# Equal contribution; * Co-corresponding author

Kaushik, A., Nuthanakanti, A., Serganov, A.


Growing a garden of fluorescent RNAs

Nat Chem Biol. Dec 22. doi: 10.1038/s41589-021-00921-4

Ariza-Mateos, A., Nuthanakanti, A., Serganov, A.


Riboswitch 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.


Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance

Science 372: 1169-1175

Peselis, A., Serganov, A.


Cooperativity and allostery in RNA systems

Methods Mol Biol. 2253: 255-271

Gao, A.#, Vasilyev, N.#, Kaushik, A.,  Duan, W. and Serganov, A.


Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH

Nucleic Acids Res. 48: 776-3788


Weaver, J.W., & Serganov, A.


T-box RNA gets boxed

Nat. Struct. Mol. Biol. 26: 1081-1083

Zhu, Y.,# Gao, A.,# Zhan, Q., Wang, Y., Feng, H., Liu, S., Gao, G., Serganov, A.,* Gao, P.*


Diverse mechanisms of CRISPR-Cas9 inhibition by type IIC anti-CRISPR proteins.

Mol. Cell. 201974: 296-309.e7

Peselis, A., Serganov, A.


ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands

Nat Chem Biol., 14: 887-894.

Vasilyev, N., Gao, A., Serganov, A.


Noncanonical 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.


Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF

Nucleic Acids Res., 46: 6841-6856.

Luciano, D.J., Vasilyev, N., Richards, J., Serganov, A., Belasco, J.G.


Importance 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.


A novel RNA phosphorylation state enables 5′ end-dependent degradation in Escherichia coli

Mol. Cell, 67: 44-54. e6.

Peselis, A., Gao, A., Serganov, A.


Preparation 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.


Long-range ‘linchpin’ G-C pair formation in the glnA riboswitch highlights a molecular signature of a ligand-dependent tertiary RNA switch

Cell Rep., 13: 1800-13

Vasilyev, N., Polonskaia, A., Darnell, J., Darnell, R., Patel, D.J. & Serganov, A.


Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

Proc. 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.


RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

RNA, 21: 1066-84

Peselis, A., Gao, A., Serganov, A.


Cooperativity, allostery and synergism in ligand binding to riboswitches

Biochimie, 117: 100-9.

Peselis, A. & Serganov, A.


Structure and function of pseudoknots involved in gene expression control

WIREs RNA, 5: 803-22

Peselis, A. & Serganov, A.


Themes and variations in riboswitch structure and function

Biochim. Biophys. Acta, 1839: 908-918

Gao, A. & Serganov, A.


Structural insights into recognition of c-di-AMP by the ydaO riboswitch

Nat. Chem. Biol., 10: 787-792

Serganov, A. * & Nudler, E.


A decade of riboswitches

Cell, 152: 17-24

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.


RNA-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.


Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Annu. Rev. Biophys., 41:343-70

Serganov, A.* & Patel, D.J.


Molecular recognition and function of riboswitches

Curr. Opin. Struct. Biol., 22: 279-286

Peselis, A. & Serganov, A.


Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch

Nat. 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.


Structure-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.


Structural 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.


Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch.

Proc. Natl. Acad. Sci. USA, 108: 14801-14806

Serganov, A.


Determination 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.


Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch

Mol. Cell, 40: 774-786. (Reviewed in Faculty of 1000)

Pikovskaya, O., Serganov, A.A., Polonskaia, A., Serganov, A.*, Patel, D.J.


Preparation 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.


A 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.


Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

Nature, 458: 233-237. (Reviewed in Faculty of 1000)

Serganov, A.


The long and the short of riboswitches

Curr. Opin. Struct. Biol., 19: 251-259

Serganov, A.* & Patel, D.J.


Amino acid recognition and gene regulation by riboswitches

Biochim. Biophys. Acta/Gene Regulatory Mechanisms (special issue), 1789: 592-611

Serganov, A.* & Patel, D.J.


