Publications

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

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