Publications

# Equal contribution; * Co-corresponding author

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

2017

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.

2016

Preparation and crystallization of riboswitches

Methods Mol. Biol., 1320: 21-36.

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

2015

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.

2015

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.

2015

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.

2015

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.

2014

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

Nat. Chem. Biol., 10: 787-792

Peselis, A. & Serganov, A.

2014

Structure and function of pseudoknots involved in gene expression control

WIREs RNA, 5: 803-22

Peselis, A. & Serganov, A.

2014

Themes and variations in riboswitch structure and function

Biochim. Biophys. Acta, 1839: 908-918

Serganov, A. * & Nudler, E.

2013

A decade of riboswitches

Cell, 152: 17-24

Peselis, A. & Serganov, A.

2012

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.

2012

Molecular recognition and function of riboswitches

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

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

2012

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.

2012

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.

2011

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.

2011

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.

2011

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.

2010

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.

2010

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.

2009

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.

2009

Amino acid recognition and gene regulation by riboswitches

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

Serganov, A.

2009

The long and the short of riboswitches

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

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

2009

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.

2009

Preparation and crystallization of riboswitch-ligand complexes

Methods Mol. Biol., 540: 115-128

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

2008

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.

2008

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.

2007

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

2007

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.

2006

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.

2006

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.

2006

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.

2005

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.

2005

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.

2004

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.

2004

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.

2004

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.

2004

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.

2004

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.

2003

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.

2003

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.

2002

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.

2002

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.

2002

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.

2002

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

2001

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.

2001

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.

2001

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.

2000

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.

2000

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.

1999

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).

1997

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.

1997

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.

1996

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.

1996

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

J. Cryst. Growth., 168: 301-307