• Rafael G. Viegas, Murilo N. Sanches, Alan A. Chen, Fernando V. Paulovich, Angel E. Garcia, and Vitor B.P. Leite (2023) “Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop” J. Chem. Inf. Model.  doi: 10.1021/acs.jcim.3c00426

• Samadrita Biswas, Simi Kaur, Christopher A. Myers, Alan A. Chen and John T. Welch (2023) “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” ACS Omega  doi: 10.1021/acsomega.3c02019

• Jibin Punnoose, Kevin Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan A. Chen, Thomas Banco, and Ken Halvorsen (2023) “High-throughput single-molecule quantification of individual base stacking energies in nucleic acids” Nature Communications doi: 10.1038/s41467-023-36373-8

• Hiba Faheem, Johnsi Mathivanan, Hannah Talbot,  Hana Zeghal, Sweta Vangaveti, Jia Sheng, Alan A. Chen, and Arun Richard Chandrasekaran (2023) “Toehold clipping: A mechanism for remote control of DNA strand displacement ” Nucleic Acids Research doi:10.1093/nar/gkac1152

• Johnsi Mathivanan, Zhixue Bai, Alan A. Chen, and Jia Sheng (2022) “Design, Synthesis, and Characterization of a Novel 2′–5′-Linked Amikacin-Binding Aptamer: An Experimental and MD Simulation Study ” ACS Chemical Biolology doi:10.1021/acschembio.2c00653

• Mengwen Yan, Christopher A. Myers, Gregory M. John, Vincent E. Meyers, Alan A. Chen, and Jeremy I. Feldblyum* (2022) “Probing the Edges between Stability and Degradation of a Series of ZnSe-Based Layered Hybrid Semiconductors ” Advanced Materials Interfaces 9 (20) doi:10.1002/admi202200347

Luyi Cheng, Elise N White, Naomi L Brandt, M Yu Angela, Alan A Chen, Julius B Lucks. (2022) “Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch” Nucleic Acids Reseach “Breakthrough Article” doi:10.1093/nar/gkac102

News Coverage:

• Exceptional research recordings display RNA switching “on” and “off” (AZO Life Sciences)
• Catching an RNA Switch in Action (Labroots)
• Unprecedented videos show RNA switching ‘on’ and ‘off’ (Phys.org)
• In Published Study, Chen Lab Elevates Understanding of Genetic Expression

• Rebecca J D’Esposito, Christopher A Myers, Alan A Chen, Sweta Vangaveti (2022) “Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches” Genes 13 (3) p. 540   doi: 10.3390/genes13030540

• Loah Huynh and Alan A Chen (2021) “Design of a protein-targeted DNA aptamer using atomistic simulation” Journal of Biomolecular Structure and Dynamics 13 (3) p. 540   doi: 10.1080/07391102.2021.2011414

• Vibhav Valsangkar, Sweta Vangaveti, Goh Woon Lee, Walid M Fahssi, Waqas S Awan, Yicheng Huang, Alan A Chen, Jia Sheng (2021) “Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)” Molecules 26 (15) p. 4620   doi: 10.3390/molecules26154620

Yu, Angela; Gasper, Paul; Cheng, Luyi; Lai, Lien; Kaur, Simi; Gopalan, Venkat; Chen, Alan. A* and Lucks, Julius B*. (2021) “Computationally Reconstructing Cotranscriptional RNA Folding from Experimental Data Reveals Rearrangement of Non-Native Folding Intermediates” Molecular Cell doi:10.1016/j.molcel.2020.12.017

News Coverage:

• Using R2D2 to Understand RNA Folding (NIH Director Francis Collins’s Blog)
• Ground-breaking films show RNA’s complex curves take shape (Research highlights- Nature)
• RNA ties itself in knots, then unties itself in mesmerizing video (LiveScience)
• Mesmerizing Video Reveals RNA Folding in All Its Strange, Tangled Glory (ScienceAlert)
• Amazing Videos Of RNA Folding Made By R2D2 Method (IFLScience)
• DR. ALAN CHEN PRESENTS R2D2- A NEW METHOD FOR INVESTIGATING RNA FOLDING PATHWAYS (RNA Institute)

• Phensinee Haruehanroengra, Sweta Vangaveti, Srivathsan V Ranganathan, Song Mao, Max Daniel Su, Alan A Chen, Jia Sheng (2020) “Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex” Iscience 23 (12) p. 101866 doi: 10.1016/j.isci.2020.101866

Ebrahimi, Parisa*; Kaur, Simi*; Baronti, Lorenzo; Petzold, Katja and Chen, Alan A. (2019) “A Multi-dimensional Hamiltonian Replica-Exchange method for simulating RNA Folding using experimental constraints” Methods (162/163) pp. 96-107   doi: 1016/j.ymeth.2019.05.001

