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

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

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

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

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

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

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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