A STUDY ON THE INTERACTION BETWEEN RHAU PEPTIDE AND G-QUADRUPLEX FOR DEVELOPING FUNCTIONAL PROTEINS THAT TARGET G-QUADRUPLEX
Main Article Content
Abstract
G-quadruplex (G4) is a secondary structure of acid nucleic which is formed in Guanine-rich sequence. The formation of the G4 structure involves many cellular biological processes such as replication, transcription, translation, and maintenance of telomeres. Therefore, the G4 has been considered a target molecule for the design of drugs that can control these biological processes. Currently, RHAU peptide has emerged as a molecule that can specifically recognize and bind to a parallel G4 structure. In particular, the fusion of RHAU peptides with functional protein domains can target the G4 structure and play their biological functions. In this review, we discuss the applications of specific interactions between RHAU peptides and parallel G4 in biochemical processes.
Keywords
G-quadruplex, peptide RHAU, RHAU/G-quadruplex interaction, fusion protein, biochemical process
Article Details
References
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Dang, D. T., Nguyen, L. T. A., Truong, T. T. T., Nguyen, H. D., & Phan, A. T. (2021). Construction of a G-quadruplex-specific DNA endonuclease. Chem Commun (Camb), 57(37), 4568-4571. https:/doi.org/10.1039/d0cc05890d
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Di Antonio, M., Ponjavic, A., Radzevicius, A., Ranasinghe, R. T., Catalano, M., Zhang, X., Shen J, Needham, L. M., Lee, S. F., Klenerman, D, & Balasubramanian S. (2020). Single-molecule visualization of DNA G-quadruplex formation in live cells. Nat Chem, 12(9), 832-837. https:/doi.org/10.1038/s41557-020-0506-4
Dutta, D., Debnath, M., Müller, D., Paul, R., Das, T., Bessi, I., Schwalbe, H., & Dash, J. (2018). Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex. Nucleic acids research, 46(11), 5355-5365.
Gaur, P., Bain, F. E., Honda, M., Granger, S. L., & Spies, M. (2023). Single-Molecule Analysis of the Improved Variants of the G-Quadruplex Recognition Protein G4P. Int J Mol Sci, 24(12). https:/doi.org/10.3390/ijms241210274
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Marzano, M., Falanga, A. P., Marasco, D., Borbone, N., D'Errico, S., Piccialli, G., Roviello, G. N., & Oliviero, G. (2020). Evaluation of an Analogue of the Marine ε-PLL Peptide as a Ligand of G-quadruplex DNA Structures. Marine drugs, 18(1), Article 49. https://doi.org/10.3390/md18010049
Meier, M., Patel, T. R., Booy, E. P., Marushchak, O., Okun, N., Deo, S., Howard, R., McEleney, K., Harding, S. E., Stetefeld, J., & McKenna, S. A. (2013). Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU). The Journal of biological chemistry, 288(49), 35014-35027.
Ngo, K. H., Yang, R., Das, P., Nguyen, G. K. T., Lim, K. W., Tam, J. P., Wu, B., & Phan, A. T. (2020). Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chemical Commun, 56(7), 1082-1084. https://doi.org/10.1039/c9cc06748e
Nguyen, L. T. A., & Dang, D. T. (2023). RHAU Peptides Specific for Parallel G-Quadruplexes: Potential Applications in Chemical Biology. Mol Biotechnol, 65(3), 291-299. https:/doi.org/10.1007/s12033-022-00552-7
Pany, S. P. P., Sapra, M., Sharma, J., Dhamodharan, V., Patankar, S., & Pradeepkumar, P. I. (2019). Presence of Potential G-Quadruplex RNA-Forming Motifs at the 5'-UTR of PP2Acalpha mRNA Repress Translation. Chembiochem, 20(23), 2955-2960. https:/doi.org/10.1002/cbic.201900336
Patel, D. J., Phan, A. T., & Kuryavyi, V. (2007). Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res, 35(22), 7429-7455. https:/doi.org/10.1093/nar/gkm711
Phan, A. T. (2010). Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J, 277(5), 1107-1117.
