Research at The RNA Institute

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Research Collaboration and Excellence

Our modern LEEDS-certified building on UAlbany's uptown campus houses researchers that are making scientific breakthroughs in the broad field of Ribonucleic Acid (RNA). RNA has a multitude of essential biological functions and can be used as a tool for scientific discovery and disease treatment. Research at The RNA Institute is discovering new roles for RNA in biology and chemical processes, and is being developed as a tool for therapeutic advances.

The RNA Institute is more than just a modern research facility, we are a collection of diverse and talented researchers united by a common goal in understanding the role of RNA across different fields, including biology, chemistry, biomedical sciences, physics, and nanobiosciences. 

See Current Research Opportunities at The RNA Institute

RNA intern David Bunn, undergraduate, Belfort Lab (photo by Paul Miller)


The RNA Institute Labs

The RNA Institute Publications
Recent Publications

The structure of a hibernating ribosome in a Lyme disease pathogen

Sharma, M. R., Manjari, S. R., Agrawal, E. K., Keshavan, P., Koripella, R. K., Majumdar, S., Marcinkiewicz, A. L., Lin, Y., Agrawal, R. K., & Banavali, N. K., (2023), Nature Communications, 14(1), 6961.

Evolution: Mitochondrial Ribosomes Across Species

Agrawal, R. K., & Majumdar, S. (2023) Methods in molecular biology (pp. 7–21)


Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales

Ikhimiukor, O. O., Souza, S. S. R., Akintayo, I., Marcovici, M. M., Workman, A., Martin, I. W., & Andam, C. P., 2023, Microbiology Spectrum, 11(5)


Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation

Li, Y., Majumdar, S., Treen, R., Sharma, M. R., Corro, J., Gamper, H., Manjari, S. R., Prusa, J., Banavali, N. K., Stallings, C. L., Hou, Y., Agrawal, R. K., & Ojha, A. K. (2023). Proceedings of the National Academy of Sciences of the United States of America, 120(22)


Multi-host infection and phylogenetically diverse lineages shape the recombination and gene pool dynamics of Staphylococcus aureus

Souza, S. S. R., Smith, J. T., Bruce, S. A., Gibson, R. J., Martin, I. W., & Andam, C. P. (2023), BMC Microbiology, 23(1). 


Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria

Lee, I. P. A., Eldakar, O. T., Gogarten, J. P., & Andam, C. P. (2023),  iScience, 26(8), 107344.


Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species

Ikhimiukor, O. O., Souza, S. S. R., Marcovici, M. M., Nye, G. J., Gibson, R. J., & Andam, C. P. (2023), Communications Biology, 6(1).


Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes

Moser, B., Moore, D., Khadka, B., Lyons, C., Foxall, T., Andam, C. P., Parker, C. J., Ochin, C., Garelnabi, M., Sevigny, J., Thomas, W. K., Bigornia, S., & Dao, M. C. (2023). Frontiers in Nutrition, 9. 


Mycobacterial phosphodiesterase Rv0805 is a virulence determinant and its cyclic nucleotide hydrolytic activity is required for propionate detoxification

McDowell, J. R., Bai, G., Lasek‐Nesselquist, E., Eisele, L. E., Yan, W., Hurteau, G. J., Johnson, R., Bai, Y., Chen, Y., Chan, J., & McDonough, K. A. (2023), Molecular Microbiology, 119(4), 401–422.


Maintenance of a host-specific minority mutation in the West Nile virus NS3

Caldwell, H. S., Kuo, L., Pata, J. D., Dupuis, A. P., Arnold, J. J., Yeager, C., Stout, J., Koetzner, C. A., Payne, A., Bialosuknia, S., Banker, E., Nolen, T. A., Cameron, C. Ε., & Ciota, A. T. (2023), iScience, 26(8), 107468.


Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC

Nelson-Rigg, R., Fagan, S. P., Jaremko, W. J., & Pata, J. D. (2023), Antimicrobial Agents and Chemotherapy, 67(6). 


Disruption of the productive encounter complex results in dysregulation of DIAPH1 activity

Theophall, G. G., Ramirez, L., Premo, A., Reverdatto, S., Manigrasso, M. B., Yepuri, G., Burz, D. S., Ramasamy, R., Schmidt, A. M., & Shekhtman, A. (2023), Journal of Biological Chemistry/Journal of Biological Chemistry, 299(11), 105342.


DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress

Yepuri, G., Ramirez, L., Theophall, G. G., Reverdatto, S., Quadri, N., Hasan, S. N., Bu, L., Thiagarajan, D., Wilson, R. A., López‐Díez, R., Gugger, P. F., Mangar, K., Narula, N., Katz, S. D., Zhou, B., Li, H., Stotland, A., Gottlieb, R. A., Schmidt, A. M., . . . Ramasamy, R. (2023), Nature Communications, 14(1).


RAGE/DIAPH1 and atherosclerosis through an evolving lens: Viewing the cell from the “Inside – Out”

Ramasamy, R., Shekhtman, A., & Schmidt, A. M. (2023), Atherosclerosis, 117304.


Measuring the Reversible Oxidation of Protein Tyrosine Phosphatases Using a Modified Cysteinyl-Labeling Assay

Londhe, A. D., & Boivin, B. (2023), Methods in molecular biology (pp. 223–237).


Interfacing neural cells with typical microelectronics materials for future manufacturing

Torres, F., Tokranova, N., Amodeo, E., Bertucci, T., Kiehl, T. R., Xie, Y., Cady, N. C., & Sharfstein, S. T. (2023), Biosensors & Bioelectronics/Biosensors & Bioelectronics (Online), 242, 115749. 


Material to system-level benchmarking of CMOS-integrated RRAM with ultra-fast switching for low power on-chip learning

Abedin, M., Gong, N., Beckmann, K., Liehr, M., Saraf, I., Van Der Straten, O., Ando, T., & Cady, N. C. (2023), Scientific Reports, 13(1). 


Emerging tickborne viruses vectored by Amblyomma americanum (Ixodida: Ixodidae): Heartland and Bourbon viruses

Dupuis, A. P., Lange, R., & Ciota, A. T. (2023), Journal of Medical Entomology, 60(6), 1183–1196.


Diversification of Bourbon Virus in New York State

Lange, R., Dupuis, A. P., & Ciota, A. T. (2023), Microorganisms, 11(6), 1590.


Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States

Vogels, C. B., Brackney, D. E., Dupuis, A. P., Robich, R. M., Fauver, J. R., Brito, A., Williams, S. C., Anderson, J. F., Lubelczyk, C. B., Lange, R., Prusinski, M. A., Kramer, L. D., Gangloff-Kaufmann, J., Goodman, L. B., Baele, G., Smith, R. P., Armstrong, P. M., Ciota, A. T., Dellicour, S., & Grubaugh, N. D. (2023), Proceedings of the National Academy of Sciences of the United States of America, 120(16).


Intrapulmonary Treatment with Mycobacteriophage LysB Rapidly Reduces Mycobacterium abscessus Burden

Hurst-Hess, K., Walz, A., Yang, Y., McGuirk, H., González-Juarrero, M., Hatfull, G. F., Ghosh, P., & Ojha, A. K. (2023), Antimicrobial Agents and Chemotherapy, 67(6).


Mab2780c, a TetV-like efflux pump, confers high-level spectinomycin resistance in mycobacterium abscessus

Hurst-Hess, K., Phelps, G. A., Wilt, L. A., Lee, R., & Ghosh, P. (2023), Tuberculosis, 138, 102295.


