Lupták Group Publications

Passalacqua LFM, Jimenez RM, Fong JY, Luptak A. (2017) Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6‑Phosphate: The Substrate of the Adjacent Gene Product. Biochemistry., 56 (45), pp 6006–6014 doi: 10.1021/acs.biochem.7b00879.

Abdelsayed, MM; Ho, BT; Vu, MMK; Polanco, J; Spitale, RC; Lupták, A. (2017) Multiplex aptamer discovery through Apta-Seq and its application to ATP aptamers derived from human-genomic SELEX. ACS Chem. Biol., 12 (8), pp 2149–2156. http://pubs.acs.org/doi/10.1021/acschembio.7b00001

Manuel, G, Lupták, A, Corn, RM. (2016) A microwell–printing fabrication strategy for the on-chip templated biosynthesis of protein microarrays for surface plasmon resonance imaging. J Phys Chem C. 2016, 120, 20984−20990 doi: 10.1021/acs.jpcc.6b03307

Webb CH, Nguyen D, Myszka M, Lupták A. (2016) Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes. Sci Rep. 6:28179. doi: 10.1038/srep28179.

Rampášek L, Jimenez RM, Lupták A, Vinar T, Brejová B. (2016) RNA motif search with data-driven element ordering. BMC Bioinformatics 17:216. doi:10.1186/s12859-016-1074-x

Kozlyuk N, Sengupta S, Lupták A, Martin RW. (2016) In situ NMR measurement of macromolecule-bound metal ion concentrations. J Biomol NMR 64(4):269-273. doi: 10.1007/s10858-016-0031-3

Pobanz K and Lupták A. (2016) Improving the odds: Influence of starting pools on in vitro selection outcomes. Methods Methods 106:14-20

Kozlyuk N, Sengupta S, Lupták A, Martin RW. (2016) In situ NMR measurement of macromolecule-bound metal ion concentrations. J Biomol NMR. doi:10.?1007/?s10858-016-0031-3 [Epub ahead of print].

Jimenez RM, Polanco JA, Lupták A. (2015) Chemistry and Biology of Self-Cleaving Ribozymes. Trends in Biochemical Sciences 40(11):648-61.

Long A, Liti G, Luptak A, Tenaillon O. (2015) Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nature Reviews Genetics 16(10):567-82.

Lupták, A. (2015) Catalytic properties of RNA. in Discoveries in modern science: Exploration, invention, technology. Trefil, J. (ed.) Macmillan reference.

Ho, B., Polanco, J., Jimenez, R.M. & Lupták, A. (2014) Discovering human RNA aptamers by structure-based bioinformatics and genome-based in vitro selection.
Methods Enzymol. 2014;549:29-46.

Riccitelli, N.J., Delwart, E. & Lupták, A. (2014) Identification of minimal HDV-like ribozymes with unique divalent metal ion dependence in the human microbiome.
Biochemistry 53: 16-16-1626.

Riccitelli, N.J. & Lupták, A. (2013) HDV family of self-cleaving ribozymes.
Prog Mol Biol Transl Sci. 120:123-71.

Vu, MMK, Jameson, NE, Masuda, SJ, Lin, D, Larralde-Ridaura, R & Lupták, A. (2012) Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX. Chemistry & Biology; 19:1247-54.

Hammann C, Lupták A, Perreault J, de la Pena M. (2012) The uniquitous hammerhead ribozyme. RNA; 18(5): 871-85.

Jimenez RM, Rampá¹ek L, Brejová B, Vina? T, Lupták A. (2012) Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences. Methods Mol Biol; 848:145-58.

Jimenez RM, Lupták A. (2012) Structure-based search and in vitro analysis of self-cleaving ribozymes. Methods Mol Biol; 848:131-43.

Xiao Z, Levy-Nissenbaum E, Alexis F, Lupták A, Teply BA, Chan JM, Shi J, Digga E, Cheng J, Langer R, Farokhzad OC. (2012) Engineering of Targeted Nanoparticles for Cancer Therapy Using Internalizing Aptamers Isolated by Cell-Uptake Selection. ACS Nano; 6(1):696-704.

Ruminski DJ, Webb C-HT, Riccitelli NJ, Lupták A. (2011) Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes. J Biol Chem; 286(48):41286-95.

Trevino S, Zhang N, Elenko M, Lupták A and Szostak JW. (2011) Evolution of functional nucleic acids in the presence of non-heritable backbone heterogeneity. Proc Natl Acad Sci USA; 108(33):13492-7.

Webb C-H T and Lupták A. (2011) RNA Families: HDV-like Self-cleaving Ribozymes. RNA Biology; 8(5):719-727.

Sendroiu I, Gifford L, Lupták A, Corn R. (2011) Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging. Journal of the American Chemical Society133(12):4271-4273.

Jimenez RM, Delwart E, and Lupták A. (2011) Structure-based search reveals hammerhead ribozymes in the human microbiome. Journal of Biological Chemistry286(10):7737-7743Paper of the week and see Randi’s profile at JBCBest of 2011 – RNA.

Gifford L, Sendroiu I, Corn R, Lupták A. (2010) Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced SPR imaging on glassified gold surfaces. Journal of the American Chemical Society132(27):9265-9267.

Riccitelli, N.J., Lupták, A. (2010) Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods; 52:133-140.
Webb, C-H.T., Riccitelli, N.J.; Ruminski, D.J.; Lupták, A. (2009) Widespread occurence of self-cleaving ribozymes. Science326(5955):953Full Text   Online Supplement

Lupták, A., Szostak, J.W. (2007) Mammalian self-cleaving ribozymes. in Ribozymes and RNA Catalysis, eds D. Lilley and F. Eckstein.

Monnard, P.A., Lupták, A., Deamer, D.W. (2007) Models of primitive cellular life: polymerases and templates in liposomes. Philosophical Transactions of the Royal Society of London, Series B Biological Sciences; 362(1486):1741-50.

Salehi-Ashtiani, K., Lupták, A., Litovchick, A., Szostak, J.W. (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science313(5794):1788-92.

Lupták, A., Doudna, J.A. (2004) Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron. Nucleic Acids Research32(7):2272-80.

Lupták, A., Ferre-D’Amare, A.R., Zhou, K., Zilm, K.W., Doudna, J.A. (2001) Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. Journal of the American Chemical Society123(35):8447-52.