muñoz-Cánoves, P. & Wang, H. Translational control by DHX36 binding to 5’UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun 12, 5043 (2021). https://doi.org/10.1038/s41467-021-25170-w


42. Ji, D., Lyu, K., Zhao, H. & Kwok, C.K. Circular L-RNA aptamer promotes target recognition and controls gene activity. Nucleic Acids Res.  49, 7280-7291 (2021). https://doi.org/10.1093/nar/gkab593


41. Zhang, Y., Wu, Y., Zheng, H., Xi, H., Ye, T., Chan, C. Y. & Kwok, C.K. Proteomic and Transcriptome Profiling of G-Quadruplex Aptamers Developed for Cell Internalization. Anal. Chem. 93, 5744-5753 (2021). https://doi.org/10.1021/acs.analchem.0c04862


40. Lyu, K., Chow, E.Y.C., Mou, X., Chan, T. & Kwok, C.K. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res.  49, 5426-5450 (2021). https://doi.org/10.1093/nar/gkab187


39. Zhao, H. & Kwok, C.K. Bringing distant DNA together. Nature Chem. Bio. 17, 125-126 (2021). ​https://doi.org/10.1038/s41589-020-00705-2

2020

38. Mou, X. & Kwok, C.K. Effect of RNA sequence context and stereochemistry on G-quadruplex-RHAU53 interaction. Biochem. Biophys. Res. Commun. 533, 1135-1141 (2020). https://doi.org/10.1016/j.bbrc.2020.09.045

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37. Umar, M.I. & Kwok, C.K. Specific suppression of D-RNA G-quadruplex–protein interaction with an L-RNA aptamer. Nucleic Acids Res. 48, 10125-10141 (2020). https://doi.org/10.1093/nar/gkaa759


36. Yang, X., Cheema, J., Zhang, Y., Deng, H., Duncan, S., Umar, M. I., Zhao, J., Liu, Q., Cao, X., Kwok, C. K. & Ding, Y. RNA G-quadruplex structures exist and function in vivo in plants. Genome Biol. 21, 226 (2020). https://doi.org/10.1186/s13059-020-02142-9


35. Ji, D., Juhas, M., Tsang, C. M., Kwok, C. K., Li, Y. & Zhang, Y. Discovery of G-quadruplex-forming sequences in SARS-CoV-2. Briefings in Bioinformatics. 22, 1150-1160 (2020). https://doi.org/10.1093/bib/bbaa114


34. Chow, E.Y.C., Lyu, K., Kwok, C. K. & Chan, T.F. rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments. RNA Biology. 17, 903-917 (2020). https://doi.org/10.1080/15476286.2020.1740470


33. Chan, C. Y., & Kwok, C. K. Specific Binding of a D‐RNA G‐Quadruplex Structure with an L‐RNA Aptamer. Angew. Chem. Int. Ed. 59, 5293 –5297​ (2020). https://doi.org/10.1002/anie.201914955


​32. Shao, X., Zhang, W., Umar, M. I., Wong, H. Y., Seng, Z., Xie, Y., Zhang, Y., Yang, L., Kwok, C. K. & Deng, X. RNA G-Quadruplex Structures Mediate Gene Regulation in Bacteria. mBio 11, 1 (2020). https://doi.org/10.1128/mbio.02926-19

2019

31. Ji, D., Li, Z., & Kwok, C. K. Rational design and development of a universal baby spinach-based sensing platform for the detection of biomolecules. Analyst. 144, 7173 - 7177​ (2019). https://doi.org/10.1039/c9an02061f

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​30. Lyu, K., Chen, S. B., Chan, C. Y., Tan, J. H., & Kwok, C. K. Structural analysis and cellular visualization of APP RNA G-quadruplex. Chemical Science. 10, 11095 - 11102 (2019). https://doi.org/10.1039/c9sc02768h


29. Ji, D., Mou, X., Kwok, C.K. Label-free and ratiometric detection of microRNA based on target-induced catalytic hairpin assembly and two fluorescent dyes. Analytical Methods​  11, 4808 - 4813​ (2019). https://doi.org/10.1039/C9AY01891C

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28. Umar, M.I.; Ji, D.; Chan, C.-Y.; Kwok, C.K. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 24, 2416 (2019). https://doi.org/10.3390/molecules24132416