Promoter selectivity of the RhlR quorum-sensing transcription factor receptor in Pseudomonas aeruginosa is coordinated by distinct and overlapping dependencies on C4-homoserine lactone and PqsE

Keegan, N. R., Torres, N., Stringer, A. M., Prager, L. I., Brockley, M., McManaman, C., Wade, J. T., & Paczkowski, J. E. (2023), PLOS Genetics, 19(12), e1010900.


Quorum-sensing synthase mutations re-calibrate autoinducer concentrations in clinical isolates of Pseudomonas aeruginosa to enhance pathogenesis

Simanek, K. A., Schumacher, M. L., Mallery, C., Shen, S., Li, L., & Paczkowski, J. E. (2023), Nature Communications, 14(1).


Widespread alternative splicing dysregulation occurs presymptomatically in CAG expansion spinocerebellar ataxias

Shorrock, H. K., Lennon, C., Aliyeva, A., Davey, E., DeMeo, C. C., Pritchard, C. E., Planco, L., Vélez, J. M., Mascorro-Huamancaja, A., Shin, D. S., Cleary, J. D., & Berglund, J. A. (2023),  Brain.


Alternative Splicing Outcomes Across an RNA-Binding Protein Concentration Gradient

Ellis, J. A., Hale, M. A., Cleary, J. D., Wang, E., & Berglund, J. A. (2023), Journal of Molecular Biology/Journal of Molecular Biology, 435(15), 168156. 


Resolving altered base-pairing of RNA modifications with DNA nanoswitches

Todkari, I. A., Chandrasekaran, A. R., Punnoose, J. A., Mao, S., Haruehanroengra, P., Beckles, C., Sheng, J., & Halvorsen, K. (2023), Nucleic Acids Research, 51(20), 11291–11297. 


siRNA-loaded DNA nanostructures restore endothelial leakiness

Chandrasekaran, A. R. (2023), Nanoscale Horizons, 8(12), 1606–1607.


Introduction to emerging concepts in nucleic acids: structures, functions and applications

Bhatia, D., Maiti, P. K., Liu, X., & Chandrasekaran, A. R. (2023), Nanoscale, 15(31), 12785–12786.


Fluorometric Determination of DNA Nanostructure Biostability

Talbot, H., Madhanagopal, B. R., Hayden, A., Halvorsen, K., & Chandrasekaran, A. R. (2023), ACS Applied Bio Materials, 6(8), 3074–3078.


Self-Assembly of DNA Nanostructures in Different Cations

Rodriguez, A., Gandavadi, D., Mathivanan, J., Song, T., Madhanagopal, B. R., Talbot, H., Sheng, J., Wang, X., & Chandrasekaran, A. R. (2023), Small, 19(39).


Caffeine-induced release of small molecules from DNA nanostructures

Madhanagopal, B. R., Chen, S., Platt, C., & Chandrasekaran, A. R. (2023), iScience, 26(5), 106564. 


High-throughput single-molecule quantification of individual base stacking energies in nucleic acids

Punnoose, J. A., Thomas, K. J., Chandrasekaran, A. R., Vilcapoma, J., Hayden, A., Kilpatrick, K., Vangaveti, S., Chen, A., Banco, T., & Halvorsen, K. (2023), Nature Communications, 14(1).


The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals

Zhao, Y., Chandrasekaran, A. R., Rusling, D. A., Woloszyn, K., Hao, Y., Hernandez, C., Vecchioni, S., Ohayon, Y. P., Mao, C., Seeman, N. C., & Sha, R. (2023), Journal of the American Chemical Society, 145(6), 3599–3605. 


Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop

Viegas, R. G., Sanches, M. N., Chen, A., Paulovich, F. V., Garcı́A, A. E., & Leite, V. B. P. (2023), Journal of Chemical Information and Modeling, 63(17), 5641–5649. 


Aggregation in Aqueous Solutions of 2-(Tetrafluoro(trifluoromethyl)-λ6-sulfanyl-ethan-1-ol (CF3SF4-ethanol)): A Comparison with Aqueous Trifluoroethanol and Hexafluoroisopropanol Using Molecular Dynamics Simulations and Dynamic Light Scattering Experiments

Biswas, S., Kaur, S., Myers, C. A., Chen, A., & Welch, J. T. (2023), ACS Omega, 8(33), 30037–30047. 


Loss of function of male-specific lethal 3 (Msl3) does not affect spermatogenesis in rodents

Mitchell, T. A., Lin, J. M., Hicks, S. M., James, J. R., Rangan, P., & Forni, P. E. (2023), Developmental Dynamics.


Identifying fibrogenic cells following salivary gland obstructive injury

Altrieth, A. L., O’Keefe, K. J., Gellatly, V., Tavarez, J. R., Feminella, S., Moskwa, N., Cordi, C. V., Turrieta, J. C., Nelson, D. A., & Larsen, M. (2023), Frontiers in Cell and Developmental Biology, 11.


Stand-off Raman spectroscopy is a promising approach for the detection and identification of bloodstains for forensic purposes

Almehmadi, L. M., & Lednev, I. K. (2023), Journal of Raman Spectroscopy, 55(2), 227–231.


Diagnosing COVID-19 in nasopharyngeal secretion through Raman spectroscopy: a feasibility study

Goulart, A. C. C., Zângaro, R. A., Carvalho, H. C., Lednev, I. K., & Silveira, L. (2023), Lasers in Medical Science, 38(1).


Discrimination of smokers and nonsmokers based on the analysis of fingermarks for forensic purposes

Amin, M. O., Al‐Hetlani, E., & Lednev, I. K. (2023), Microchemical Journal, 188, 108466.


Soil from footwear is a newly rediscovered type of forensic evidence due to the application of modern analytical techniques: A review

Ogilvie, R. H., & Lednev, I. K. (2023), TrAC. Trends in Analytical Chemistry, 163, 117081. 


Identification and highly selective differentiation of organic gunshot residues utilizing their elemental and molecular signatures Author links open overlay panel

Khandasammy, S. R., Halámková, L., Baudelet, M., & Lednev, I. K. (2023), Spectrochimica Acta. Part a, Molecular and Biomolecular Spectroscopy, 291, 122316.


A novel Raman spectroscopic method for detecting traces of blood on an interfering substrate

Kistenev, Y. V., Borisov, A. V., Samarinova, A. A., Colón‐Rodríguez, S., & Lednev, I. K. (2023), Scientific Reports, 13(1).


Raman spectroscopy for the identification of body fluid traces: Semen and vaginal fluid mixture

Sikirzhytskaya, A., Sikirzhytski, V., Pérez-Almodóvar, L., & Lednev, I. K. (2023), Forensic Chemistry, 32, 100468.


Innovative Vibrational Spectroscopy Research for Forensic Application

Weber, A. R., Hoplight, B., Ogilvie, R. H., Muro, C. K., Khandasammy, S. R., Pérez-Almodóvar, L., Sears, S. F., & Lednev, I. K. (2023), Analytical Chemistry, 95(1), 167–205.


Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function

Schroader, J. H., Handley, M., & Reddy, K. (2023), Wiley Interdisciplinary Reviews. RNA, 14(5).


Quercetin selectively reduces expanded repeat RNA levels in models of myotonic dystrophy

Mishra, S. K., Hicks, S. M., Frías, J., Vangaveti, S., Nakamori, M., Cleary, J. D., Reddy, K., & Berglund, J. A. (2023), bioRxiv (Cold Spring Harbor Laboratory). 