Phan, A. T., Kuryavyi, V., & Patel, D. J. (2006). DNA architecture: from G to Z. Curr Opin Struct Biol, 16(3), 288-298.
Reddy Chichili, V. P., Kumar, V., & Sivaraman, J. (2013). Linkers in the structural biology of protein-protein interactions. Protein Sci, 22(2), 153-167. https:/doi.org/10.1002/pro.2206
Rhodes, D., & Lipps, H. J. (2015). G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res, 43(18), 8627-8637.
Sengupta, P., Banerjee, N., Roychowdhury, T., Dutta, A., Chattopadhyay, S., & Chatterjee, S. (2018). Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells. Nucleic Acids Res, 46(19), 9932-9950. https:/doi.org/10.1093/nar/gky824
Simonsson, T. (2001). G-quadruplex DNA structures--variations on a theme. Biol Chem, 382(4), 621-628. doi:10.1515/BC.2001.073
Spiegel, J., Adhikari, S., & Balasubramanian, S. (2020). The Structure and Function of DNA G-Quadruplexes. Trends Chem, 2(2), 123-136. https:/doi.org/10.1016/j.trechm.2019.07.002
Storz, G. (2002). An expanding universe of noncoding RNAs. Science, 296(5571), 1260-1263. https:/doi.org/10.1126/science.1072249
Sulej, A. A., Tuszynska, I., Skowronek, K. J., Nowotny, M., & Bujnicki, J. M. (2012). Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger. Nucleic Acids Res, 40(22), 11563-11570. https:/doi.org/10.1093/nar/gks885
Sun, Z. Y., Wang, X. N., Cheng, S. Q., Su, X. X., & Ou, T. M. (2019). Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid(-)Protein Interaction. Molecules, 24(3), Article 396. https:/doi.org/10.3390/molecules24030396
Truong,T. T. T., Cao, C., & Dang, D. T. (2020). Parallel G-quadruplex-mediated protein dimerization and activation. RSC Adv, 10(50), 29957-29960. https:/doi.org/10.1039/d0ra06173e
Truong,T. T. T., Phan, T. P. T., Le, T. R. L., Nguyen, H. D., Nguyen, D. H., & Dang, D. T. (2018). Engineering yellow fluorescent protein probe for visualization of parallel DNA G-quadruplex. Science and Technology Development Journal, 21(3-4), 84-89.
Walton, C. M., Wu, C. H., & Wu, G. Y. (2001). A ribonuclease H-oligo DNA conjugate that specifically cleaves hepatitis B viral messenger RNA. Bioconjug Chem, 12(5), 770-775. https:/doi.org/10.1021/bc010018e
Wu, T. Y., Huang, Q., Huang, Z. S., Hu, M. H., & Tan, J. H. (2020). A drug-like imidazole-benzothiazole conjugate inhibits malignant melanoma by stabilizing the c-MYC G-quadruplex. Bioorg Chem, 99, Article 103866. https:/doi.org/10.1016/j.bioorg.2020.103866
Wu, Y., & Brosh, R. M., Jr. (2010). G-quadruplex nucleic acids and human disease. FEBS J, 277(17), 3470-3488. https:/doi.org/10.1111/j.1742-4658.2010.07760.x
Zheng, K. W., Zhang, J. Y., He, Y. D., Gong, J. Y., Wen, C. J., Chen, J. N., Hao, Y. H., Zhao, Y., & Tan, Z. (2020). Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic acids research, 48(20), 11706-11720. https://doi.org/10.1093/nar/gkaa841
Breaker, R. R., & Joyce, G. F. (2014). The expanding view of RNA and DNA function. Chem Biol, 21(9), 1059-1065. https:/doi.org/10.1016/j.chembiol.2014.07.008
Chen, B. J., Wu, Y. L., Tanaka, Y., & Zhang, W. (2014). Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics. Int J Biol Sci, 10(10), 1084-1096.
