Publications
2025
2024
Ng KK, Cole KH, Halbers LH, Chen C, Barhoosh AA, Reid-McLaughlin E, Metcalfe M, Kent AD, Steward O, Lupták A, Prescher JA (2024)
A modular platform for bioluminescent RNA tracking. Nature Communications 15, Article number: 9992
Abiri A, Chen X, Latifi B, Hsu FPK, Lupták A, Khine M, Kuan EC. (2024)
In vitro selection of human cerebrospinal fluid-specific aptamers using clinical samples. Rhinology 2024 Oct 15. doi: 10.4193/Rhin24.341.
Chen S, Sibley CD, Latifi B, Balaratnam S, Dorn RS, Lupták A, Schneekloth JS, Prescher JA. (2024)
Bioorthogonal cyclopropenones for investigating RNA structure. ACS Chem Biol 19, 12, 2406–2411.
Inhibition of Cpeb3 ribozyme elevates CPEB3 protein expression and polyadenylation of its target mRNAs, and enhances object location memory. eLife 13:e90116
2023
Cole, KH, Mogannam, K, Lupták A (2023)
Choreography of a self-splicing ribozyme (News & Views). Nature Catalysis 6, 291–293
2022
Kent A.D, Yang L.L., Lee I.A., Lupták A. (2022). Pyrophosphate-Mediated Repair of Damaged and Mismatched RNA by a Polymerase Ribozyme. bioRxiv 2022.11.01.514781. https://doi.org/10.1101/2022.11.01.514781
Cole, K. H., Bouin, A., Ruiz, C., Semler, B. L., Inlay, M. A., & Lupták, A. (2022). Single-Tube Collection and nucleic acid analysis of clinical samples for SARS-COV-2 saliva testing – scientific reports. Sci Rep. https://doi.org/10.1038/s41598-022-07871-4
2021
Peng, H., Latifi, B., Müller, S., Lupták, A., & Chen, I. A. (2021). Self-cleaving ribozymes: Substrate specificity and synthetic biology applications. RSC Chemical Biology, 2(5), 1370–1383. https://doi.org/10.1039/d0cb00207k
Chen, C. C., Han, J., Chinn, C. A., Li, X., Nikan, M., Myszka, M., Tong, L., Bredy, T. W., Wood, M. A., & Lupták, A. (2021). The CPEB3 ribozyme modulates hippocampal-dependent memory. https://doi.org/10.1101/2021.01.23.426448
Chen, C. C., & Lupták, A. (2021). Hunting for human ribozymes. Nature Chemical Biology, 17(5), 507–508. https://doi.org/10.1038/s41589-021-00778-7
Chizzolini, F., Kent, A., Passalacqua, L. F., & Lupták, A. (2021). Enzymatic RNA production from NTPs synthesized from nucleosides and trimetaphosphate. ChemBioChem 22: 2098–2101. https://doi.org/10.1002/cbic.202100085
2020
Passalacqua, L. F. M., Dingilian, A. I., & Lupták, A. (2020). Single-pass transcription by T7 RNA polymerase. RNA, 26(12), 2062–2071. https://doi.org/10.1261/rna.076778.120
Rotstan, K. A., Abdelsayed, M. M., Passalacqua, L. F. M., Chizzolini, F., Sudarshan, K., Chamberlin, A. R., Míšek, J., & Luptak, A. (2020). Regulation of mrna translation by a photoriboswitch. ELife, 9. https://doi.org/10.7554/elife.51737
Passalacqua, L. F., & Lupták, A. (2020). Co-transcriptional analysis of self-cleaving ribozymes and their ligand dependence. Methods in Molecular Biology, 13–24. https://doi.org/10.1007/978-1-0716-0716-9_2
2019