Towards deciphering the principles underlying an mRNA recognition code

Curr. Opin. Struct. Biol., 18: 120-129

Serganov, A.*#, Huang, L.# & Patel, D.J.


Structural 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.


Structured 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


Ribozymes, 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.


Synthesis, oxidation behavior, crystallization and structure of 2′-methylseleno guanosine containing RNAs

J. Am. Chem. Soc., 128: 9909-9918

Serganov, A.*, Polonskaia, A., Phan, A.T., Breaker, R.R. & Patel, D.J.


Structural 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.


Control 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.


Syntheses of RNAs with up to 100 nucleotides containing site-specific 2′-methylseleno labels for use in X-ray crystallography

J. 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.


Structural 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.


Molecular 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.


Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

Chem. 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.


Molecular imaging of temporal dynamics and spatial heterogeneity of hypoxia-inducible factor-1 signal transduction activity in tumors in living mice

Cancer Research,  64: 6101-6108

Pitt, S.W., Majumdar, A., Serganov, A., Patel, D.J. & Al-Hashimi, H.M.


Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+ induced conformational stabilization

J. Mol. Biol., 338: 7-16

Mathy, N., Pellegrini, O., Serganov, A., Patel, D.J., Ehresmann, C. & Portier, C.


Specific recognition of rpsO mRNA and 16S rRNA by E. coli ribosomal protein S15 relies on both mimicry and site differentiation.

Mol. Microbiol., 52: 661-675

Zhang, Q., Throolin, R., Pitt, S., Serganov, A. & Al-Hashimi, H.


Probing motions between equivalent RNA domains using magnetic field induced residual dipolar couplings: accounting for correlations between motions and alignment

J. Amer. Chemical Society, 125: 10530-10531

Serganov, A., Polonskaia, A., Ehresmann, B., Ehresmann, C. & Patel, D.J.


Ribosomal protein S15 represses its own translation via adaptation of an rRNA-like fold within its mRNA

EMBO 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.


Crystallization of RNA/protein complexes

Acta Crystallogr. D, 58: 1664-1669

Ye, K., Serganov, A., Hu, W., Garber, M. & Patel, D.J.


Ribosome-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.


Do mRNA and rRNA binding sites of E. coli ribosomal protein S15 share common structural determinants?

J. Mol. Biol., 320: 963-978

Serganova, I., Ksenzenko, V., Serganov, A., Meshcheryakova, I., Pyatibratov, M., Vakhrusheva, O., Metlina, A. & Fedorov, O.


Sequencing of flagellin genes from Natrialba magadii provides new insight into evolutionary aspects of archaeal flagellins

J. 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.


Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin

Biochemistry (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.


The Thermus thermophilus 5S rRNA-protein complex: identification of specific binding sites for proteins L5 and L18 in the 5S rRNA

Molecular Biology (Moscow), 35: 521-526

Serganov, A., Benard, L., Portier, C., Ennifar, E., Garber, M., Ehresmann B. & C. Ehresmann


Role 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.


The 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.


Crystal 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.


N-terminal domain, residues 1-91, of ribosomal protein TL5 from Thermus thermophilus binds specifically and strongly to the region of 5S rRNA containing loop E

FEBS Lett., 451: 51-55

Serganov, A., Rak, A., Garber, M., Reinbolt, J., Ehresmann, B., Ehresmann, C., Grunberg-Manago, M. & Portier, C.


Ribosomal protein S15 from Thermus thermophilus: cloning, sequencing, overexpression of the gene and RNA binding features of the protein

Eur. 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).


Solution 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.


Crystallization and structural studies of components of the protein-synthesizing system from Thermus thermophilus

J. Cryst. Growth., 168: 301-307

Serganov, A., Masquida, B., Westhof, E., Cachia, C., Portier, C., Garber, M., Ehresmann, B. & Ehresmann C.


The 16S rRNA binding site of Thermus thermophilus ribosomal protein S15: comparison with Escherichia coli, minimum site and structure

RNA, 2: 1124-1138