Cooper, T. A., Wan, L., & Dreyfuss, G. (2009). RNA and disease. Cell, 136(4), 777-793. https:/doi.org/10.1016/j.cell.2009.02.011
Dang, D. T. (2022). Molecular Approaches to Protein Dimerization: Opportunities for Supramolecular Chemistry. Front Chem, 10, Article 829312. https:/doi.org/10.3389/fchem.2022.829312
Dang, D. T., Nguyen, L. T. A., Truong, T. T. T., Nguyen, H. D., & Phan, A. T. (2021). Construction of a G-quadruplex-specific DNA endonuclease. Chem Commun (Camb), 57(37), 4568-4571. https:/doi.org/10.1039/d0cc05890d
Dang, D. T., & Phan, A. T. (2016). Development of Fluorescent Protein Probes Specific for Parallel DNA and RNA G-Quadruplexes. Chembiochem, 17(1), 42-45. https:/doi.org/10.1002/cbic.201500503
Dang, D. T., & Phan, A. T. (2019). Development of a ribonuclease containing a G4-specific binding motif for programmable RNA cleavage. Sci Rep, 9(1), Article 7432. https:/doi.org/10.1038/s41598-019-42143-8
Dang, D. T., Thao, N. T. T. (2018). G-quadruplex: Mục tiêu tiềm năng cho những phân tử nhỏ và protein trong việc tạo thuốc trị ung thư. [G-quadruplex: A potential target for small molecules and proteins in anti-cancer drug investigation]. Ho Chi Minh City Open University Journal of Science, 13(1), 81-92.
Di Antonio, M., Ponjavic, A., Radzevicius, A., Ranasinghe, R. T., Catalano, M., Zhang, X., Shen J, Needham, L. M., Lee, S. F., Klenerman, D, & Balasubramanian S. (2020). Single-molecule visualization of DNA G-quadruplex formation in live cells. Nat Chem, 12(9), 832-837. https:/doi.org/10.1038/s41557-020-0506-4
Dutta, D., Debnath, M., Müller, D., Paul, R., Das, T., Bessi, I., Schwalbe, H., & Dash, J. (2018). Cell penetrating thiazole peptides inhibit c-MYC expression via site-specific targeting of c-MYC G-quadruplex. Nucleic acids research, 46(11), 5355-5365.
Gaur, P., Bain, F. E., Honda, M., Granger, S. L., & Spies, M. (2023). Single-Molecule Analysis of the Improved Variants of the G-Quadruplex Recognition Protein G4P. Int J Mol Sci, 24(12). https:/doi.org/10.3390/ijms241210274
Gellert, M., Lipsett, M. N., & Davies, D. R. (1962). Helix formation by guanylic acid. Proc Natl Acad Sci U S A, 48(12), 2013-2018. https:/doi.org/10.1073/pnas.48.12.2013
Heddi, B., Cheong, V. V., Martadinata, H., & Phan, A. T. (2015). Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex. Proc Natl Acad Sci U S A, 112(31), 9608-9613. https:/doi.org/10.1073/pnas.1422605112
Marzano, M., Falanga, A. P., Marasco, D., Borbone, N., D'Errico, S., Piccialli, G., Roviello, G. N., & Oliviero, G. (2020). Evaluation of an Analogue of the Marine ε-PLL Peptide as a Ligand of G-quadruplex DNA Structures. Marine drugs, 18(1), Article 49. https://doi.org/10.3390/md18010049
Meier, M., Patel, T. R., Booy, E. P., Marushchak, O., Okun, N., Deo, S., Howard, R., McEleney, K., Harding, S. E., Stetefeld, J., & McKenna, S. A. (2013). Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU). The Journal of biological chemistry, 288(49), 35014-35027.
Ngo, K. H., Yang, R., Das, P., Nguyen, G. K. T., Lim, K. W., Tam, J. P., Wu, B., & Phan, A. T. (2020). Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chemical Commun, 56(7), 1082-1084. https://doi.org/10.1039/c9cc06748e
Nguyen, L. T. A., & Dang, D. T. (2023). RHAU Peptides Specific for Parallel G-Quadruplexes: Potential Applications in Chemical Biology. Mol Biotechnol, 65(3), 291-299. https:/doi.org/10.1007/s12033-022-00552-7
Pany, S. P. P., Sapra, M., Sharma, J., Dhamodharan, V., Patankar, S., & Pradeepkumar, P. I. (2019). Presence of Potential G-Quadruplex RNA-Forming Motifs at the 5'-UTR of PP2Acalpha mRNA Repress Translation. Chembiochem, 20(23), 2955-2960. https:/doi.org/10.1002/cbic.201900336
Patel, D. J., Phan, A. T., & Kuryavyi, V. (2007). Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res, 35(22), 7429-7455. https:/doi.org/10.1093/nar/gkm711
Phan, A. T. (2010). Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J, 277(5), 1107-1117.
