Publications

• Ganguly, C., Aribam, S.D., Santos, A.M.D., Martin, L., Thomas, L.M., Shao, Y., Rajan, R. Bridge helix of Cas12a is an allosteric regulator of R-loop formation and RuvC activation. (2026) Nat. Commun. 17(1):2126 DOI: 10.1038/s41467-026-68657-0. Link to article

• Aiswarya, N., Remya, C., Sajitha, K., Rajan, R., Vasudevan, D. M., K.V. Dileep, K. V. Methyl eugenol as a multitarget-directed ligand for Alzheimer disease: a promising lead for drug design. (2026) ASPET Discovery 2,100019, Link to article

• Wu, D., Snead, S., Ganguly, C., Babu, K., Li, Y., Kathiresan, V., Shen, R., Zhang, X., Rajan, R. Qin, P.Z. Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination. (2025) Nucleic Acids Res. 53(12):gkaf557. DOI: 10.1093/nar/gkaf557. Link to article

• Benedict, A., Aquino, A., Buckner, B.A., Aribam, S.D., Ganguly, C., Thomas, L.M., Bourne, P., Rajan, R., Downs, D.M., Somalinga, V. Biochemical and structural characterization of a reactive intermediate deaminase A homolog from Streptococcus sanguinis. (2025) Sci. Rep. 15(1):22017. DOI: 10.1038/s41598-025-05264-x. Link to article

• Hima, S., Remya, C., Abhithaj, J., Arun, K. G., Sabu, A., Sajitha, K., Rajan, R., Vasudevan, D. M., Dileep, K. V. Insights into the structural and biophysical mechanisms of benzamidine-driven inhibition of human lysozyme aggregation. (2025) Int J Biol Macromol. 305(Pt 2):141139. doi: 10.1016/j.ijbiomac.2025.141139. Link to article

• Van, R., Pan, X., Rostami, S., Liu, J., Agarwal, P.K., Brooks, B., Rajan, R., Shao, Y. Exploring CRISPR-Cas9 HNH-domain-catalyzed DNA cleavage using accelerated quantum mechanical molecular mechanical free energy simulation. (2024) Biochemistry. 64(1):289-299. doi: 10.1021/acs.biochem.4c00651. Link to article

• Ganguly, C., Rostami, R., Long, K., Aribam, S.D., Rajan, R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. (2024) J Biol Chem. 300(6):107295. doi: 10.1016/j.jbc.2024.107295. Link to article

• Park, J.H., Prasad, V., Newsom, S.N., Najar, F., Rajan, R. An interactive motif identification in protein sequences. (2024) IEEE Comput Graph Appl. 44(3):114-125. doi: 10.1109/MCG.2023.3345742. Link to article

• Newsom, S.N., Wang, D-S., Rostami, S., Schuster, I., Parameshwaran, H.P., Joseph, Y,G., Qin, P.Z., Liu,J., Rajan, R. Differential divalent metal binding by SpyCas9's RuvC active site contributes to nonspecific DNA cleavage. (2023) CRISPR J. 6(6):527-542.. doi: 10.1089/crispr.2023.0022. Link to article

• Martin, L., Rostami, R., Rajan, R. Optimized protocols for the characterization of Cas12a activities. (2023) Methods Enzymol. 679:97-129. doi: 10.1016/bs.mie.2022.08.048. Link to article

• Flusche, T., Rajan, R. Molecular details of DNA integration by CRISPR-associated proteins during adaptation in bacteria and archaea. (2022). Adv. Exp. Med. Biol., doi: 10.1007/5584_2022_730. Link to article

• Zuo, Z., Babu, K., Zolekar, A., Rajan, R., Wang, Y. C., Liu, J. Rational engineering of CRISPR-Cas9 nuclease to attenuate position-dependent off-target effects. (2022). CRISPR J. 5(2):329-340. Link to article

• Babu, K., Kathiresan, V., Kumari, P., Newsom, S., Parameshwaran, H.P., Chen, X., Liu, J., Qin, P.Z., Rajan, R. (2021). Coordinated actions of Cas9 HNH and RuvC nuclease domains are regulated by the bridge helix and the target DNA sequence. Biochemistry, 60(49):3783-3800. Link to article

• Parameshwaran, H.P., Babu, K., Tran, C., Guan, K., Allen, A., Kathiresan, V., Qin, P.Z., Rajan, R. (2021). Bridge helix of Cas12a imparts selectivity in cis-DNA cleavage and regulates trans-DNA cleavage. FEBS Lett. 595(7):892-912. doi: 10.1002/1873-3468.14051. Link to article

• Newsom, S., Parameshwaran, H.P., Martin, L., Rajan, R. (2021). The CRISPR-Cas mechanism for adaptive immunity and alternate bacterial functions fuels diverse biotechnologies. Front. Cell. Infect. Microbiol. 10:619763. doi: 10.3389/fcimb.2020.619763. eCollection 2020. Link to article

• Van Orden M. J., Newsom, S., Rajan, R. (2020) CRISPR type II-A subgroups exhibit phylogenetically distinct mechanisms for prespacer insertion. J. Biol. Chem. 295(32):10956-10968. doi: 10.1074/jbc.RA120.013554. PMID: 32513871. Link to article 

• Jiang, W., Singh, J., Allen, A., Li, Y., Kathiresan, V., Qureshi, O., Tangprasertchai, N., Zhang, X., Parameshwaran, H. P., Rajan, R., & Qin, P. Z. (2019) CRISPR-Cas12a nucleases bind flexible DNA duplexes without RNA/DNA complementarity. ACS Omega. 4(17):17140-17147. doi: 10.1021/acsomega.9b01469; PubMed PMID: 31656887. Link to article 

