# Equal contribution; * Co-corresponding author

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.

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


Cooperativity, allostery and synergism in ligand binding to riboswitches

Biochimie, 117: 100-9.

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

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

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

Gao, A. & Serganov, A.


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

Nat. Chem. Biol., 10: 787-792

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

Serganov, A. * & Nudler, E.


A decade of riboswitches

Cell, 152: 17-24

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).

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


Molecular recognition and function of riboswitches

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

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


Metabolite recognition principles and molecular mechanisms underlying riboswitch function

Annu. Rev. Biophys., 41:343-70

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)

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

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).

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

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)

Serganov, A.


Determination of riboswitch structures: light at the end of the tunnel?

RNA Biology (special issue), 7: 98-103. (January/February cover)

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.* & Patel, D.J.


Amino acid recognition and gene regulation by riboswitches

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

Serganov, A.


The long and the short of riboswitches

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

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)

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

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)

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


Towards deciphering the principles underlying an mRNA recognition code

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

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

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

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)

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., 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).

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

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

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

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

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)

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., 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).

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

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

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

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

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

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

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

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

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)

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

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

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)

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

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

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