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

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

G3: GENES, GENOMES, GENETICS · May 04, 2020

 

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

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