Chizzolini, F., Passalacqua, L. F., Oumais, M., Dingilian, A. I., Szostak, J. W., & Lupták, A. (2019). Large phenotypic enhancement of structured random RNA pools. Journal of the American Chemical Society, 142(4), 1941–1951. https://doi.org/10.1021/jacs.9b11396
Cole, K. H., & Lupták, A. (2019). High-throughput methods in Aptamer Discovery and analysis. Methods in Enzymology, 329–346. https://doi.org/10.1016/bs.mie.2019.02.009
2018
Webb, C.-H. T., & Lupták, A. (2018). Kinetic parameters of trans scission by extended HDV-like ribozymes and the prospect for the discovery of genomic trans-cleaving RNAS. Biochemistry, 57(9), 1440–1450. https://doi.org/10.1021/acs.biochem.7b00789
Burke, C. R., & Lupták, A. (2018). DNA synthesis from diphosphate substrates by DNA polymerases. Proceedings of the National Academy of Sciences, 115(5), 980–985. https://doi.org/10.1073/pnas.1712193115
2017
Passalacqua, L. F., Jimenez, R. M., Fong, J. Y., & Lupták, 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), 6006–6014. https://doi.org/10.1021/acs.biochem.7b00879
Abdelsayed, M. M., Ho, B. T., Vu, M. M., Polanco, J., Spitale, R. C., & Lupták, A. (2017). Multiplex aptamer discovery through APTA-Seq and its application to ATP aptamers derived from human-genomic Selex. ACS Chemical Biology, 12(8), 2149–2156. https://doi.org/10.1021/acschembio.7b00001
2016
Manuel, G., Lupták, A., & Corn, R. M. (2016). A Microwell–printing fabrication strategy for the on-chip templated biosynthesis of protein microarrays for surface plasmon resonance imaging. The Journal of Physical Chemistry C, 120(37), 20984–20990. https://doi.org/10.1021/acs.jpcc.6b03307
Webb, C.-H. T., Nguyen, D., Myszka, M., & Lupták, A. (2016). Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes. Scientific Reports, 6(1). https://doi.org/10.1038/srep28179
Rampášek, L., Jimenez, R. M., Lupták, A., Vinař, T., & Brejová, B. (2016). RNA motif search with data-driven element ordering. BMC Bioinformatics, 17(1). https://doi.org/10.1186/s12859-016-1074-x
Kozlyuk, N., Sengupta, S., Lupták, A., & Martin, R. W. (2016). In situ NMR measurement of macromolecule-bound metal ion concentrations. Journal of Biomolecular NMR, 64(4), 269–273. https://doi.org/10.1007/s10858-016-0031-3
Pobanz, K., & Lupták, A. (2016). Improving the odds: Influence of starting pools on in vitro selection outcomes. Methods, 106, 14–20. https://doi.org/10.1016/j.ymeth.2016.04.021
2015
Jimenez, R. M., Polanco, J. A., & Lupták, A. (2015). Chemistry and biology of self-cleaving ribozymes. Trends in Biochemical Sciences, 40(11), 648–661. https://doi.org/10.1016/j.tibs.2015.09.001
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), 567–582. https://doi.org/10.1038/nrg3937
Lupták, A. (2015). Catalytic properties of RNA. in Discoveries in modern science: Exploration, invention, technology. Macmillan Reference.