27. Yeung, P.Y., Zhao, J., Chow, E.Y.C., Mou, X., Hong, H.Q., Chen, L.L., Chan, T.F., Kwok, C.K. Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing. Sci. Rep. 9, 8091 (2019). https://doi.org/10.1038/s41598-019-44541-4


26. Zhao, J., Qian, X., Yeung, P.Y., Zhang, Q.F.C., Kwok, C.K. Mapping In Vivo RNA Structures and Interactions. Trends Biochem. Sci.  44, 555-556 (2019). https://doi.org/10.1016/j.tibs.2019.01.012


25. Chan, C.-Y., Umar, M.I., Kwok, C.K. Spectroscopic analysis reveals the effect of a single nucleotide bulge on G-quadruplex structures. Chem Comm. 55, 2616-2619 (2019). https://doi.org/10.1039/c8cc09929d  


24. Qian, X., Zhao, J., Yeung, P.Y., Zhang, Q.F.C., Kwok, C.K. Revealing LncRNA Structures and Interactions by Sequencing-Based Approaches. Trends Biochem. Sci. 44, 33-52 (2019)​. https://doi.org/10.1016/j.tibs.2018.09.012

2018

23. Ziv, O., Gabryelska, M.M., Lun, A.T.L., Gebert, L.F.R., Sheu-Gruttadauria, J., Meredith, L.W., Liu, Z.Y., Kwok, C.K., Qin, C.F., MacRae, I.J., Goodfellow, I., Marioni, J.C., Kudla, G., Miska, E.A. COMRADES determines in vivo RNA structures and interactions. Nat Methods. 15, 785-788 (2018). https://doi.org/10.1038/s41592-018-0121-0 

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22. Chan, K.L., Peng, B., Umar, M.I., Chan, C.-Y., Sahakyan, A.B., Le, M.T.N., Kwok, C.K. Structural Analysis Reveals Formation and Role of RNA G-Quadruplex Structures in Human Mature MicroRNAs. Chem Comm. 54, 10878-10881 (2018). https://doi.org/10.1039/c8cc04635b 


21. ​Kwok, CK., Marsico, G., Balasubramanian, S. Detecting RNA G-quadruplexes (rG4s) in the Transcriptome. Cold Spring Harb Perspect Biol. 10:a032284 (2018). https://doi.org/10.1101/cshperspect.a032284


20. Ding, Y., Kwok, CK. Emergence of Vascular Plants. Nature Plants 4, 325–326 (2018). https://doi.org/10.1038/s41477-018-0159-0

2017

​19. Kwok, CK., Merrick, C.J. G-Quadruplexes: Prediction, Characterization, and Biological Application. Trends Biotechnol. 35, 997–1013 (2017). https://doi.org/10.1016/j.tibtech.2017.06.012

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18. ​Norris, M., Kwok, CK., Cheema J., Hartley M., Morris R.J., Aviran S., Ding, Y. FoldAtlas: A Repository for Genome-Wide RNA Structure Probing Data. Bioinformatics. 33, 306-308 (2017). https://doi.org/10.1093/bioinformatics/btw611

2016

​17. Kwok, CK., Dawn of the In Vivo RNA Structuome and Interactome. Biochem Soc. Trans. 44, 1395-1410 (2016). https://doi.org/10.1042/bst20160075

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16. Kwok, CK., Marsico, G., Sahakyan, A., Chambers V.S., Balasubramanian, S. rG4-Seq Reveals Widespread Formation of G-Quadruplex Structures in the Human Transcriptome. Nat. Methods. 13, 841-844 (2016). https://doi.org/10.1038/nmeth.3965 


15. Kwok, CK., Sahakyan, A., Balasubramanian, S. Structural Analysis using SHALiPE to Reveal RNA G-Quadruplex Formation in Human Precursor MicroRNA. Angew. Chem. Int. Ed. 55, 8958-8961 (2016). https://doi.org/10.1002/anie.201603562
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14. Sherlock, M.E., Rumble, C., Kwok, CK., Breffke, J., Maroncelli, M., & Bevilacqua, P.C. Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes. J. Phy. Chem. B 120, 5146-5158. (2016). https://doi.org/10.1021/acs.jpcb.6b03790

2015

13. Crenshaw, E., Leung, B.P., Kwok, CK., Olson, K., Sebastian, N.P., Ansaloni, S., Schweitzer-Stenner, R., Akins, M.P., Bevilacqua, P.C., & Saunders, A.J. Amyloid Precursor Protein Translation is Regulated by a 3’UTR Guanine Quadruplex. PloS One. 10(11): e0143160. (2015). https://doi.org/10.1371/journal.pone.0143160