Pharmacological antagonism of receptor for advanced glycation end products signaling promotes thermogenesis, healthful body mass and composition, and metabolism in mice

Wilson, R. A., Arivazhagan, L., Ruiz, H. H., Zhou, B., Qian, K., Manigrasso, M. B., Bernadin, R., Mangar, K., Shekhtman, A., Li, H., Ramasamy, R., & Schmidt, A. M. (2023), Obesity, 31(7), 1825–1843.


DIAPH1 mediates progression of atherosclerosis and regulates hepatic lipid metabolism in mice

Senatus, L. M., Egaña-Gorroño, L., López‐Díez, R., Bergaya, S., Aranda, J., Amengual, J., Arivazhagan, L., Manigrasso, M. B., Yepuri, G., Nimma, R., Mangar, K. N., Bernadin, R., Zhou, B., Gugger, P. F., Li, H., Friedman, R. A., Theise, N. D., Shekhtman, A., Fisher, E. A., . . . Schmidt, A. M. (2023), Communications Biology, 6(1). 


Crystal structures and identification of novel Cd2+-specific DNA aptamer

Liu, H., Yun-Sheng, G., Mathivanan, J., Armour-Garb, Z., Shao, Z., Zhang, Y., Zhao, X., Shao, Q., Zhang, W., Yang, J., Cao, C., Li, H., Sheng, J., & Gan, J. (2023), Nucleic Acids Research, 51(9), 4625–4636.


Design, synthesis, and evaluation of 4′-phosphonomethoxy pyrimidine ribonucleosides as potential anti-influenza agents

Hassan, A. E. A., Hegazy, H. A., Zaki, I., Hassan, M. M. A., Ramadan, M., Haikal, A., Sheng, J., & Abou‐Elkhair, R. a. I. (2023), Archiv Der Pharmazie, 356(6).


Development of Nitroso-Based Probes for Labeling and Regulation of RAS Proteins in Cancer Cells via Sequential Ene-Ligation and Oxime Condensation

Yuanyuan Li, Hongling Zhou, Huili Liu, Youfang Gan, Yaying Zheng, Jia Sheng, and Rui Wang Li, Y., Zhou, H., Liu, H., Gan, Y., Zheng, Y., Sheng, J., & Wang, R. (2023), Journal of Organic Chemistry, 88(3), 1762–1771.


Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections

Joshua T. Smith, Elissa M. Eckhardt, Nicole B. Hansel, Tahmineh Rahmani Eliato, Isabella W. Martin & Cheryl P. Andam. BMC Infectious Diseases. June 21, 2021

Aptamer-Programmed DNA Nanodevices for Advanced, Targeted Cancer Theranostics

Shanka Walia, Arun Richard Chandrasekaran, Banani Chakraborty, and Dhiraj Bhatia. ACS Appl. Bio Mater. June 18, 2021

Recognition of DNA Target Formulations by CRISPR-Cas12a Using a dsDNA Reporter.

Smith CW, Kachwala MJ, Nandu N, Yigit MV. ACS Synth Biol. June 18, 2021

p63 and p53: collaborative partners or dueling rivals?

Dana L. Woodstock, Morgan A. Sammons, and Martin Fischer. Frontiers in Cell and Developmental Biology. June 14, 2021

A mini DNA–RNA hybrid origami nanobrick

Lifeng Zhou, Arun Richard Chandrasekaran, Mengwen Yan, Vibhav A. Valsangkar, Jeremy I. Feldblyum, Jia Sheng and  Ken Halvorsen. Nanoscale Adv. June 11, 2021

Towards development of a novel screening method for identifying Alzheimer’s disease risk: Raman spectroscopy of blood serum and machine learning

Nicole M. Ralbovsky, Greg S. Fitzgerald, Ewan C. McNay, Igor K. Lednev. Spectrochimica Acta. June 5, 2021 

Determining the stages of cellular differentiation using deep ultraviolet resonance Raman spectroscopy

Nicole M. Ralbovsky, Paromita Dey, Bijan K.Dey, Igor K. Lednev. Talanta. May 15, 2021

EXPRESS: Vibrational Spectroscopy for Detection of Diabetes: A Review

Nicole M. Ralbovsky, Igor K. Lednev. Applied Spectroscopy. May 14, 2021

Detecting the epitranscriptome

Anwesha Sarkar  William Gasperi  Ulrike Begley  Steven Nevins  Sabrina M. Huber  Peter C. Dedon  Thomas J. Begley. WIREs RNA. May 13, 2021

RNA degradation is required for the germ-cell to maternal transition in Drosophila

Patrick Blatt, Siu Wah Wong-Deyrup, Alicia McCarthy, Justin Camacho, Miler T. Lee 5, Prashanth Rangan. Current Biology. May 13, 2021

Undergraduate students in research: Accommodating undergraduates in the lab is a mutually beneficial relationship

Chandrasekaran AR. EMBO Rep. May 9, 2021

DNA-based ribonuclease detection assays

Arun Richard Chandrasekaran J. Mater. Chem. B, April 26, 2021

DNA Functionality with Photoswitchable Hydrazone Cytidine*

Song Mao, Zhihua Chang, Ya Ying Zheng, Alexander Shekhtman, Jia Sheng. Chemistry. April 19, 2021


Mechanisms underlying pre- and postnatal development of the vomeronasal organ

Raghu Ram Katreddi, Paolo E Forni. Cell Mol Life Sci. April 19, 2021


Quantitative mapping of the cellular small RNA landscape with AQRNA-seq

Jennifer F. Hu, Daniel Yim, Duanduan Ma, Sabrina M. Huber, Nick Davis, Jo Marie Bacusmo, Sidney Vermeulen, Jieliang Zhou, Thomas J. Begley, Michael S. DeMott, Stuart S. Levine, Valérie de Crécy-Lagard, Peter C. Dedon & Bo Cao. Nature Biotechnology. April 15, 2021 

A translation control module coordinates germline stem cell differentiation with ribosome biogenesis during Drosophila oogenesis

Elliot T Martin, Patrick Blatt, Elaine Ngyuen, Roni Lahr, Sangeetha Selvam, Hyun Ah M Yoon, Tyler Pocchiari, Shamsi Emtenani,  Daria Siekhaus, Andrea Jeanne Berman, Gabriele Fuchs, Prashanth Rangan. BioRxiv. April 04, 2021

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator

Shruti Nagaraja, Maggi W Cai, [..], Thomas J Begley, et. al. mBio. March 9, 2021

Methylation of rRNA as a host defense against rampant group II intron retrotransposition

Waldern JM, Smith D, Piazza CL, Bailey EJ, Schiraldi NJ, Nemati R, Fabris D, Belfort M, Novikova O. Mob DNA. March 7, 2021


Pop-culture references in peer-reviewed scientific articles

Arun Richard Chandrasekara. Matter. March 3, 2021


A genetic program boosts mitochondrial function to power macrophage tissue invasion

Shamsi Emtenani,  Elliott T Martin, Attila Gyoergy, Julia Bicher, Jakob Wendelin-Genger, Thomas Koecher, Thomas Hurd, Andreas Bergthaler, Prashanth Rangan, Daria E Siekhaus. bioRxiv. February 18, 2021


Regulation of the Peroxidase-Like Activity of nGO, MoS 2 and WS 2 Nanozymes by Using Metal Cations

Nidhi Nandu, Christopher W Smith, Mahera J Kachwala, Mehmet V Yigit. Chembiochem. February 15, 2021


