Publications
# Equal contribution; * Co-corresponding author
Shiu, P.K., Illieva, M., Holm, A., Uchida, S., DiStefano, J.K., Bronisz, A., Yang, L., Asahi, Y., Goel, A., Yang, L., Nuthanakanti, A., Serganov, A., Alahari, S.K., Lin, C., Pardini, B., Naccarati, A., Jin, J., Armanios, B., Zhong, X., Sideris, N., Bayraktar, S., Castellano, L., Gerber, A., Lin, H., Conn, S., Sleem, D., Timmons, L.
2023The Non-Coding RNA Journal Club: Highlights on Recent Papers-12
Noncoding RNA, 9: 28.
#Weaver, J.W., #Proshkin, S., Duan, W., Epshtein, V., Gowder, M., Bharati, B.K., Afanaseva, E., Mironov, A., Serganov, A., Nudler, E.
2023Control of transcription elongation and DNA repair by alarmone ppGpp
Nat. Struct. Mol. Biol., 30: 600-607.
Nuthanakanti, A., Ariza-Mateos, A., Serganov, A.
2022X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch
Methods Mol. Biol., 2568: 213-232.
Bonnet, H., Bogard, B., Hubé, F., Ilieva, M., Uchida, S., Ariza-Mateos, A., Serganov, A., Pardini, B., Naccarati, A., Santulli, G., Varzideh, F., Xiao, H., Shiu, P.K.
2022The Non-Coding RNA Journal Club: Highlights on Recent Papers-11
Noncoding RNA., 8: 31.
Zeller, M.J., Favorov, O., Li, K., Nuthanakanti, A., Hussein, D., Michaud, A., Lafontaine, D.A., Busan, S., Serganov, A., Aubé, J., Weeks, K.M.
2022SHAPE-enabled fragment-based ligand discovery for RNA
Proc. Natl. Acad. Sci. U. S. A., 119: e2122660119.
Levenson-Palmer, R., Luciano, D.J., Vasilyev, N., Nuthanakanti, A., Serganov, A., Belasco, J.G.
2022A distinct RNA recognition mechanism governs Np4 decapping by RppH
Proc. Natl. Acad. Sci. U. S. A., 119: e2117318119.
Zeller, M.J., Nuthanakanti, A., Li, K., Aubé, J., Serganov, A., Weeks, K.M.
2022ACS Chem. Biol., 17(2): 438-448.
Kaushik, A., Nuthanakanti, A., Serganov, A.
2021Growing a garden of fluorescent RNAs
Nat. Chem. Biol. 18: 120-122.
Ariza-Mateos, A., Nuthanakanti, A., Serganov, A.
2021Riboswitch mechanisms: new tricks for an old dog.
Biochemistry (Mosc). 86: 962-975.
#Shatalin, K., #Nuthanakanti, A., Kaushik, A., Shishov, D., Peselis, A., Shamovsky, I., Pani, B., Lechpammer, M., Vasilyev, N., Shatalina, E., Rebatchouk, D., Mironov, A., Fedichev, P., Serganov, A., Nudler, E.
2021Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance
Science. 372: 1169-1175.
Peselis, A., Serganov, A.
2021Cooperativity and allostery in RNA systems
Methods Mol. Biol. 2253: 255-271.
Gao, A., Vasilyev, N., Kaushik, A., Duan, W., Serganov, A.
2020Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH
Nucleic Acids Res. 48: 776-3788.
Zhu, Y., #Gao, A.,#Zhan, Q., Wang, Y., Feng, H., Liu, S., Gao, G., Serganov, A.,* Gao, P.*
2019Diverse mechanisms of CRISPR-Cas9 inhibition by type IIC anti-CRISPR proteins.
Mol. Cell. 74: 296-309.e7.
Peselis, A., Serganov, A.
2018ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands
Nat Chem Biol., 14: 887-894.
Vasilyev, N., Gao, A., Serganov, A.
2018Noncanonical features and modifications on the 5′-end of bacterial sRNAs and mRNAs
Wiley Interdiscip. Rev. RNA, 10: e1509
Gao, A., Vasilyev, N., Luciano, D.J., Levenson-Palmer, R., Richards, J., Marsiglia, W.M., Traaseth, N.J., Belasco, J.G., Serganov, A.
2018Nucleic Acids Res., 46: 6841-6856.
Luciano, D.J., Vasilyev, N., Richards, J., Serganov, A., Belasco, J.G.
2018Importance of a diphosphorylated intermediate for RppH-dependent RNA degradation
RNA Biol., 15: 703-706.
Luciano, D.J., Vasilyev, N., Richards, J., Serganov, A., Belasco, J.G.
