Indian Institute of Science Education and Research

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Publications

Srivatsan Group

Publications

 

 

1. George, J. T.; Srivatsan, S. G.* Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem. Commun. 2020, doi.org/10.1039/D0CC05228K.

2. George, J. T.; Srivatsan, S. G.* Responsive fluorescent nucleotides serve as efficient substrates to probe terminal uridylyl transferase. Chem. Commun. 2020, doi.org/10.1039/D0CC05092J.

3. George, J. T.; Mohd. Azhar; Aich, M.; Sinha, D.; Ambi, U. B.; Maiti, S.;* Chakraborty, D.;* Srivatsan, S. G.* Terminal uridylyl transferase mediated site-directed access to clickable chromatin employing CRISPR-dCas9. J. Am. Chem. Soc. 2020, 142, 13954-13965.

4. Sontakke, V. A.; Srivatsan, S. G.* Bioorganic & Medicinal Chemistry Letters, 2020, 30, 127345.

5. Nuthanakanti, A.; Srivatsan, S. G.* Multi-stimuli responsive heterotypic hydrogels based on nucleolipids show selective dye adsorption. Nanoscale Adv. 2020, 2, 4161-4171 .

6. Nuthanakanti, A.; Srivatsan, S. G.* Synthesis of DNA and RNA oligonucleotides containing a dual-purpose selenium-modified fluorescent nucleoside probe. Current Protocols in Nucleic Acid Chemistry, 2020, 81, e106.

7. Walunj, M. B.; Srivatsan, S. G.* Posttranscriptional Suzuki-Miyaura cross-coupling yields labeled RNA for conformational analysis and imaging. Methods in Molecular Biology, 2020, 2166, 473-486.

8. Manna, S.; Srivatsan, S. G.* Synthesis and enzymatic incorporation of a responsive ribonucleoside probe that enables quantitative detection of metallo-base pairs. Org. Lett. 2019, 21, 4646-4650.

9. Ashok, N.; Ishtiyaq, A.; Saddam, Y. K.; Kayarat, S.;* Srivatsan, S. G.* Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucl. Acid. Res. 2019, 47, 6059-6072.

10. Ashok, N.; Walunj, M. B.; Arun, T. A. T.; Badiger, M. V.; Srivatsan, S. G.* Self-assemblies of nucleolipid supramolecular synthons show unique self-sorting and cooperative assembling process. Nanoscale 2019, 11, 11956-11966.

11. Manna, S.; Sarkar, D.; Srivatsan, S. G.* A Dual-app nucleoside probe provides structural insights into the human telomeric overhang in live cells. J. Am. Chem. Soc. 2018, 140, 12622-12633.

12. Sabale, P. M.; Ambi, U. B.; Srivatsan, S. G.* Clickable PNA probes for imaging human telomeres and poly(A) RNAs. ACS Omega 2018, 3, 15343-15352.

13. Manna, S.; Srivatsan, S. G. Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments. RSC Adv. 2018, 8, 25673-25694.

14. Sabale, P. M.; Tanpure, A. A.; Srivatsan, S. G. Probing the competition between duplex and G-quadruplex/i-motif structures using a conformation-sensitive fluorescent nucleoside probe. Org. Biomol. Chem. 2018, 16, 4141-4150.

15. Walunj, M. B.; Tanpure, A. A.; Srivatsan, S. G.* Posttranscriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes. Nucl. Acid. Res. 2018, 46, e65. DOI: 10.1093/nar/gky185.

16. Sabale, P. M.; Ambi, U. B.; Srivatsan, S. G.* A Lucifer-based environment-sensitive fluorescent PNA probe for imaging poly(A) RNAs. ChemBioChem 2018, 19, 826-835 (cover page article).

17. Walunj, M. B.; Sabale, P. M.; Srivatsan, S. G. Advances in the application of Pd-mediated transformations in nucleotides and oligonucleotides: a book chapter in Palladium-catalyzed modification of nucleosides, nucleotides and oligonucleotides. Elsevier Inc, 2018, 269-293.

18. Sawant, A. A.; Galande, S.; Srivatsan, S. G. Imaging newly transcribed RNA in cells by using a clickable azide-modified UTP analog. Methods in Molecular Biology 2018, 1649, 359-371.