2014
Ho, B., Polanco, J., Jimenez, R., & Lupták, A. (2014). Discovering human RNA aptamers by structure-based bioinformatics and genome-based in vitro selection. Methods in Enzymology, 29–46. https://doi.org/10.1016/b978-0-12-801122-5.00002-7
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(10), 1616–1626. https://doi.org/10.1021/bi401717w
2013
Riccitelli, N., & Lupták, A. (2013). HDV family of self-cleaving ribozymes. Progress in Molecular Biology and Translational Science, 123–171. https://doi.org/10.1016/b978-0-12-381286-5.00004-4
2012
Vu, M. M. K., Jameson, N. E., Masuda, S. J., 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(10), 1247–1254. https://doi.org/10.1016/j.chembiol.2012.08.010
Hammann, C., Luptak, A., Perreault, J., & de la Peña, M. (2012). The ubiquitous Hammerhead ribozyme. RNA, 18(5), 871–885. https://doi.org/10.1261/rna.031401.111
Jimenez, R. M., Rampášek, L., Brejová, B., Vinař, T., & Lupták, A. (2012). Discovery of RNA motifs using a computational pipeline that allows insertions in paired regions and filtering of candidate sequences. Methods in Molecular Biology, 145–158. https://doi.org/10.1007/978-1-61779-545-9_10
Jimenez, R. M., & Lupták, A. (2012). Structure-based search and in vitro analysis of self-cleaving ribozymes. Methods in Molecular Biology, 131–143. https://doi.org/10.1007/978-1-61779-545-9_9
Xiao, Z., Levy-Nissenbaum, E., Alexis, F., Lupták, A., Teply, B. A., Chan, J. M., Shi, J., Digga, E., Cheng, J., Langer, R., & Farokhzad, O. C. (2012). Engineering of targeted nanoparticles for cancer therapy using internalizing aptamers isolated by cell-uptake selection. ACS Nano, 6(1), 696–704. https://doi.org/10.1021/nn204165v
2011
Ruminski, D. J., Webb, C.-H. T., Riccitelli, N. J., & Lupták, A. (2011). Processing and translation initiation of non-long terminal repeat retrotransposons by Hepatitis Delta virus (hdv)-like self-cleaving ribozymes. Journal of Biological Chemistry, 286(48), 41286–41295. https://doi.org/10.1074/jbc.m111.297283
Trevino, S. G., Zhang, N., Elenko, M. P., Lupták, A., & Szostak, J. W. (2011). Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity. Proceedings of the National Academy of Sciences, 108(33), 13492–13497. https://doi.org/10.1073/pnas.1107113108
Webb, C.-H. T., & Lupták, A. (2011). HDV-like self-cleaving ribozymes. RNA Biology, 8(5), 719–727. https://doi.org/10.4161/rna.8.5.16226
Sendroiu, I. E., Gifford, L. K., Lupták, A., & Corn, R. M. (2011). Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR Imaging. Journal of the American Chemical Society, 133(12), 4271–4273. https://doi.org/10.1021/ja2005576
Jimenez, R. M., Delwart, E., & Lupták, A. (2011). Structure-based search reveals hammerhead ribozymes in the human microbiome*. Journal of Biological Chemistry, 286(10), 7737–7743. https://doi.org/10.1074/jbc.c110.209288
2010
Gifford, L. K., Sendroiu, I. E., Corn, R. M., & Lupták, A. (2010). Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced surface plasmon resonance imaging on glassified Gold Surfaces. Journal of the American Chemical Society, 132(27), 9265–9267. https://doi.org/10.1021/ja103043p
Riccitelli, N. J., & Lupták, A. (2010). Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods, 52(2), 133–140. https://doi.org/10.1016/j.ymeth.2010.06.005
2009
Webb, C.-H. T., Riccitelli, N. J., Ruminski, D. J., & Lupták, A. (2009). Widespread occurrence of self-cleaving ribozymes. Science, 326(5955), 953–953. https://doi.org/10.1126/science.1178084
2007
Lupták, A., & Szostak, J. W. (2007). Chapter 7. Mammalian Self-Cleaving Ribozymes. Ribozymes and RNA Catalysis, 123–133. https://doi.org/10.1039/9781847557988-00123
Monnard, P.-A., Luptak, A., & Deamer, D. W. (2007). Models of primitive cellular life: Polymerases and templates in liposomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 362(1486), 1741–1750. https://doi.org/10.1098/rstb.2007.2066
2006
Salehi-Ashtiani, K., Lupták Andrej, Litovchick, A., & Szostak, J. W. (2006). A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science, 313(5794), 1788–1792. https://doi.org/10.1126/science.1129308
2004
Luptak, A., & Doudna, J. A. (2004). Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena Group I intron. Nucleic Acids Research, 32(7), 2272–2280. https://doi.org/10.1093/nar/gkh548
2001
Lupták, A., Ferré-D’Amaré, A. R., Zhou, K., Zilm, K. W., & Doudna, J. A. (2001). Direct PKA measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme. Journal of the American Chemical Society, 123(35), 8447–8452. https://doi.org/10.1021/ja016091x