Nuclease resistance of DNA nanostructures

Arun Richard Chandrasekaran. Nature Reviews Chemistry. February 10, 2021


Silencing of the tRNA Modification Enzyme Cdkal1 Effects Functional Insulin Synthesis in NIT-1 Cells: tRNA Lys3 Lacking ms 2- (ms 2 t 6 A 37) is Unable to Establish Sufficient Anticodon:Codon Interactions to Decode the Wobble Codon AAG

Amithi Narendran, Sweta Vangaveti, Srivathsan V Ranganathan, Emily Eruysal, Miranda Craft, Omar Alrifai, Fu Yee Chua, Kathryn Sarachan, Breann Litwa, Sheetal Ramachandran, Paul F Agris. Front Mol Biosci. February 9, 2021


SQ3370 Activates Cytotoxic Drug via Click Chemistry at Tumor and Elicits Sustained Responses in Injected and Non‐Injected Lesions

Sangeetha Srinivasan, Nathan Alexander Yee, Kui Wu, Michael Zakharian, Amir Mahmoodi, Maksim Royzen, José Manuel Mejía Oneto. Advanced Therapeutics. January 20, 2021


Orthogonal Control of DNA Nanoswitches with Mixed Physical and Biochemical Cues 

Nathan T. Forrest, Javier Vilcapoma, Kristina Alejos, Ken Halvorsen and Arun Richard Chandrasekaran. Biochemistry. January 19, 2021.


Computationally reconstructing cotranscriptional RNA folding pathways from experimental data reveals rearrangement of non-native folding intermediates 

Angela M. Yu, Paul M. Gasper, Luyi Cheng, …Venkat Gopalan, Alan A. Chen, Julius B. Lucks. Molecular Cell. January 15, 2021.


Small-molecule inhibitors for the Prp8 intein as antifungal agents

Zhong Li, Anil Mathew Tharappel, Jimin Xu, Yuekun Lang, Cathleen M. Green, Jing Zhang, Qishan Lin, Sudha Chaturvedi, Jia Zhou, Marlene Belfort, and Hongmin Li. PNAS. January 12, 2021.


Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction

Mahera J. Kachwala, Christopher W. Smith, Nidhi Nandu, and Mehmet V. Yigit. Anal. Chem. January 6, 2021


Click Activated Protodrugs Against Cancer Increase the Therapeutic Potential of Chemotherapy through Local Capture and Activation

Kui Wu, Nathan Yee, Sangeetha Srinivasan, Amir Mahmoodi, Michael Zakharian, Jose M. Mejia Oneto, Maksim Royzen

Chemical Science · January 5, 2021


DNA Nanoswitch Barcodes for Multiplexed Biomarker Profiling 

Arun Richard Chandrasekaran, Molly MacIsaac, Javier Vilcapoma, Clinton H. Hansen, Darren Yang, Wesley P. Wong, Ken Halvorsen. Nano Lett. January 4, 2021.


Multiplexed detection and quantification of human antibody response to COVID-19 infection using a plasmon enhanced biosensor platform

Nathaniel C.Cady, Natalya Tokranova, Armond Minor, Nima Nikvand, Klemen Strle, William T. Lee, William Page, Ernest Guignon, Arturo Pilar, George N.Gibson. Biosensors and Bioelectronics. January 1, 2021


Diverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance

J.Park, Jinfeng Li, Xinglu Zhang, Fengxiang Gao, Christopher S. Benton, Cheryl P. Andam. Infection, Genetics and Evolution. January, 2021 


Melanin pigments extracted from horsehair as antibacterial agents

Tahmineh Rahmani Eliato, Joshua T Smith, Zhen Tian, Eun-Sik Kim, Wonseok Hwang, Cheryl P Andam, Young Jo Kim. J Mater Chem B. January, 2021


Analysis of individual red blood cells for Celiac disease diagnosis

Nicole M Ralbovsky, Igor K Lednev. Talanta. January 1, 2021


Machine-Learning Single-Stranded DNA Nanoparticles for Bacterial Analysis

Nidhi Nandu, Christopher W. Smith, Taha Bilal Uyar, Yu-Sheng Chen, Mahera J. Kachwala, Muhan He, and Mehmet V. Yigit. ACS Appl. Nano Mater. December 14, 2020


Discrimination between human and animal blood by attenuated total reflection Fourier transform-infrared spectroscopy 

Ewelina Mistek-Morabito & Igor K. Lednev. Communications Chemistry. December 10, 2020. 


Repeat length increases disease penetrance and severity in C9orf72 ALS/FTD BAC transgenic mice

Pattamatta A, Nguyen L, Olafson HR, Scotti MM, Laboissonniere LA, Richardson J, Berglund JA, Zu T, Wang ET, Ranum LPW. Hum Mol Genet. December 31, 2020


RNA structure probing to characterize RNA-protein interactions on a low abundance pre-mRNA in living cells

Bubenik JL, Hale M, McConnell O, Wang E, Swanson MS, Spitale R, Berglund JA. RNA. December 11, 2020


Rapid one-step detection of SARS-CoV-2 RNA 

Arun Richard Chandrasekaran, Lifeng Zhou and Ken Halvorsen. Nature Biomedical Engineering. December 8, 2020


DNA-Functionalized Nanoparticles for Targeted Biosensing and Biological Applications

Udisha Singh, Vinod Morya, Anjali Rajwar, Arun Richard Chandrasekaran, Bhaskar Datta, Chinmay Ghoroi, and Dhiraj Bhatia.

ACS Omega 2020, November 28, 2020


Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex 

Phensinee Haruehanroengra, Sweta Vangaveti, Srivathsan V. Ranganathan, Song Mao, Max Daniel Su, Alan A. Chen, Jia Sheng. iScience. November 26, 2020. 


MicroRNA-24-3p promotes skeletal muscle differentiation and regeneration by regulating high mobility group AT-hook 1

Paromita Dey, Bijan K. Dey. BioRxiv. November 11, 2020


Determining the stages of cellular differentiation using Deep Ultraviolet Resonance Raman Spectroscopy.

Nicole K Ralbovsky, Paromita Dey, Bijan K Dey, Igor Lednev

bioRxiv · November 08, 2020


Short DNA Oligonucleotide as a Ag+ Binding Detector

Fusheng Shen, Song Mao, Johnsi Mathivanan, Ying Wu, Arun Richard Chandrasekaran, Hehua Liu, Jianhua Gan and Jia Sheng

ACS Omega · October 28, 2020


A Wi-Fi live streaming Centrifuge Force Microscope (CFM) for benchtop single-molecule experiments

Jibin Abraham Punnoose, Andrew Hayden, Lifeng Zhou, Ken Halvorsen

Biophysical Journal · October 27, 2020


Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems

Anjali Rajwar, Sumit Kharbanda, Arun Richard Chandrasekaran, Sharad Gupta, and Dhiraj Bhatia

ACS Appl. Bio Mater. · October 26, 2020


Hybrid DNA/RNA nanostructures with 2′-5′ linkages

Arun Richard Chandrasekaran, Johnsi Mathivanan, Parisa Ebrahimi, Javier Vilcapoma,  Alan A. Chen, Ken Halvorsen and  Jia Sheng

Nanoscale · October 22, 2020


2-Hydroxyimino-6-aza-pyrimidine nucleosides: synthesis, DFT calculations, and antiviral evaluations 

Abou-Elkhair, R.A.I.;  Wasfy,A. A.;  Mao, S.;  Du,J.;  Eladl, S.;  Metwally, K.;   Hassan, A.E.A.;  Sheng, J. New J. Chem. October 21, 2020. 