19. Nuthanakanti, A.; Srivatsan, S. G. Surface-tuned and metal-ion-responsive supramolecular gels based on nucleolipids. ACS Appl. Mater. Interfaces 2017, 9, 22864-22874.

20. Manna, S.; Panse, C. H.; Sontakke, V. A.; Sangamesh, S.; Srivatsan, S. G. Probing human telomeric DNA and RNA topology and ligand binding in a cellular model by using responsive fluorescent nucleoside probes. ChemBioChem 2017, 18, 1604-1615.

21.  George, J. T.; Srivatsan, S. G. Vinyluridine as a Versatile Chemoselective Handle for the Posttranscriptional Chemical Functionalization of RNA. Bioconjugate Chem. 2017, 28, 1529-1536.

22.  Nuthanakanti, A.; Boerneke, M. A.; Hermann, T.; Srivatsan S. G. Structure of the ribosomal decoding site RNA containing a Se-modified responsive fluorescent ribonucleoside probe. Angew. Chem. Int. Ed. 2017, 56, 2640-2644.

23.  George, J. T.; Srivatsan, S. G. Posttranscriptional chemical labeling of RNA by using bioorthogonal chemistry. Methods 2017, 120, 28-38.

24.  Sabale, P. M.; Srivatsan, S. G. Responsive fluorescent PNA analog as a tool for detecting G-quadruplex motifs of oncogenes and activity of toxic ribosome inactivating proteins. ChemBioChem 2016, 17, 1665-1673.

25.  Sawant, A. A.; Mukherjee, P. P.; Jangid, R. K.; Galande, S.; Srivatsan, S. G. Clickable UTP analog for the posttranscriptional chemical labeling and imaging of RNA. Org. Biomol. Chem., 2016, 14, 5832-5842.

26.  Nuthanakanti, A.; Srivatsan, S. G. Hierarchical self-assembly of switchable nucleolipid supramolecular gels based on environment-sensitive fluorescent nucleoside analogs, Nanoscale 2016, 8, 3607-3619.

27.  Sawant, A. A.; Tanpure, A. A.; Mukherjee, P. P.; Athavale, S.; Kelkar, A.; Galande, S.; Srivatsan, S. G. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucl. Acid. Res. 2016, 44, e16.

28.  Tanpure, A. A.; Srivatsan, S. G. Conformation-sensitive nucleoside analogues as topology-specific fluorescence turn-on probes for DNA and RNA G-quadruplexes. Nucl. Acid. Res. 2015, 43, e149.

29.  Sabale, P. M.; George, J. T.; Srivatsan, S. G. Base-modified PNA-graphene oxide platform as a turn-On fluorescence sensor for the detection of human telomeric repeats. Nanoscale 2014, 6, 10460-10469.

30.  Tanpure, A. A.; Srivatsan, S. G. Synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue based on the lucifer chromophore. ChemBioChem 2014, 15, 1309-1316.

31.  Pawar, M. G.; Srivatsan, S. G. Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model cell-like compartment. J. Phys. Chem. B 2013, 117, 14273-14282.

32.  Peters, J. P.; Yelgaonkar, S. P.; Srivatsan, S. G.; Tor, Y.; Maher III, L. J. Mechanical properties of DNA-like polymers. Nucl. Acid. Res. 2013, 41, 10593-10604.

33.  Pawar, M. G.; Nuthanakanti, A.; Srivatsan, S. G. Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding. Bioconjugate Chem. 2013, 24, 1367-1377.

34.  Sabale, P.M.; Nuthanakanti, A.; Srivatsan, S. G. Synthesis and fluorescence properties of a full set of extended RNA base analogues. Ind. J. Chem. 2013, 52A, 1004-1013 (invited research article for the thematic special issue on Complex Chemical Systems).

35.  Tanpure, A. A.; Pawar, M. G.; Srivatsan, S. G. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr. J. Chem. 2013, 53, 366-378.

36.  Tanpure, A. A.; Srivatsan, S. G. Synthesis and photophysical characterization of a fluorescent nucleoside analogue that signals the presence of an abasic site in RNA. ChemBioChem 2012, 13, 2392-2399.