2017A novel RNA phosphorylation state enables 5′ end-dependent degradation in Escherichia coli
Mol. Cell, 67: 44-54. e6.
Vasilyev, N. & Serganov, A.
2016Methods Mol. Biol., 1320: 11-20.
Peselis, A., Gao, A., Serganov, A.
2016Preparation and crystallization of riboswitches
Methods Mol. Biol., 1320: 21-36.
Ren, A., Xue, Y., Peselis, A., Serganov, A., Al-Hashimi, H.M. and Patel, D. J.
2015Cell Rep., 13: 1800-13
Vasilyev, N., Polonskaia, A., Darnell, J., Darnell, R., Patel, D.J. & Serganov, A.
2015Proc. Natl. Acad. Sci. U.S.A., 112: E5391-400
Miao, Z., Adamiak, R.W., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cheng, C., Chojnowski, G., Chou, F.C., Cordero, P., Cruz, J.A., Ferré-D’amaré, A.R., Das, R., Ding, F., Dokholyan, N.V., Dunin-Horkawicz, S., Kladwang, W., Krokhotin, A., Lach, G., Magnus, M., Major, F., Mann, T.H., Masquida, B., Matelska, D., Meyer, M., Peselis, A., Popenda, M., Purzycka, K.J., Serganov, A., Stasiewicz, J., Szachniuk, M., Tandon, A., Tian, S., Wang, J., Xiao, Y., Xu, X., Zhang, Zhao, P., Zok, T., Westhof, E.
2015RNA, 21: 1066-84
Vasilyev, N. & Serganov, A.
2015J Biol. Chem., 290: 9487-99
Peselis, A., Gao, A., Serganov, A.
2015Cooperativity, allostery and synergism in ligand binding to riboswitches
Biochimie, 117: 100-9.
Peselis, A. & Serganov, A.
2014Structure and function of pseudoknots involved in gene expression control
WIREs RNA, 5: 803-22
Peselis, A. & Serganov, A.
2014Themes and variations in riboswitch structure and function
Biochim. Biophys. Acta, 1839: 908-918
Gao, A. & Serganov, A.
2014Structural insights into recognition of c-di-AMP by the ydaO riboswitch
Nat. Chem. Biol., 10: 787-792
Cruz, J.A., Blanchet, M.F., Boniecki, M., Bujnicki, J.M., Chen, S.J., Cao, S., Das, R., Ding, F., Dokholyan, N.V., Flores, S.C., Huang, L., Lavender, C.A., Lisi, V., Major, F., Mikolajczak, K., Patel, D.J., Philips, A., Puton, T., Santalucia, J., Sijenyi, F., Hermann, T., Rother, K., Rother, M., Serganov, A., Skorupski, M., Soltysinski, T., Sripakdeevong, P., Tuszynska, I., Weeks, K.M., Waldsich, C., Wildauer, M., Leontis, N.B., & Westhof, E.
2012RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction
RNA 18, 610-625. (Reviewed in Faculty of 1000)
Serganov, A.* & Patel, D.J.
2012Metabolite recognition principles and molecular mechanisms underlying riboswitch function
Annu. Rev. Biophys., 41:343-70
Serganov, A.* & Patel, D.J.
2012Molecular recognition and function of riboswitches
Curr. Opin. Struct. Biol., 22: 279-286
Peselis, A. & Serganov, A.
2012Nat. Struct. Mol. Biol., 19: 1182-1184. (News & Views, in Breaker, R., 2012, Nat. Struct. Mol. Biol., 19: 1208-1209; Highlight, in Micura, R., 2013, Angewandte Chemie, 52: 1874-1877).
Phan, A.T., Kuryavyi, V., Darnell, J.C., Serganov, A., Majumdar, A., Ilin, S., Raslin, T., Polonskaia, A., Chen, C., Clain, D., Darnell, R.B. & Patel, D.J.
2011Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction
Nat. Struct. Mol. Biol., 18: 774-804
Pikovskaya, O., Polonskaya, A., Patel, D.J. & Serganov, A.
2011Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch
Nat. Chem. Biol., 7: 748-755. (News & Views in Dann, C.E., III., Nat. Chem. Biol., 7: 748-755).
Huang, L., Ishibe-Murakami, S., Patel, D.J. & Serganov, A.
2011Proc. Natl. Acad. Sci. USA, 108: 14801-14806
Serganov, A.
2010Determination of riboswitch structures: light at the end of the tunnel?
RNA Biology (special issue), 7: 98-103. (January/February cover)
Huang, L. #, Serganov, A. #* & Patel, D.J.
