Publications

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.

The Non-Coding RNA Journal Club: Highlights on Recent Papers-12

#Weaver, J.W., #Proshkin, S., Duan, W., Epshtein, V., Gowder, M., Bharati, B.K., Afanaseva, E., Mironov, A., Serganov, A., Nudler, E.

Control of transcription elongation and DNA repair by alarmone ppGpp

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

X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch

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.

The Non-Coding RNA Journal Club: Highlights on Recent Papers-11

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.

SHAPE-enabled fragment-based ligand discovery for RNA

Levenson-Palmer, R., Luciano, D.J., Vasilyev, N., Nuthanakanti, A., Serganov, A., Belasco, J.G.

A distinct RNA recognition mechanism governs Np4 decapping by RppH

Zeller, M.J., Nuthanakanti, A., Li, K., Aubé, J., Serganov, A., Weeks, K.M.

Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery

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

Growing a garden of fluorescent RNAs

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

Riboswitch mechanisms: new tricks for an old dog.

#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

Peselis, A., Serganov, A.

Cooperativity and allostery in RNA systems

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

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

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

T-box RNA gets boxed

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.

Peselis, A., Serganov, A.

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

Vasilyev, N., Gao, A., Serganov, A.

Noncanonical features and modifications on the 5′-end of bacterial sRNAs and mRNAs

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

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

Importance of a diphosphorylated intermediate for RppH-dependent RNA degradation

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

Vasilyev, N. & Serganov, A.

Preparation of short 5′-triphosphorylated oligoribonucleotides for crystallographic and biochemical studies

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

Preparation and crystallization of riboswitches

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

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

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

Vasilyev, N. & Serganov, A.

Structures of RNA Complexes with the Escherichia coli RNA pyrophosphohydrolase RppH unveil the basis for specific 5′-end-dependent mRNA decay

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

Cooperativity, allostery and synergism in ligand binding to riboswitches

Peselis, A. & Serganov, A.

Structure and function of pseudoknots involved in gene expression control

Peselis, A. & Serganov, A.

Themes and variations in riboswitch structure and function

Gao, A. & Serganov, A.

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

Serganov, A. * & Nudler, E.

A decade of riboswitches

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

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

Metabolite recognition principles and molecular mechanisms underlying riboswitch function

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

Molecular recognition and function of riboswitches

Peselis, A. & Serganov, A.

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

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

Pikovskaya, O., Polonskaya, A., Patel, D.J. & Serganov, A.

Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch

Huang, L., Ishibe-Murakami, S., Patel, D.J. & Serganov, A.

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

Serganov, A.

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

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

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

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

Preparation and crystallization of riboswitch-ligand complexes

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

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

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

Serganov, A.

The long and the short of riboswitches

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

Amino acid recognition and gene regulation by riboswitches

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

Towards deciphering the principles underlying an mRNA recognition code

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

Structural insights into amino acid binding and gene control by a lysine riboswitch

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

Serganov, A.* & Patel, D.J

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

Moroder, H., Kreutz, C., Lang, K., Serganov, A.* & Micura, R.

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

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

Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch

Wombacher, R., Keiper, S., Suhm., S., Serganov, A., Patel, D.J. & Jaschke, A.

Control of stereoselectivity in an enzymatic reaction by backdoor access

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

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

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

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

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

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

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.

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

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

Garber, M., Gongadze, G., Meshcheryakov, V., Nikonov, O., Nikulin, A., Perederina, A., Piendl, W., Serganov, A. & Tishchenko, S.

Crystallization of RNA/protein complexes

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

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?

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

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

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

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

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

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

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

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

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

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

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

Friguet, B., Fedorov, A., Serganov, A., Navon, A. & Goldberg, M.

A radioimmunoassay-based method for measuring the true affinity of a monoclonal antibody with trace amounts of radioactive antigen: illustration with the products of a cell-free protein synthesis system