37.  Rao, H.; Tanpure A. A.; Sawant, A. A.; Srivatsan, S. G. Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization. Nature Protocols 2012, 7, 10971112.

38.  Tanpure, A. A.; Patheja, P.; Srivatsan, S. G. Label-free fluorescence detection of the depurination activity of ribosome inactivating protein toxins. Chem. Commun., 2012, 48, 501503. Selected as a Hot Article for Chem. Commun: see http://blogs.rsc.org/cc/2011/12/06/simple-detection-of-rna-depurination-by-rips/

39.  Rao, H.; Sawant, A. A.; Tanpure A. A.; Srivatsan, S. G. Posttranscriptional chemical functionalization of azide-modified oligoribonucleotides by bioorthogonal click and Staudinger reactions, Chem. Commun., 2012, 48, 498500. Cover page article; Selected as a Hot Article for Chem. Commun: See http://blogs.rsc.org/cc/2011/11/02/overcoming-obstacles-in-labelling-rna/; Also Faculty of 1000 (F1000) places this article in their library of the top 2% of published articles in biology and medicine.

40.  Tanpure, A. A.; Srivatsan, S. G. A Microenvironment-Sensitive Fluorescent Pyrimidine Ribonucleoside Analogue: Synthesis, Enzymatic Incorporation, and Fluorescence Detection of a DNA Abasic Site. Chem. Eur. J. 2011, 17, 1282012827.

41.  Pawar, M. G.; Srivatsan, S. G. Synthesis, Photophysical Charaterization, and Enzymatic Incorporation of a Microenvironment-Sensitive Fluorescent Uridine Analog. Org. Lett., 2011, 13, 11141117.

42.  Srivatsan, S. G.; Sawant, A. A. Fluorescent Ribonucleoside Analogues as Probes for Investigating RNA Structure and Function. Pure Appl. Chem., 2011, 1, 213232.

43.  Srivatsan, S. G. and Tor, Y.: Enzymatic Incorporation of Emissive Pyrimidine Ribonucleotides. Chemistry Asian J., 2009, 4, 419427.

44.  Srivatsan, S. G., Greco, N. J. and Tor, Y.: Highly Emissive Fluorescent Nucleoside Signals the Activity of Toxic Ribosome Inactivating Proteins. Angew. Chem., 2008, 47, 6661−6665. Cover page article; Spotlight feature article: ACS Chemical Biology 2008, 3, 520. Science & Technology Concentrates, CN&E, 2008, 86, 35−36.

45.  Fusz, S., Srivatsan, S. G., Ackermann, D., and Famulok M.: Photocleavable initiator nucleotide substrates for an aldolase ribozyme. J. Org. Chem., 2008, 73, 5069−5077.

46.  Srivatsan, S. G., Weizman, H. and Tor, Y.: Highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine positively senses mismatched pairing. Org. Biomol. Chem., 2008, 6, 1334−1338.

47.  Srivatsan, S. G. and Tor, Y.: Synthesis and enzymatic incorporation of a fluorescent pyrimidine ribonucleotide. Nature Protocols 2007, 2, 1547−1555.

48.  Srivatsan, S. G. and Tor, Y.: Fluorescent pyrimidine ribonucleotide: synthesis, enzymatic incorporation and utilization. J. Am. Chem. Soc., 2007, 129, 2044−2053. Spotlight feature article: ACS Chemical Biology 2007, 2, 83.

49.  Srivatsan, S. G. and Tor, Y.: Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs. Tetrahedron 2007, 63, 36013607.

50.  Tor, Y., Valle, S. D., Jaramillo, D., Srivatsan, S. G., Rios, A. and Weizman, H.: Designing new isomorphic fluorescent nucleobase analogues: the thieno[3,2-d]pyrimidine core. Tetrahedron 2007, 63, 3608−3614.

51.  Hafner, M., Schmitz, A., Grune, I., Srivatsan, S. G., Paul, B., Kolanus, W., Quast, T., Kremmer, E., Bauer, I. and Famulok, M.: Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance. Nature 2006, 444, 941−944.

52.  Fusz, S., Eisenfuhr, A., Srivatsan, S. G., Heckel, A. and Famulok M.: A ribozyme for the aldol reaction. Chemistry and Biology 2005, 12, 941−950. Highlighted in Nature news and views: Nature 2005, 438, 40.

