Publications

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

Ng, K.K., Cole, K.H., Halbers, L.H., Chen, C., Barhoosh, A. A., Reid-McLaughlin, E., Metcalfe, M., Kent, A.D., Steward, O., Lupták, A., Prescher, J.A. (2022). A modular platform for bioluminescent RNA tracking. bioRxiv 2022.07.02.498144. https://doi.org/10.1101/2022.07.02.498144

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

 

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