Sai Krishnan Kayarat

Publications

1. Adhav, V.A. & Saikrishnan, K. (2023).  The realm of unconventional noncovalent interactions in proteins: their significance in structure and function. ACS Omega, 8, 22268-22284.

2. Adhav, V.A., Sanket, S.S., Balanarayan, P. & Saikrishnan, K. (2023). Sulfur-mediated chalcogen versus hydrogen bonds in proteins: a seesaw effect in the conformational space. Quat. Rev. Biophys. Disc. DOI: https://doi.org/10.1017/qrd.2023.3.

3. Adhav, V.A., Balanarayan, P. & Saikrishnan, K. (2022). Probing the directionality of S···O/N chalcogen bond and its interplay with weak C–H···O/N/S hydrogen bond using molecular electrostatic potential. J. Phys. Chem. B, 126, 40, 7818-7832.

4. Tumuluri, V.S., Saikrishnan, K. (2022). Heterologous Expression and high degree purification of the restriction endonuclease SauUSI. Bio-Protocol, 12(1).e4275.,doi:10.21769/BioProtoc.4275.

5. Tumuluri, V.S., Rajgor, V., Xu, S-Y., Chouhan, O. P., Saikrishnan, K. (2021). Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res., 49, 2161–2178.

6. Chand, M. K. Carle, V., Anuvind, K. G. & Saikrishnan, K. (2020). DNA-mediated coupling of ATPase, translocase and nuclease activities of a Type ISP restriction-modification enzyme. Nucleic Acids Res. 48, 2594-2603.

7. Gopinath, A., Kulkarni, M., Ahmed, I., Chouhan, O.P. & Saikrishnan, K. (2020). The conserved aspartate in motif III of b family AdoMet-dependent DNA methyltransferase is important for methylation. J. Biosciences, 45, https://www.ias.ac.in/article/fulltext/jbsc/045/0010.

8. Nirwan, N., Itoh, Y., Singh, P., Bandyopadhyay, S., Vinothkumar, K. R., Amunts, A., & Saikrishnan, K. (2019) Structure-based mechanism for activation of the AAA+ GTPase McrB0 by the endonuclease McrC, Nature Communications. doi.org/10.1038/s41467-019-11084-1.

9. Nuthankanti, A. Ahmed, I. Saikrishnan, K.* & Srivatsan, S.G. (2019) Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app fluorescent and X-ray probe,  Nucleic Acids Res. 47, 6059-6072. (* Co-corresponding author)

10. Nirwan, N., Singh, P., Mishra, G. G., Johnson, C. M., Szczelkun, M. D., Inoue, K., Vinothkumar, K. R. & Saikrishnan, K.  (2019) Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity. Nucleic Acids Res. 47, 868-882.

11. Ahmad, I., Kulkarni, M., Gopinath, A. & Saikrishnan, K. (2018)  Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated. Nucleic Acids Res. 46, 6229 -6237.

12. Kadam, V. N., Saikrishnan, K. & Ganesh, K. N. (2018)  5-Amidodansyl-U (U D ) peptide nucleic acid (PNA) as a fluorescent sensor of the local dielectric constant (ε) in PNA duplexes: major grooves in PNA duplexes are more hydrophobic than major grooves in DNA–DNA duplexes.  J. Phys. Chem. C, 122, 14004-14013.

13. Kulkarni, M., Nirwan, N., van Aelst, K., Szczelkun, M. & Saikrishnan, K. (2016). Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes. Nucleic Acids Res. 44, 4396-4408.

14. van Aelst, K., Saikrishnan, K.*, & Szczelkun, M. (2015). Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations. Nucleic Acid Res. 43, 10430-10443 (* Co-corresponding author).

15. Chand, M. K., Nirwan, N., Diffin, F., van Aelst, K., Kulkarni, M., Pernstich, C., Szczelkun, M. & Saikrishnan, K. (2015). Translocation-coupled DNA cleavage by the Type ISP restriction- modification enzymes. Nature Chemical Biol. 11, 870-877.

16. Saikrishnan, K., Yeeles, J.T., Gilhooly, N.S., Krajewski, W.W., Dillingham, M.S. & Wigley, D.B. (2012). Insights into Chi recognition from the structure of an AddAB-type helicase- nuclease complex. EMBO J. 31, 1568-1578.

17. Saikrishnan, K., Powell, B., Cook, N., Webb, R. M. & Wigley, D.B. (2009). Mechanistic basis of 5’-3’ translocation by SF1B helicases. Cell. 137, 849-859.

18. Saikrishnan, K. Griffiths, S. P., Cook, N., Court, R. & Wigley, D.B. (2008). DNA binding to RecD: role of the 1B domain in SF1B helicase activity. EMBO J. 27, 2222-2229.

19. Court, R., Cook, N., Saikrishnan, K. & Wigley, D.B. (2007). The crystal structure of -Gam protein suggests a model for RecBCD inhibition. J. Mol. Biol. 371, 25-33.

20. Saikrishnan, K., Manjunath, G. P., Singh, P., Jeyakanthan, J., Dauter, Z., Sekar, K., Muniyappa, K. & Vijayan, M. (2005). Crystal structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs. Biological implications of structural plasticity and variability in quaternary association. Acta Crystallogr. D61, 1140-1148.

21. Singh, D. D., Saikrishnan, K., Kumar. P., Sekar, K., Surolia, A. & Vijayan, M. (2005). Unusual sugar specificity of banana lectin from Musa paradisiaca and its probable evolutionary origin. Crystallographic and modeling studies. Glycobiology. 15, 1025-1032.

22. Saikrishnan, K., Kalapala, S. K., Varshney, U. & Vijayan, M. (2005). X-ray structural studies of Mycobacterium tuberculosis RRF and a comparative study of RRFs of known structure. Molecular plasticity and biological implications. J. Mol. Biol. 345, 29-38.

23. Singh, D. D., Saikrishnan, K., Kumar. P., Sekar, K., Surolia, A. & Vijayan, M. (2004). Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca. Acta Crystallogr. D60, 2104-2106.

24. Saikrishnan, K., Kalapala, S. K., Bidya Sagar, M., Rao, A. R., Varshney, U. & Vijayan, M. (2004). Purification, crystallization and preliminary X-ray studies of Mycobacterium tuberculosis RRF. Acta Crystallogr. D60, 368-370.

25. Acharya, N., Talwar, R. K., Saikrishnan, K., Vijayan, M. & Varshney, U. (2003). Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition. Nucleic Acids Res. 31, 7216-7226.

26. Saikrishnan, K., Jeyakanthan, J., Venkatesh, J., Acharya, N., Sekar, K., Varshney, U. & Vijayan, M. (2003). Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications. J. Mol. Biol. 331, 385-393.

27. Saikrishnan, K., Bidya Sagar, M., Ravishankar, R., Roy, S., Purnapatre, K., Handa P., Varshney U. & Vijayan, M. (2002). Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG. Acta Crystallogr. D58, 1269-76.

28. Saikrishnan, K., Jeyakanthan, J., Venkatesh, J., Acharya, N., Purnapatre, K., Sekar, K., Varshney, U. & Vijayan, M. (2002). Crystallization and preliminary X-ray studies of the single- stranded DNA-binding protein from Mycobacterium tuberculosis. Acta Crystallogr. D58, 327-329.