Phan, A. T., Kuryavyi, V., & Patel, D. J. (2006). DNA architecture: from G to Z. Curr Opin Struct Biol, 16(3), 288-298.
Reddy Chichili, V. P., Kumar, V., & Sivaraman, J. (2013). Linkers in the structural biology of protein-protein interactions. Protein Sci, 22(2), 153-167. https:/doi.org/10.1002/pro.2206
Rhodes, D., & Lipps, H. J. (2015). G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res, 43(18), 8627-8637.
Sengupta, P., Banerjee, N., Roychowdhury, T., Dutta, A., Chattopadhyay, S., & Chatterjee, S. (2018). Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells. Nucleic Acids Res, 46(19), 9932-9950. https:/doi.org/10.1093/nar/gky824
Simonsson, T. (2001). G-quadruplex DNA structures--variations on a theme. Biol Chem, 382(4), 621-628. doi:10.1515/BC.2001.073
Spiegel, J., Adhikari, S., & Balasubramanian, S. (2020). The Structure and Function of DNA G-Quadruplexes. Trends Chem, 2(2), 123-136. https:/doi.org/10.1016/j.trechm.2019.07.002
Storz, G. (2002). An expanding universe of noncoding RNAs. Science, 296(5571), 1260-1263. https:/doi.org/10.1126/science.1072249
Sulej, A. A., Tuszynska, I., Skowronek, K. J., Nowotny, M., & Bujnicki, J. M. (2012). Sequence-specific cleavage of the RNA strand in DNA-RNA hybrids by the fusion of ribonuclease H with a zinc finger. Nucleic Acids Res, 40(22), 11563-11570. https:/doi.org/10.1093/nar/gks885
Sun, Z. Y., Wang, X. N., Cheng, S. Q., Su, X. X., & Ou, T. M. (2019). Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid(-)Protein Interaction. Molecules, 24(3), Article 396. https:/doi.org/10.3390/molecules24030396
Truong,T. T. T., Cao, C., & Dang, D. T. (2020). Parallel G-quadruplex-mediated protein dimerization and activation. RSC Adv, 10(50), 29957-29960. https:/doi.org/10.1039/d0ra06173e
Truong,T. T. T., Phan, T. P. T., Le, T. R. L., Nguyen, H. D., Nguyen, D. H., & Dang, D. T. (2018). Engineering yellow fluorescent protein probe for visualization of parallel DNA G-quadruplex. Science and Technology Development Journal, 21(3-4), 84-89.
Walton, C. M., Wu, C. H., & Wu, G. Y. (2001). A ribonuclease H-oligo DNA conjugate that specifically cleaves hepatitis B viral messenger RNA. Bioconjug Chem, 12(5), 770-775. https:/doi.org/10.1021/bc010018e
Wu, T. Y., Huang, Q., Huang, Z. S., Hu, M. H., & Tan, J. H. (2020). A drug-like imidazole-benzothiazole conjugate inhibits malignant melanoma by stabilizing the c-MYC G-quadruplex. Bioorg Chem, 99, Article 103866. https:/doi.org/10.1016/j.bioorg.2020.103866
Wu, Y., & Brosh, R. M., Jr. (2010). G-quadruplex nucleic acids and human disease. FEBS J, 277(17), 3470-3488. https:/doi.org/10.1111/j.1742-4658.2010.07760.x
Zheng, K. W., Zhang, J. Y., He, Y. D., Gong, J. Y., Wen, C. J., Chen, J. N., Hao, Y. H., Zhao, Y., & Tan, Z. (2020). Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic acids research, 48(20), 11706-11720. https://doi.org/10.1093/nar/gkaa841