Identifying Isl1 Genetic Lineage in the Developing Olfactory System and in GnRH-1 Neurons

Ed Zandro M. Taroc, Raghu Ram Katreddi and Paolo E. Forni

Front. Physiol. · October 21, 2020


Forensic Phenotype Profiling Based on the Attenuated Total Reflection Fourier Transform-Infrared Spectroscopy of Blood: Chronological Age of the Donor

Samantha Giuliano, Ewelina Mistek-Morabito and Igor K. Lednev

ACS Omega · October 14, 2020


Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing

Nan Liu, Xiaolong Dong, Cuixia Hu, Jianwei Zeng, Jiawei Wang, Jia Wang, Hong-Wei Wang, Marlene Belfort 

Nucleic Acids Research · October 06, 2020


Regulation of the Peroxidase‐Like Activity of nGO, MoS2 and WS2 Nanozymes by Using Metal Cations

Nidhi Nandu, Christopher W. Smith, Mahera J. Kachwala, Mehmet V. Yigit. ChemBioChem. October 6, 2020


Myh11+ microvascular mural cells and derived mesenchymal stem cells promote retinal fibrosis

H. Clifton Ray, Bruce A. Corliss, Anthony C. Bruce, Sam Kesting, Paromita Dey, Jennifer Mansour, Scott A. Seaman, Christian M. Smolko, Corbin Mathews, Bijan K. Dey, Gary K. Owens, Shayn M. Peirce & Paul A. Yates

Scientific Reports · September 25, 2020


DNA nanoswitch barcodes for multiplexed biomarker profiling

Arun Richard Chandrasekaran, Molly MacIsaac, Javier Vilcapoma, Clinton H Hansen, Darren Yang, Wesley P Wong, Ken Halvorsen

BioRxiv · September 22, 2020


Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.

 Mao S, Sekula B, Ruszkowski M, Ranganathan SV, Haruehanroengra P, Wu Y, Shen F, Sheng J.

Nucleic Acids Research · September 17, 2020


Nuclease Degradation Analysis of DNA Nanostructures Using Gel Electrophoresis

Arun Richard Chandrasekaran and Ken Halvorsen

Current Protocols · September 15, 2020


Multiplexed Detection and Quantification of Human Antibody Response to COVID-19 Infection Using a Plasmon Enhanced Biosensor Platform

Nathaniel C Cady, Natalya Tokranova, Armond Minor, Nima Nikvand, Klemen Strle, William T Lee, William Page, Ernest Guignon, Arturo Pilar, George N Gibson

BioRxiv · September 02, 2020


Synthesis of 5-Cyanomethyluridine (cnm 5 U) and 5-Cyanouridine (cn 5 U) Phosphoramidites and Their Incorporation into RNA Oligonucleotides

Mao S, Tsai HC, Sheng J.

Curr Protoc Nucleic Acid Chem. · September 01, 2020


Detection and Quantification of RNA Phosphorothioate Modifications Using Mass Spectrometry.

Wu Y, Zheng YY, Lin Q, Sheng J. 

Curr Protoc Nucleic Acid Chem. · September 01, 2020


Base Pairing and Functional Insights into N3-methylcytidine (m3C) in RNA 

Mao, S.; Haruehanroengra, P.; Ranganathan, S.V.; Shen, F.; Begley, T.; Sheng, J. ACS Chemical Biology, August 28, 2020, in press. 


Programmable low-cost DNA-based platform for viral RNA detection

Lifeng Zhou, Arun Richard Chandrasekaran, Jibin Abraham Punnoose, Gaston Bonenfant, Stephon Charles, Oksana Levchenko, Pheonah Badu, Cassandra Cavaliere, Cara T. Pager and Ken Halvorsen

Science Advances · August 21, 2020


Tumor suppressor p53: from engaging DNA to target gene regulation

Morgan A Sammons, Thuy-Ai T Nguyen, Simon S McDade, Martin Fischer

Nucleic Acids Research · August 14, 2020


Ribonuclease-Responsive DNA Nanoswitches

Arun Richard Chandrasekara, Ruju Trivedi, Ken Halvorsen.

Cell Reports. Physical Science · July 22, 2020


Fatal attraction: The roles of ribosomal proteins in the viral life cycle.

Clare M. Miller, Sangeetha Selvam, Gabriele Fuchs.

WiresRNA · July 12, 2020


Diagnosis of a model of Duchenne muscular dystrophy in blood serum of mdx mice using Raman hyperspectroscopy.

Nicole M. Ralbovsky, Paromita Dey, Andrew Galfano, Bijan K. Dey, Igor K. Lednev

Nature Scientific Reports · July 16, 2020


Conditional DnaB Protein Splicing Is Reversibly Inhibited by Zinc in Mycobacteria

Daniel Woods, Sweta Vangaveti, Ikechukwu Egbanum, Allison M. Sweeney, Zhong Li, Valjean Bacot-Davis, Danielle S. LeSassier, Matthew Stanger, Gabrielle E. Hardison, Hongmin Li, Marlene Belfort, Christopher W. Lennon

American Society for Microbiology · July 14, 2020


A Wi-Fi live streaming Centrifuge Force Microscope for benchtop single-molecule experiments

Jibin A Punnoose, Andrew Hayden,  Lifeng Zhou,  Ken Halvorsen.

bioRxiv Preprint · July 07, 2020


Single species RNA purification with DNA nanoswitches

Lifeng Zhou, Cassandra Cavaliere, Andrew Hayden, Paromita Dey, Song Mao, Arun Richard Chandrasekaran, Jia Sheng, Bijan K Dey, Ken Halvorsen

bioRxiv · July 07, 2020


Long noncoding RNA BHLHE40‐AS1 promotes early breast cancer progression through modulating IL‐6/STAT3 signaling

Rebecca S. DeVaux, Ali S. Ropri, Sandra L. Grimm, Peter A. Hall, Emilio O. Herrera, Sridar V. Chittur, William P. Smith, Cristian Coarfa, Fariba Behbod, Jason I. Herschkowitz

Journal of Cellular Biochemistry · July 01, 2020


RNA degradation sculpts the maternal transcriptome during Drosophila oogenesis

Patrick Blatt, Siu Wah Wong-Deyrup, Alicia McCarthy, Shane Breznak, Matthew D. Hurton, Maitreyi Upadhyay, Benjamin Bennink, Justin Camacho, Miler T. Lee, Prashanth Rangan

bioRxiv · June 30, 2020


Processing DNA-Based Molecular Signals into Graphical Displays.

Arun Richard Chandrasekaran

ACS Synth. Biol · June 25, 2020


Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

Aldema Sas-Chen, Justin M. Thomas, […], Qishan Lin, Schraga Schwartz

Nature · June 17, 2020


New Twists on Long Noncoding RNAs: From Mobile Elements to Motile Cancer Cells.

Tuan M Nguyen, Sumayya Alchalabi, Adewunmi Oluwatoyosi, Ali S Ropri, Jason I Herschkowitz, Jeffrey M Rosen.

RNA Biol. · June 10, 2020


How Anionic Lipids Affect Spatiotemporal Properties of KRAS4B on Model Membranes

Ngo VA, Sarkar S, Neale C, Garcia AE

J Phys Chem B. · June 08, 2020


Cell Type-Specific In Vitro Gene Expression Profiling of Stem Cell-Derived Neural Models

James A Gregory, Emily Hoelzli, Rawan Abdelaal, Catherine Braine, Miguel Cuevas, Madeline Halpern, Natalie Barretto, Nadine Schrode, Güney Akbalik, Kristy Kang, Esther Cheng, Kathryn Bowles, Steven Lotz, Susan Goderie, Celeste M Karch, Sally Temple, Alison Goate, Kristen J Brennand, Hemali Phatnani

Cells. · June 05, 2020


Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel.