Myers, Christopher; D’Esposito, Rebecca; Fabris, Daniele; Ranganathan, Srivathsan; and Chen, Alan A. (2019) “CoSIMS: An Optimized Trajectory Based Collision Simulator for Ion Mobility Spectrometry” Journal of Physical Chemistry B 123 (20), pp. 4347-4357 doi: 10.1021/acs.jpcb.9b01018

Note: the CoSIMS code can be downloaded here

Mao, Song; Ranganathan, Srivathsan V.; Tsai, Hsu-Chun; Haruehanroengra, Phensinee; Shen, Fusheng; Valsangkar, Vibhav A.; Han, Bo; Hassan, Abdalla E.; Chen, Alan and Sheng, Jia. (2018) “Cyano‐modification on Uridine Decrease the Base Pairing Stability and Specificity through Neighbouring Disruption in RNA Duplex” ChemBioChem, 19(24), pp. 2558-2565 10.1002/cbic.201800399

 Wang, Rui; Ranganathan, Srivathsan V.; Haruehanroengra, Phensinee; Mao, Song; Scalabrin, Matteo; Fabris, Daniele; Chen, Alan A.; Lui, Hehua; Hassan, Abdalla; Gan, Jianhua and Sheng, Jia. (2018) “Construction and Structure Studies of DNA-bipyridine Complexes as Versatile Scaffolds for Site-Specific Incorporation of Metal Ions into DNA” Journal of Biomolecular Structure and Dynamics, 37 (3), pp. 551-561 10.1080/07391102.2018.1441071

Seebald, Leah; DeMott, Christopher; Ranganathan, Srivathsan; Okai, Papa Nii; Glazunova, Anastasia; Chen, Alan; Shekhtman, Alexander; and Royzen, Maksim (2017) “Cobalt-Based Paramagnetic Probe to Study RNA–Protein Interactions by NMR” Inorganic Biochemistry 170, pp. 202-208 10.1016/j.jinorgbio.2017.02.024

Seebald, Leah; DeMott, Christopher; Ranganathan, Srivathsan; Okai, Papa Nii; Glazunova, Anastasia; Chen, Alan; Shekhtman, Alexander; and Royzen, Maksim (2017) “Cu(II)-Based Paramagnetic Probe to Study RNA–Protein Interactions by NMR” Inorganic Chemistry 56 (7), pp. 3773-3780 10.1021/acs.inorgchem.6b02286

Vangaveti, Sweta; Ranganathan, Sri; and Chen, Alan A. (2016) “Advances in RNA Molecular Dynamics: A Simulator’s Guide to RNA Force-fields” Wiley Interdisciplinary Reviews: RNA 8 (2), pp. e1396 10.1002/wrna.1396

 Wang, Rui.; Vangaveti, Sweta; Ranganathan, Sri; Basanta-Sanchez, Maria; Haruehanroengra, Phensinee ; Chen, Alan; and Sheng, Jia (2016) “Synthesis, Base Pairing and Structure Studies of Geranylated RNA” Nucleic Acids Research 44 (13): 6036-6045 PMCID: PMC4889945

Ranganathan, S. V.; Halvorsen, K.; Myers, C. A.; Robertson, N. M.; Yigit, M. Y.; and Chen, A. A., (2016) “Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces” Langmuir 32 (24), pp 6028–6034 DOI:10.1021/acs.langmuir.6b00456 

Takahashi, Melissa K.; Watters, Kyle E.; Gasper, Paul; Abbott, Timothy R.; Chen, Alan A.; Lucks, Julius B. (2016) “Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators” RNA Vol. 22, pp. 920-933 DOI: 10.1261/rna.054916.115 

Jacob C Miner, Alan A Chen, Angel E Garcia (2016) “The free-energy landscape of a hyperstable RNA tetraloop” Proceedings of the National Academy of Sciences, U.S.A. 113 (24) 6665-6670 DOI: 10.1073/pnas.1603154113 PMCID: PMC4914146

R. Wang, S. Ranganathan, M. Basanta Sanchez, F. Shen, A. Chen and J. Sheng, (2015), Synthesis and Base Pairing Studies of Geranylated 2-thiothymidine, a Natural Variant of Thymidine. Chem. Commun., (51) 16369-16372 DOI:10.1039/C5CC07479G 

R. Wang, S. Ranganathan, V. A. Valsankar, S. M. Magliocco, F. Shen, A. Chen and J. Sheng, (2015), Water-bridged hydrogen bond formation between 5-hydroxymethylcytosine (5-hmC) and its 3’-neighboring bases in A- and B-form DNA Duplexes. Chem. Commun., (51) 16389-16392 DOI: 10.1039/C5CC06563A