12. Ding, Y., Kwok, CK., Tang, Y., Bevilacqua, P.C., & Assmann, S.M. Structure-Seq: Genome-Wide Profiling of In Vivo RNA Structure at Single Nucleotide Resolution. Nat. Protoc. 10, 1050-1066 (2015). https://doi.org/10.1038/nprot.2015.064


11. Tang, Y., Bouvier, E., Kwok, CK., Ding, Y., Nekrutenko, A., Bevilacqua, P.C., & Assmann, S.M. StructureFold: Genome-Wide RNA Secondary Structure Mapping and Reconstruction In Vivo. Bioinformatics. 31, 2668-2675 (2015). https://doi.org/10.1093/bioinformatics/btv213


10. Kwok, CK., & Balasubramanian, S. Targeted Detection of G-Quadruplexes in Cellular RNAs. Angew. Chem. Int. Ed. 54, 6751-6754 (2015). (Selected as Hot Paper.) https://doi.org/10.1002/anie.201500891


9. Kwok, CK., Tang, Y., Assmann, S.M., & Bevilacqua, P.C. The RNA Structurome: Transcriptome-Wide Structure Probing using Next-Gen Sequencing. Trends Biochem. Sci. 40, 221-232 (2015). (Featured on the cover) https://doi.org/10.1016/j.tibs.2015.02.005

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8. Kwok, CK., Ding, Y., Shahid, S., Assmann, S.M., & Bevilacqua, P.C. A Stable RNA G-Quadruplex within the 5’UTR of Arabidopsis Thaliana ATR mRNA Inhibits Translation. Biochem. J. 467, 91-102 (2015). (Featured in HFSP website) https://doi.org/10.1042/bj20141063

2014

7.  Ding, Y., Tang, Y., Kwok, CK., Zhang, Y., Bevilacqua, P.C. Assmann, S.M. In vivo Genome-Wide Profiling of RNA Secondary Structures Reveal Novel Regulatory Features. Nature. 505, 696-700 (2014). (Featured on the cover, F1000 site http://f1000.com/prime/718185620, Nature 505, 621-622 (2014), Nat. Meth.11, 11 (2014) and Nat. Chem. Biol. 10, 87 (2014).) https://doi.org/10.1038/nature12756

2013


​6. Kwok, CK., Ding, Y., Tang, Y., Assmann, S.M., Bevilacqua, P.C. Determination of in vivo RNA Structure in Low-Abundance Transcripts. Nat. Commun. 4, 2971 (2013). (Featured in Nat. Meth.11, 11 (2014).) https://doi.org/10.1038/ncomms3971 
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5. Kwok, CK., Lam, SL. NMR Proton Chemical Shift Prediction of T∙T Mismatches in B-DNA Duplexes. J. Magn. Reson. 234, 184-189 (2013). https://doi.org/10.1016/j.jmr.2013.06.022
  

4. Kwok, CK., Sherlock, M.E. & Bevilacqua, P.C. Effect of Loop Sequence and Loop Length on the Intrinsic Fluorescence of G-Quadruplexes. Biochemistry 52, 3019-3021 (2013). https://doi.org/10.1021/bi400139e   


3. Kwok, CK., Ding, Y., Sherlock, M.E., Assmann, S.M. & Bevilacqua, P.C. A Hybridization-Based Approach for Quantitative and Low-Bias Single-Stranded DNA Ligation. Anal. Biochem. 435, 181-186 (2013). Featured on the cover. https://doi.org/10.1016/j.ab.2013.01.008    

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2.  Kwok, CK., Sherlock, M.E. & Bevilacqua, P.C. Decrease in RNA Folding Cooperativity by Deliberate Population of Intermediates in RNA G-Quadruplexes. Angew. Chem., Int. Ed. 52, 683-686 (2013). (Featured in F1000 site. http://f1000.com/prime/717970147.) https://doi.org/10.1002/anie.201206475

2011

1.  He, G., Kwok, CK. & Lam, SL. Preferential Base Pairing Modes of T.T Mismatches. FEBS Lett. 585, 3953-3958 (2011). https://doi.org/10.1016/j.febslet.2011.10.044
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