Zheng X, Fu Z, Su D, Zhang Y, Li M, Pan Y, Li H, Li S, Grassucci RA, Ren Z, Hu Z, Li X, Zhou M, Li G, Frank J, Yang J.

Nat Struct Mol Biol. · June 01, 2020


Ribosomal protein RACK1 enhances translation of poliovirus and other viral IRESs

Ethan LaFontaine, Clare M. Miller, Natasha Permaul, Elliot T. Martin, Gabriele Fuchs

Virology · June 01, 2020


SNAP/CLIP-Tags and Strain-Promoted Azide–Alkyne Cycloaddition (SPAAC)/Inverse Electron Demand Diels–Alder (IEDDA) for Intracellular Orthogonal/Bioorthogonal Labeling

Miguel Macias-Contreras , Huan He, Kevin N. Little, Justin P. Lee, Ryan P. Campbell, Maksim Royzen, and Lei Zhu

Bioconjugate Chem. · May 31, 2020


Base-Pair Conformational Switch Modulates miR-34a Targeting of Sirt1 mRNA

Lorenzo Baronti, Ileana Guzzetti, Parisa Ebrahimi, Sarah Friebe Sandoz, Emilie Steiner, Judith Schlagnitweit, Bastian Fromm, Luis Silva, Carolina Fontana, Alan A. Chen and Katja Petzold

Nature · May 27, 2020


Small molecule-induced DNA hydrogel with encapsulation and release properties

Muhan He, Nidhi Nandu, Taha Bilal Uyar, Maksim Royzen and Mehmet V. Yigit

Chemical Communications · May 26, 2020


Sex-dependent effects of chronic variable stress on discrete corticotropin-releasing factor receptor 1 cell populations.

Rosinger ZJ, De Guzman RM, Jacobskind JS, Saglimbeni B, Malone M, Fico D, Justice NJ, Forni PE, Zuloaga DG

.Physiol Behav. · May 15, 2020


Reaction mechanism, energetics, and kinetics of the water-assisted thioformaldehyde + ˙OH reaction and the fate of its product radical under tropospheric conditions.

Arathala P, Katz M, Musah RA

Phys Chem Chem Phys. · May 13, 2020


A kainate receptor-selective RNA aptamer.

Jaremko W, Huang Z, Karl N, Pierce VD, Lynch J, Niu L.

J Biol Chem. · May 08, 2020


Specificity in the Biosynthesis of the Universal tRNA Nucleoside N6-Threonylcarbamoyl Adenosine (t6A) - TsaD is the Gatekeeper.

Swinehart WE, Deutsch CW, Sarachan KL, Luthra A, Bacusmo JM, de Crécy-Lagard V, Swairjo MA, Agris PF, Iwata-Reuyl D.

RNA · May 08, 2020


Group II intron as cold sensor for self-preservation and bacterial conjugation

Xiaolong Dong, Guosheng Qu, Carol Lyn Piazza, Marlene Belfort

Nucleic Acids Research · May 07, 2020


Asian Zika Virus Isolate Significantly Changes the Transcriptional Profile and Alternative RNA Splicing Events in a Neuroblastoma Cell Line

Gaston Bonenfant, Ryan Meng, Carl Shotwell, Pheonah Badu, Anne F. Payne, Alexander T. Ciota, Morgan A. Sammons, J. Andrew Berglund, Cara T. Pager.

Viruses · May 05, 2020


Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster

Victoria Jorgensen, Jingxun Chen, Helen Vander Wende, Devon E Harris, Alicia McCarthy, Shane Breznak, Siu Wah Wong-Deyrup, Yuzhang Chen, Prashanth Rangan , Gloria Ann Brar, Eric M Sawyer, Leon Y Chan, Elçin Ünal



Epitranscriptomic marks: Emerging modulators of RNA virus gene expression

Netzband R, Pager CT.

Wiley Interdiscip Rev RNA. · May 01, 2020


Smad4-dependent morphogenic signals control the maturation and axonal targeting of basal vomeronasal sensory neurons to the accessory olfactory bulb

Naik AS, Lin JM, Taroc EZM, Katreddi RR, Frias JA, Lemus AA, Sammons MA, Forni PE.

Development · April 27, 2020


Probing CRISPR-Cas12a Nuclease Activity Using Double-Stranded DNA-Templated Fluorescent Substrates

Smith CW, Nandu N, Kachwala MJ, Chen YS, Uyar TB, Yigit MV.

Biochemistry · April 21, 2020


The epitranscriptomic writer ALKBH8 drives tolerance and protects mouse lungs from the environmental pollutant naphthalene

Leonardi A, Kovalchuk N, Yin L, Endres L, Evke S, Nevins S, Martin S, Dedon PC, Melendez JA, Van Winkle L, Zhang QY, Ding X, Begley TJ.

Epigenetics · April 17, 2020


Epigenomic and Transcriptomic Changes During Human RPE EMT in a Stem Cell Model of Epiretinal Membrane Pathogenesis and Prevention by Nicotinamide

Nathan C Boles, Marie Fernandes, Tomasz Swigut, Rajini Srinivasan, Lauren Schiff, Alvaro Rada-Iglesias, Qingjie Wang, Janmeet S Saini, Thomas Kiehl, Jeffrey H Stern, Joanna Wysocka, Timothy A Blenkinsop, Sally Temple

Stem Cell Reports. · April 14, 2020


RNA Phosphorothioate Modification in Prokaryotes and Eukaryotes

Ying Wu, Yaning Tang, Xiaolong Dong, Ya Ying Zheng, Phensinee Haruehanroengra, Song Mao, Qishan Lin, Jia Sheng

ACS Chem. Biol. · April 10, 2020


DNA Nanotechnology in the Undergraduate Laboratory: Analysis of Molecular Topology Using DNA Nanoswitches

Jibin Abraham Punnoose, Ken Halvorsen, Arun Richard Chandrasekaran

Journal of Chemical Education · April 10, 2020


How Nanopore Translocation Experiments Can Measure RNA Unfolding

Prasad Bandarkar, Huan Yang, Robert Y Henley, Meni Wanunu, Paul C Whitford

Biophys J. · April 07, 2020


Activation of Group 2 Innate Lymphoid Cells Alleviates Aging-Associated Cognitive Decline

Ivan Ting Hin Fung, Poornima Sankar, Yuanyue Zhang, Lisa S Robison, Xiuli Zhao, Shanti S D'Souza, Abigail E Salinero, Yue Wang, Jiang Qian, Marcy L Kuentzel, Sridar V Chittur, Sally Temple, Kristen L Zuloaga, Qi Yang

J Exp Med. · April 06, 2020


Switchable Fluorescence of Doxorubicin for Label-Free Imaging of Bioorthogonal Drug Release

Uyar TB, Wu K, He M, Khan I, Royzen M, Yigit MV.

ChemMedChem · March 26, 2020


Exceptional Nuclease Resistance of Paranemic Crossover (PX) DNA and Crossover-Dependent Biostability of DNA Motifs

Arun Richard Chandrasekaran, Javier Vilcapoma, Paromita Dey, Siu Wah Wong-Deyrup, Bijan K. Dey, Ken Halvorsen

J. Am. Chem. Soc. · March 25, 2020


Polycysteine-encoding leaderless short ORFs function as cysteine-responsive attenuators of operonic gene expression in mycobacteria.