• Chan, C. W., Badong, D., Rajan, R., Mondragòn, A. (2020) Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of folded tRNAs. RNA 26(3):278-289. Link to article 

• Zuo, Z., Zolekar, A., Babu, K., Lin, V. J., Hayatshahi, H. S., Rajan, R., Wang, Y. C., & Liu, J. (2019) Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. Elife. 30;8. pii: e46500. doi: 10.7554/eLife.46500; PMID: 31361218. Link to article 

• Babu, K., Amrani, N., Jiang, W., Yogesha, S.D., Nguyen, R., Qin, P.Z. & Rajan, R. (2019) Bridge helix of Cas9 modulates target DNA cleavage and mismatch tolerance. Biochemistry 58(24): 1905-1917. doi: 10.1021/acs.biochem.8b01241; PMID: 30916546. Link to article 

• Sundaresan, R.†, Parameshwaran, H. P.†, Yogesha, S. D., Keilbarth, M. W., Rajan, R. (2017). RNA-independent DNA cleavage activities of Cas9 and Cas12a. Cell Rep., 21(13): 3728-3739. PMID: 29281823. (†equal contribution). Link to article 

• Murugan, K., Babu, K., Sundaresan, R., Rajan, R., Sashital, D. G. (2017). The revolution continues: newly discovered systems expand the CRISPR-Cas Toolkit. Mol. Cell, 68:15-25. PMID: 28985502. Link to article

• Van Orden, M.†, Klein, P.†, Babu, K., Najar, F.Z., Rajan, R. (2017). Conserved DNA motifs in the type II-A CRISPR leader region. Peer J. DOI 10.7717/peerj.3161. PMID: 28392985. (†equal contribution). Link to article 

• Vazquez Reyes, C. V., Tangprasertchai, N. S., Yogesha, S. D., Nguyen, R. H., Zhang, X., Rajan, R. Qin, P.Z. (2017). Nucleic-acid dependent conformational changes in CRISPR-Cas9 revealed by site-directed spin labeling. Cell Biochem. Biophys., 75(2):203-210 PMID: 27342128. Link to article 

• Rajan, R., Osterman, A., Mondragòn, A. (2016). Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site. Nucleic Acids Res. 44(7):3464-3474 PMID: 26908655. Link to article

• Wakefield, N., Rajan, R., Sontheimer, E.J. (2015). Primary processing of CRISPR RNA by the endonuclease Cas6 in Staphylococcus epidermidis. FEBS Lett. 589 (20 Pt B): 3197-3204. PMID: 26364721. Link to article 

• Zhang, Y.†, Rajan, R.†, Seifert, H.S., Mondragòn, A., Sontheimer, E.J. (2015). DNase H activity of Neisseria meningitidis Cas9. Mol. Cell, 60 (2): 242-255 PMID: 26474066. (†equal contribution). Link to article 

• Rajan, R., Osterman, A.K., Gast, A.T., Mondragòn, A. (2014). Biochemical characterization of the topoisomerase domain of Methanopyrus kandleri topoisomerase V. J. Biol. Chem., 289 (42): 28898-28909. PMID: 25135643. Link to article 

• Rajan, R., Critchelow, C., Mondragòn, A. (2013). DNA Topoisomerases. Encyclopedia of Biophysics, Volume 1, (Editor: Gordon, C. K. Roberts, Published in cooperation with the European Biophysics Societies' Association (EBSA), Springer) pp 2616-2622. Link to article 

• Rajan, R., Prasad, R., Taneja, B., Wilson, S.H., Mondragòn, A. (2013). Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies. Nucleic Acids Res., 41 (1): 657-666. PMID: 23125368. Link to article 

• Rajan, R., Taneja, B., Mondragòn, A. (2010). Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding. Structure, 18 (7): 829-838. PMID: 20637419. Link to article 

• Gopishetty, B., Zhu, J., Rajan, R., Sobczak, A.J., Wnuk, S.F., Bell, C.E., Pei, D. (2009). Probing the catalytic mechanism of S-Ribosylhomocysteinase (LuxS) with catalytic intermediates and substrate analogues. J. Am. Chem. Soc., 131 (3): 1243-1250. PMID: 19099445. Link to article 

• Baker, N. M., Rajan, R., Mondragòn, A. (2009). Structural studies of type I topoisomerases. Nucleic Acids Res. 37: 693-701. PMID: 19106140. Link to article 

• Shen, G., Rajan, R., Zhu, J., Bell, C.E., Pei, D. (2006). Design and synthesis of substrate and intermediate analogue inhibitors of S-ribosylhomocysteinase. J. Med. Chem., 49 (10): 3003-3011. PMID: 16686542. Link to article 

• Rajan, R., Wisler, J.W., Bell, C.E. (2006). Probing the DNA sequence specificity of Escherichia coli RECA protein. Nucleic Acids Res., 34 (8): 2463-2471. PMID: 16684994. Link to article 

• Rajan, R., Zhu, J., Hu, X., Pei, D., Bell, C.E. (2005). Crystal structure of S-ribosylhomocyteinase (LuxS) in complex with a catalytic 2-ketone intermediate. Biochemistry, 44 (10): 3745-3753. PMID: 15751951. Link to article 

• Rajan, R., Bell, C.E. (2004). Crystal structure of RecA from Deinococcus radiodurans: insights into the structural basis of extreme radioresistance. J. Mol. Biol., 344 (4): 951-963. PMID: 15544805. Link to article