2010Mol. Cell, 40: 774-786. (Reviewed in Faculty of 1000)
Pikovskaya, O., Serganov, A.A., Polonskaia, A., Serganov, A.*, Patel, D.J.
2009Preparation and crystallization of riboswitch-ligand complexes
Methods Mol. Biol., 540: 115-128
Olieric, V., Rieder, U., Lang, K., Serganov, A, Schulze-Briese, C., Micura, R., Dumas, P. & Ennifar, E.
2009A fast selenium derivatization strategy for crystallization and phasing of RNA structures
RNA, 15: 707-715. (Reviewed in Faculty of 1000)
Serganov, A.*#, Huang, L.# & Patel, D.J.
2009Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
Nature, 458: 233-237. (Reviewed in Faculty of 1000)
Serganov, A.* & Patel, D.J.
2009Amino acid recognition and gene regulation by riboswitches
Biochim. Biophys. Acta/Gene Regulatory Mechanisms (special issue), 1789: 592-611
Serganov, A.* & Patel, D.J.
2008Towards deciphering the principles underlying an mRNA recognition code
Curr. Opin. Struct. Biol., 18: 120-129
Serganov, A.*#, Huang, L.# & Patel, D.J.
2008Structural insights into amino acid binding and gene control by a lysine riboswitch
Nature, 455: 11263-11267. (Point of View in Underwood & Gordon, 2008, ACS Chem. Biol., 3: 660–665)
Marzi, S., Myasnikov, A.G., Serganov, A., Ehresmann, C., Romby, P., Yusupov, M. & Klaholz, B.P.
2007Structured mRNAs regulate translation initiation by binding to a dedicated site on the ribosome
Cell, 130: 1019-1031. (Previewed in Boehringer & Ban, Cell, 130: 983)
Serganov, A.* & Patel, D.J
2007Ribozymes, riboswitches and beyond: regulation of gene expression without proteins
Nature Rev. Genetics, 8: 760-7
Moroder, H., Kreutz, C., Lang, K., Serganov, A.* & Micura, R.
2006J. Am. Chem. Soc., 128: 9909-9918
Serganov, A.*, Polonskaia, A., Phan, A.T., Breaker, R.R. & Patel, D.J.
2006Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
Nature, 441: 1167-1171. (News & Views in Reichow & Varani, 2006, Nature, 441: 1054-1055; preview in Nudler, 2006, Cell, 126: 19-22; Point of View in Sashital & Butcher, 2006, ACS Chemical Biology, 1: 341-345; reviewed in Faculty of 1000)
Wombacher, R., Keiper, S., Suhm., S., Serganov, A., Patel, D.J. & Jaschke, A.
2006Control of stereoselectivity in an enzymatic reaction by backdoor access
Angew. Chem. Int. Ed. Engl., 45: 2469-2472
Hobartner, C., Rieder, R., Kreutz, C., Puffer, B., Lang, K., Polonskaia, A., Serganov, A. & Micura, R.
2005J. Am. Chem. Soc., 127: 12035-12045
Serganov, A., Keiper, S., Malinina, L., Tereshko, V., Skripkin, E., Hobartner, C., Polonskaia, A., Phan, A.T., Wombacher, R., Micura, R., Dauter, Z., Jaschke, A. & Patel, D.J.
2005Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation
Nat. Struct. Mol. Biol., 12: 218-224. (March cover; News & Views in Pitt & Ferre-D’Amare, 2005, Nature Struct. Biol., 10: 206-208; reviewed in Faculty of 1000).
Ehresmann, C., Ehresmann, B., Ennifar, E., Dumas, P., Garber, M., Mathy, N., Nikulin, A., Portier, C. & Patel, D.J. & Serganov, A.
2004Molecular mimicry in translational regulation: the case of ribosomal protein S15
RNA Biology, 1: 66-73
Serganov, A., Yuan, Y.R., Pikovskaya, O., Polonskaia, A., Malinina, L., Phan, A.T., Hobartner, C., Micura, R., Breaker, R.R. & Patel, D.J.
2004Chem. Biol., 11: 1729-1741. (December cover; highlighted in Lescoute & Westhof, Chem. Biol. 2005, 12: 10-13; reviewed in Faculty of 1000)
Serganova, I., Doubrovin, M., Vider, M., Ponomarev, V., Soghomonyan, S., Beresten, T., Ageyeva, L., Serganov, A., Cai, S., Balatoni, J., Blasberg, R. & Gelovani, J.
2004Cancer Research, 64: 6101-6108
Pitt, S.W., Majumdar, A., Serganov, A., Patel, D.J. & Al-Hashimi, H.M.