Canestrari JG, Lasek-Nesselquist E, Upadhyay A, Rofaeil M, Champion MM, Wade JT, Derbyshire KM, Gray TA.

Mol Microbiol. · March 17, 2020


A Dual-Functioning 5'-PPP-NS1shRNA That Activates a RIG-I Antiviral Pathway and Suppresses Influenza NS1

Neetu Singh, Priya Ranjan, Weiping Cao, Jenish Patel, Shivaprakash Gangappa, Bruce A Davidson, John M Sullivan, Paras N Prasad, Paul R Knight, Suryaprakash Sambhara

Mol Ther Nucleic Acids. · March 06, 2020


Bacterial group II intron genomic neighborhoods reflect survival strategies: hiding and hijacking

Waldern J, Schiraldi NJ, Belfort M, Novikova O.

Mol Biol Evol · March 05, 2020


Locally acting transcription factors regulate p53-dependent cis-regulatory element activity

Allison N Catizone, Gizem Karsli Uzunbas, Petra Celadova, Sylvia Kuang, Daniel Bose, Morgan A Sammons

Nucleic Acids Research · March 05, 2020


How to Perform miRacles: A Step-by-Step microRNA Detection Protocol Using DNA Nanoswitches.

Chandrasekaran AR, Dey BK, Halvorsen K.

Curr Protoc Mol Biol. · March 01, 2020


Identification of the Species Constituents of Maggot Populations Feeding on Decomposing Remains Facilitation of the Determination of Post Mortem Interval and Time Since Tissue Infestation through Application of Machine Learning and Direct Analysis in Real Time-Mass Spectrometry.

Samira Beyramysoltan, Mónica I. Ventura, Jennifer Y. Rosati, Justine E. Giffen-Lemieux and Rabi A. Musah

Anal. Chem. · February 24, 2020


Nucleobase-Modified Triplex-Forming Peptide Nucleic Acids for Sequence-Specific Recognition of Double-Stranded RNA

Nikita Brodyagin, Dziyana Hnedzko, James A MacKay, Eriks Rozners

Peptide Nucleic Acids · February 23, 2020


West Nile Virus Fidelity Modulates the Capacity for Host Cycling and Adaptation

Haley S Caldwell, Kiet Ngo, Janice D Pata, Laura D Kramer, Alexander T Ciota

J Gen Virol. · February 18, 2020


A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.

Vangaveti S, Cantara WA, Spears JL, DeMirci H, Murphy FV 4th, Ranganathan SV, Sarachan KL, Agris PF.

J Mol Biol. · February 14, 2020


2'-O-ribose Methylation of Transfer RNA Promotes Recovery From Oxidative Stress in Saccharomyces Cerevisiae

Lauren Endres ,Rebecca E. Rose,Frank Doyle,Taylor Rahn,Bethany Lee,Jessica Seaman,William D. McIntyre,Daniele Fabris

PLoS One. · February 13, 2020


Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast.

Leticia Pollo-Oliveira, Roland Klassen, Nick Davis, Akif Ciftci, Jo Marie Bacusmo, Maria Martinelli, Michael S DeMott, Thomas J Begley, Peter C Dedon, Raffael Schaffrath, Valérie de Crécy-Lagard

Biomolecules · February 10, 2020


Probing Remote Residues Important for Catalysis in Escherichia Coli Ornithine Transcarbamoylase

Lisa Ngu, Jenifer N Winters, Kien Nguyen, Kevin E Ramos, Nicholas A DeLateur, Lee Makowski, Paul C Whitford, Mary Jo Ondrechen, Penny J Beuning

PLoS One. · February 06, 2020


Drug Screen Tugs at Common Thread for Repeat Disorders

Reddy K, Cleary JD, Berglund JA

Trends Pharmacol Sci. · February 04, 2020


Small RNA Mcr11 Requires the Transcription Factor AbmR for Stable Expression and Regulates Genes Involved in the Central Metabolism of Mycobacterium Tuberculosis

Roxie C. Girardin Kathleen A. McDonough

Mol Microbiol. · February 03, 2020


High‐resolution ion mobility spectrometry‐mass spectrometry of isomeric/isobaric ribonucleotide variants

Thomas Kenderdine Reza Nemati Andrew Baker Martin Palmer Jakub Ujma Molly FitzGibbon Limin Deng Maksim Royzen James Langridge Daniele Fabris

Journal of Mass Spectrometry · February 03, 2020


Comparisons of SOCS mRNA and protein levels in Xenopus provide insights into optic nerve regenerative success

Priscilla R, Szaro BG.

Brain Research · February 01, 2020


Drug Screen Tugs at Common Thread for Repeat Disorders.

Reddy K, Cleary JD, Berglund JA.

Trends Pharmacol Sci. · February 01, 2020


NDAT Suppresses Pro-Inflammatory Gene Expression to Enhance Resveratrol-Induced Anti-Proliferation in Oral Cancer Cells

Yih Ho, Chien-Yi Wu, Yu-Tang Chin, Zi-Lin Li, Yi-Shin Pan, Tung-Yung Huang, Po-Yu Su, Sheng-Yang Lee, Dana R Crawford, et. al.

Food Chem Toxicol. · February 01, 2020


Clarifying Glass Luminescence at Near-Infrared Excitation.

Fikiet MA, Tuschel D, Ermolenkov VV, Lednev IK.

Appl Spectrosc. · February 01, 2020


Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming

Lee MY, Leonardi A, Begley TJ, Melendez JA.

Redox Biol. · January 28, 2020


Synthesis and Biological Activity of Short Interfering RNAs Having Several Consecutive Amide Internucleoside Linkages

Venubabu Kotikam, Julien A Viel, Eriks Rozners

Chemistry · January 13, 2020


The potential of engineered eukaryotic RNA-binding proteins as molecular tools and therapeutics

Shotwell CR, Cleary JD, Berglund JA.

Wiley Interdiscip Rev RNA. · January 11, 2020


Gli3 Regulates Vomeronasal Neurogenesis, Olfactory Ensheathing Cell Formation, and GnRH-1 Neuronal Migration

Taroc EZM, Naik AS, Lin JM, Peterson NB, Keefe DL Jr, Genis E, Fuchs G, Balasubramanian R, Forni PE.

J Neurosci. · January 08, 2020


Regional Differences following Partial Salivary Gland Resection

O'Keefe KJ, DeSantis KA, Altrieth AL, Nelson DA, Taroc EZM, Stabell AR, Pham MT, Larsen M.

J Dent Res. · January 01, 2020


Sequential Regulation of Maternal mRNAs through a Conserved cis-Acting Element in Their 3′ UTRs

PoojaFlora12Siu WahWong-Deyrup1, Elliot, ToddMartin1, RyanJ.Palumbo13, MohamadNasrallah14, AndrewOligney15, PatrickBlatt1, DhruvPatel16, GabrieleFuchs1, PrashanthRangan17

Cell Reports · December 26, 2019


Repeat-associated RNA structure and aberrant splicing

Hale MA, Johnson NE, Berglund JA.

Biochim Biophys Acta Gene Regul Mech · December 01, 2019


Rationally Engineered Nucleic Acid Architectures for Biosensing Applications.

Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H.

Chem Rev. · November 27, 2019


DNA nanotechnology approaches for microRNA detection and diagnosis.

