Publications

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

      •  “Toehold clipping: A mechanism for remote control of DNA strand displacement” Faheem H., Mathivanan J., Talbot H., Zeghal H., Vangaveti S., Sheng J., Chen A. A, Chandrasekaran A. R. Nucleic Acids Research (Dec 2022)
        (https://doi.org/10.1093/nar/gkac1152)

      •  “Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches” –D’Esposito R. J, Myers C. A, Chen A. A., Vangaveti S. Genes ( Mar 2022)
        (https://doi.org/10.3390/genes13030540)

      •   “Physical Chemistry of a Single TRNA-Modified Nucleoside Regulates Decoding of the Synonymous Lysine Wobble Codon and Affects Type 2 Diabetes” – Vangaveti S., Ranganathan S. V. and Agris P. F.  The Journal of Physical Chemistry B (Feb 2022)
        (https://doi.org/10.1021/acs.jpcb.1c09053)

• • • •  “Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)” – Valsangkar V., Vangaveti S., Lee G. W., Fahssi W. M., Awan W. S., Huang Y., Chen A. A., and Sheng J. Molecules (Jul 2021)
        (https://doi.org/10.3390/molecules26154620)

• • • • “Silencing of the tRNA Modification Enzyme Cdkal1 Effects Functional Insulin Synthesis in NIT-1 Cells: tRNALys3 Lacking ms2- (ms2t6A37) is Unable to Establish Sufficient Anticodon:Codon Interactions to Decode the Wobble Codon AAG. ”  Narendran A., Vangaveti S., Ranganathan SV., Eruysal E., Craft M., Alrifai O., Chua FY, Sarachan K., Litwa B., Ramachandran S., Agris PF.  Frontiers in Molecular Biosciences ( Feb 2021

(https://doi.org/10.3389/fmolb.2020.584228)

• • • • “Terpene chain length affects the base pairing discrimination of S-geranyl-2-thiouridine in RNA duplex.” Haruehanroengra P., Vangaveti S., Ranganathan SV., Mao S., Su MD., Chen A., Sheng J. Iscience (Dec 2020)
        ( https://doi.org/10.1016/j.isci.2020.101866 )

• • • •   “Conditional DnaB Protein Splicing Is Reversibly Inhibited by Zinc in Mycobacteria” – Woods D., Vangaveti S., Egbanum I., Sweeney A. M., Li Z., Bacot-Davis V., LeSassier D.S., Stanger M., Hardison G. E., Li H., Belfort M., Lennon C.W. mBio (Jul 2020),
        (https://doi.org/10.1128/mbio.01403-20)

• • • •  “Performance of ZDOCK and IRAD in CAPRI rounds 39-45.” – Vreven T., Vangaveti S., Borrman T., Gaines J., Weng Z.  Proteins (Jan 2020) (https://doi.org/10.1002/prot.25873 )  

• • • •  “A structural basis for restricted codon recognition mediated by 2-thiocytidine in tRNA Containing a wobble position inosine”- Vangaveti S., Sarachan K., Cantara W., Spears J., Demirci H., Murphy F., Ranganathan S., Agris P., Journal of Molecular Biology (Feb 2020)

( https://doi.org/10.1016/j.jmb.2019.12.016  )

• • • •  "Modification of messenger RNA by 2’-O-methylation regulates gene expression in vivo." Elliott B., Hsiand-Ting H., Ranganathan S., Vangaveti S., Ilkayeva O., Assi A H., Choi A., Agris P., Holley C. Nature Communications (Jul 2019)
        ( https://doi.org/10.1038/s41467-019-11375-7)

• • • •  “Integrating ab initio and template-based algorithms for protein-protein structure prediction.” – Vangaveti S., Vreven T., Zhang Y., Weng Z. Bioinformatics (Aug 2019)
        (https://doi.org/10.1093/bioinformatics/btz623)

• • • • “Celebrating wobble decoding: Half a century and still much is new.”- Eruysal R. E., Narendran A., Vare V.Y.P., Vangaveti S., Ranganathan S., Agris P. RNA Biology (Aug 2017).
        (https://doi.org/10.1080/15476286.2017.1356562 )

• • • •  “A coarse-grained model for assisting the investigation of the structure and dynamics of large nucleic acid species by Ion Mobility Spectrometry- Mass Spectrometry.” - Vangaveti S., D’Esposito R., Lippens J. , Fabris D., Ranganathan S. Physical Chemistry Chemical Physics (June 2017)
        ( https://dx.doi.org /10.1039/C7CP00717E )

• • • •  “Nature’s Selection of Geranyl Group as a tRNA Modification: The Effects of Chain Length on Base-Pairing Specificity.”-  Haruehanroengra P., Vangaveti S., Ranganathan S., Wang R., Sheng J. ACS Chemical Biology (April 2017) 
        (  10.1021/acschembio.7b00108 )

• • • •  “Advances in RNA molecular dynamics : a simulator’s guide to RNA force fields.” - Vangaveti S., Ranganathan S. V., Chen A. A., Wires RNA (Oct 2016)
        (https://dx.doi.org/10.1002/wrna.1396)

• • • • “Synthesis, base pairing and structure studies of geranylated RNA” – Vangaveti S., Wang R., Ranganathan S., Basanta-Sanchez M., Haruehanroengra P., Chen A. and Sheng J., Nucleic Acids Research (Jun 2016)
        ( https://dx.doi.org/10.1093/nar/gkw544)

• • • • “Separation of the Stern and Diffuse Layer in Coarse Grained models; The cases of Phosphatidyl Serine, Phosphatidic Acid and PIP2 monolayers” – Vangaveti S., Travesset A., J Chem. Phys. (Dec 2014)
        (http://dx.doi.org/10.1063/1.4904885)
        
        

      •  “General Solution to the Electric Double Layer with Discrete Interfacial Charges” – Vangaveti S., Travesset A., J Chem. Phys. (Aug 2012) (http://dx.doi.org/10.1063/1.4739300)

• • • • “Electrostatic Correlations at the Stern Layer: Physics or Chemistry?”  – Travesset A., Vangaveti S., J Chem. Phys. (Nov 2009) (http://dx.doi.org/10.1063/1.3257735)