2004J. Mol. Biol., 338: 7-16
Mathy, N., Pellegrini, O., Serganov, A., Patel, D.J., Ehresmann, C. & Portier, C.
2004Mol. Microbiol., 52: 661-675
Zhang, Q., Throolin, R., Pitt, S., Serganov, A. & Al-Hashimi, H.
2003J. Amer. Chemical Society, 125: 10530-10531
Serganov, A., Polonskaia, A., Ehresmann, B., Ehresmann, C. & Patel, D.J.
2003EMBO J., 22: 1898-1908. (News & Views in Springer & Portier, 2003, Nature Struct. Biol., 10: 420-422).
Garber, M., Gongadze, G., Meshcheryakov, V., Nikonov, O., Nikulin, A., Perederina, A., Piendl, W., Serganov, A. & Tishchenko, S.
2002Crystallization of RNA/protein complexes
Acta Crystallogr. D, 58: 1664-1669
Ye, K., Serganov, A., Hu, W., Garber, M. & Patel, D.J.
2002Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold
Eur. J. Biochem., 269: 5182-5191
Serganov, A., Ennifar, E., Portier, C., Ehresmann, B. & Ehresmann, C.
2002J. Mol. Biol., 320: 963-978
Serganova, I., Ksenzenko, V., Serganov, A., Meshcheryakova, I., Pyatibratov, M., Vakhrusheva, O., Metlina, A. & Fedorov, O.
2002J. Bacter., 184: 318-322
Tishchenko, S.V., Vassilieva, J.M., Platonova, O.B., Serganov, A.A., Fomenkova, N.P., Mudrik, E.S., Piendl, W., Ehresmann, C., Ehresmann, B. & Garber, M.B.
2001Biochemistry (Moscow), 66: 948-953
Gongadze, G.M., Perederina, A.A., Meshcheryakov, V.A., Fedorov, R.V., Moskalenko, S.E., Rak, A.V., Serganov, A.A., Shcherbakov, D.V., Nikonov, S.V. & Garber, M.B.
2001Molecular Biology (Moscow), 35: 521-526
Serganov, A., Benard, L., Portier, C., Ennifar, E., Garber, M., Ehresmann B. & C. Ehresmann
2001Role of conserved nucleotides in building the 16S rRNA binding site for ribosomal protein S15
J. Mol. Biol., 305: 785-803
Ennifar, E., Nikulin, A., Tishchenko, S., Serganov, A., Nevskaya, N., Garber, M. Ehresmann, B., Ehresmann, C., Nikonov, S. & P. Dumas.
2000The crystal structure of UUCG tetraloop
J. Mol. Biol., 304: 35-42
Nikulin, A., Serganov, A., Ennifar, E., Tishchenko, S., Nevskaya, N., Shepard, W., Portier, C., Garber, M., Ehresmann, B., Ehresmann, C., Nikonov, S. & P. Dumas.
2000Crystal structure of the S15-rRNA complex
Nature Struct. Biol., 7: 273-277. (News & Views in Konforti, 2000, Nature Struct. Biol., 7: 355)
Gongadze, G.M., Meshcheryakov, V.A., Serganov, A.A., Fomenkova, N.P. Mudrik, E.S., Jonsson, B.-H., Liljas, A., Nikonov, S.V. & Garber, M.B.
1999FEBS Lett., 451: 51-55
Serganov, A., Rak, A., Garber, M., Reinbolt, J., Ehresmann, B., Ehresmann, C., Grunberg-Manago, M. & Portier, C.
1997Eur. J. Biochem., 246: 291-300
Berglund, H., Rak, A., Serganov, A., Garber, M., & Hard, T. . (News & Views in Yonath & Franceschi, 1997, Nature Struct. Biol., 4: 3).
1997Solution structure of the ribosomal RNA-binding protein S15 from T. thermophilus
Nature Struct. Biol., 4: 20-23. (News & Views in Yonath & Franceschi, 1997, Nature Struct. Biol., 4: 3)
Garber, M., Davydova, N., Eliseikina, I., Fomenkova, N., Gryaznova, O., Gryshkovskaya, I., Nevskaya, N., Nikonov, S., Rak, A., Sedelnikova, S., Serganov, A., Shcherbakov, D., Tishchenko, S., Zheltonosova, J., Lilias, A., Aevarsson, A. & Al-Karadaghi, S.
1996J. Cryst. Growth., 168: 301-307
Serganov, A., Masquida, B., Westhof, E., Cachia, C., Portier, C., Garber, M., Ehresmann, B. & Ehresmann C.
1996RNA, 2: 1124-1138
Friguet, B., Fedorov, A., Serganov, A., Navon, A. & Goldberg, M.
1993Analytical Biochem. 210: 344-350