Chandrasekaran AR, Punnoose JA, Zhou L, Dey P, Dey BK, Halvorsen K.

Nucleic Acids Res. · November 18, 2019


Distinguishing Biomolecular Pathways and Metastable States

Antonio B Oliveira Jr, Huan Yang, Paul C Whitford, Vitor B P Leite

J Chem Theory Comput. · November 12, 2019


Epitranscriptomic marks: Emerging modulators of RNA virus gene expression.

Netzband R, Pager CT.

Wiley Interdiscip Rev RNA. · November 06, 2019


Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins

Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ

Free Radic Biol Med · November 01, 2019


Synthesis and RNA-Binding Properties of Extended Nucleobases for Triplex-Forming Peptide Nucleic Acids

Ilze Kumpina, Nikita Brodyagin, James A MacKay, Scott D Kennedy, Martins Katkevics, Eriks Rozners

J Org Chem. · November 01, 2019


Control (Native) and Oxidized (DeMP) Mitochondrial RNA Are Proinflammatory Regulators in Human

Zoran Ilic, Abhinav R Saxena, Sivakumar Periasamy, Dana R Crawford

Free Radic Biol Med. · November 01, 2019


Leptin-derived peptides block leptin-induced proliferation by reducing expression of pro-inflammatory genes in hepatocellular carcinoma cells

Yih Ho, Shwu-Huey Wang, Yi-Ru Chen, Zi-Lin Li, Yu-Tang Chin, Yu-Chen S H Yang, Yun-Hsuan Wu, Kuan-Wei Su, Hung-Ru Chu, Hsien-Chung Chiu, Dana R Crawford, et. al.

Food Chem Toxicol · November 01, 2019


Introduction, Spread, and Establishment of West Nile Virus in the Americas.

Kramer LD, Ciota AT, Kilpatrick AM.

J Med Entomol. · October 28, 2019


A CTG repeat-selective chemical screen identifies microtubule inhibitors as selective modulators of toxic CUG RNA levels

Reddy K, Jenquin JR, McConnell OL, Cleary JD, Richardson JI, Pinto BS, Haerle MC, Delgado E, Planco L, Nakamori M, Wang ET, Berglund JA.

Proc Natl Acad Sci U S A · October 15, 2019


Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing

Green CM, Li Z, Smith AD, Novikova O, Bacot-Davis VR, Gao F, Hu S, Banavali NK, Thiele DJ, Li H, Belfort M

PLoS Biol · October 10, 2019


Molecular mechanism of poliovirus Sabin vaccine strain attenuation

Avanzino BC, Jue H, Miller CM, Cheung E, Fuchs G, Fraser CS

The Journal of Biological Chemistry · October 05, 2019


Drift-diffusion (DrDiff) Framework Determines Kinetics and Thermodynamics of Two-State Folding Trajectory and Tunes Diffusion Models

Frederico Campos Freitas, Angelica Nakagawa Lima, Vinícius de Godoi Contessoto, Paul C Whitford, Ronaldo Junio de Oliveira

J Chem Phys. · September 21, 2019


A Novel Two-Step Method for the Detection of Organic Gunshot Residue for Forensic Purposes: Fast Fluorescence Imaging Followed by Raman Microspectroscopic Identification

Khandasammy SR, Rzhevskii A, Lednev IK.

Anal Chem. · September 17, 2019


Detecting miRNAs Using DNA Nanoswitches.

Chandrasekaran AR.

Trends Biochem Sci. · September 01, 2019


Diffusion of tRNA Inside the Ribosome Is Position-Dependent

Huan Yang, Prasad Bandarkar, Ransom Horne, Vitor B P Leite, Jorge Chahine, Paul C Whitford

J Chem Phys. · August 28, 2019


Bio-orthogonal chemistry-based method for fluorescent labelling of ribosomal RNA in live mammalian cells

Wu K, He M, Khan I, Asare Okai PN, Lin Q, Fuchs G, Royzen M.

Chem Commun (Camb). · August 27, 2019


HuR counteracts miR-330 to promote STAT3 translation during inflammation-induced muscle wasting

Mubaid S, Ma JF, Omer A, Ashour K, Lian XJ, Sanchez BJ, Robinson S, Cammas A, Dormoy-Raclet V, Di Marco S, Chittur SV, Tenenbaum SA, Gallouzi IE.

Proc Natl Acad Sci U S A. · August 27, 2019


Surface Enhanced Raman Spectroscopy for Single Molecule Protein Detection

Almehmadi LM, Curley SM, Tokranova NA, Tenenbaum SA, Lednev IK.

Sci Rep. · August 26, 2019


Click and photo-release dual-functional nucleic acid nanostructures

Valsangkar VA, Chandrasekaran AR, Zhuo L, Mao S, Lee GW, Kizer M, Wang X, Halvorsen K, Sheng J.

Chem Commun (Camb). · August 21, 2019


Mitigating RNA Toxicity in Myotonic Dystrophy using Small Molecules.

Reddy K, Jenquin JR, Cleary JD, Berglund JA.

Int J Mol Sci. · August 17, 2019


Combination Treatment of Erythromycin and Furamidine Provides Additive and Synergistic Rescue of Mis-Splicing in Myotonic Dystrophy Type 1 Models

Jenquin JR, Yang H, Huigens RW 3rd, Nakamori M, Berglund JA.

ACS Pharmacol Transl Sci. · August 09, 2019


Mechanism of Single-Stranded DNA Activation of Recombinase Intein Splicing

Lennon CW, Stanger MJ, Belfort M

Biochemistry · August 06, 2019


Raman spectroscopy and chemometrics: A potential universal method for diagnosing cancer.

Ralbovsky NM, Lednev IK.

Spectrochim Acta A Mol Biomol Spectrosc. · August 05, 2019


Cisplatin protects mice from challenge of Cryptococcus neoformans by targeting the Prp8 intein

Li Z, Fu B, Green CM, Liu B, Zhang J, Lang Y, Chaturvedi S, Belfort M, Liao G, Li H.

Emerg Microbes Infect. · August 01, 2019


Modification of messenger RNA by 2'-O-methylation regulates gene expression in vivo

Elliott BA, Ho HT, Ranganathan SV, Vangaveti S, Ilkayeva O, Abou Assi H, Choi AK, Agris PF, Holley CL.

Nat Commun. · July 30, 2019


Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

Tardu M, Jones JD, Kennedy RT, Lin Q, Koutmou KS.

ACS Chem Biol. · July 19, 2019


Repeat-associated RNA structure and aberrant splicing.

Hale MA, Johnson NE, Berglund JA.

Biochim Biophys Acta Gene Regul Mech. · July 16, 2019


Masking the Peroxidase‐Like Activity of the Molybdenum Disulfide Nanozyme Enables Label‐Free Lipase Detection

Nidhi Nandu Mustafa Salih Hizir Neil M. Roberston Dr. Birol Ozturk Prof. Dr. Mehmet V. Yigit

Chem Bio Chem. · July 15, 2019


GPx3 Supports Ovarian Cancer Progression by Manipulating the Extracellular Redox Environment

Beth L Worley, Yeon Soo Kim, Jennifer Mardini, Rameez Zaman, Kelly E Leon, Piyushi Gupta Vallur, Asvelt Nduwumwami, Joshua I Warrick, Patrick F Timmins, Joshua P Kesterson, Rébécca Phaëton, Nam Y Lee, Vonn Walter, Lauren Endres, Karthikeyan Mythreye, Katherine M Aird, Nadine Hempel

Redox Biol. · July 01, 2019