53.  Chandrasekhar, V., Deria, P., Krishnan, V., Athimoolam, A., Singh, S., Madhavaiah, C., Srivatsan, S. G. and Verma, S.: Metalated hybrid polymers as catalytic reagents for phosphate ester hydrolysis and plasmid modification. Bioorg. Med. Chem. Lett., 2004, 14, 15591562.

54.  Saxena, A., Srivatsan, S. G., Saxena, V. and Verma, S.: Bioinspired modification of polystyryl matrix: single-step chemical evolution to a moderately conducting polymer. Chem. Lett., 2004, 33, 740741.

55.  Srivatsan, S. G., Parvez, M. and Verma, S.: Adenine-copper coordination polymer as an oxidative nucleozyme: Implications for simple prebiotic catalytic units. J. Inorg. Biochem., 2003, 97, 340344.

56.  Mukhopadhyay, R., Srivatsan, S. G. and Verma, S.: Surface trapping and AFM detection of DNA topological intermediates generated from an oxidative chemical nuclease. Biochem. Biophy. Res. Commun., 2003, 308, 165−169.

57.  Verma, S., Srivatsan, S. G., Claussen, C. A. and Long, E. C.: DNA Strand Scission by a Cu(I)-Adenylated Polymeric Template: Preliminary mechanistic and recycling studies. Bioorg. Med. Chem. Lett., 2003, 13, 2501−2504.

58.  Madhavaiah, C., Srivatsan, S. G. and Verma, S.: Heterogeneously active nucleolytic reagents: Flexible design of reusable catalysts for nucleic acid scission. Catal. Commun., 2003, 4, 237241.

59.  Madhavaiah, C., Srivatsan, S. G. and Verma, S.: Kinetic and mechanistic investigations of phosphodiester cleavage catalyzed by uranyl ion impregnated adenylated homopolymer. Catal. Commun., 2002, 3, 299303.

60.  Chandrasekhar, V., Athimoolam, A., Srivatsan, S. G., Sundaram, P. S., Verma, S., Steiner, A. and Zacchini, S.: Pyrazolylcyclotriphosphazene containing pendant polymers: Synthesis, characterization and phosphate ester hydrolysis using a Cu(II) metalated cross-linked polymeric catalyst. Inorg. Chem., 2002, 41, 51625173.

61.  Srivatsan, S. G., Parvez, M. and Verma, S.: Modeling prebiotic catalysis with adenylated polymeric templates: Crystal structure studies and kinetic characterization of template-assisted phosphate ester hydrolysis. Chem. Eur. J., 2002, 8, 5184−5191.

62. Srivatsan, S. G., Verma, S. and Parvez, M.: 4-vinylbezyl analogs of adenine and uracil: Reactive monomers for nucleobase polymeric resins. Acta Cryst., 2002, C58, o378o380.

63. Srivatsan, S. G., Kingsley, S. and Verma, S.: Self-assembly of 9-allyladenine hydrochloride in crystalline state: Formation of infinitely stacked molecular sheets using multiple hydrogen bonds. Chem. Lett., 2002, 240241.

64.  Madhavaiah, C., Srivatsan, S. G. and Verma, S.: Ruthenium-metallated adenine nucleobase polymers as novel reagents for catalytic cleavage of phosphate esters. Catal. Commun., 2001, 2, 9599.

65.  Srivatsan, S. G. and Verma, S.: Nucleobase containing metallated polymeric resins as artificial phosphodiesterases: Kinetics of hydrolysis, pH dependence and catalyst recycling. Chem. Eur. J., 2001, 7, 828-833.

66.  Srivatsan, S. G., Nigam, P., Rao, M. S. and Verma, S.: Phenol oxidation by copper metallated 9-allyladenine-DVB polymer: Reaction catalysis and polymer recycling. Appl. Catal. A: General 2001, 209, 327-334.

67.  Srivatsan, S.G. and Verma, S.: Synthetic Dephosphorylation Reagents: Rate Enhancement of Phosphate Monoester Hydrolysis by Cu(II)-Metallated Adenine Nucleobase Polymers. Chem. Commun., 2000, 515-516.

 

Book Chapter and Reviews

68. Srivatsan, S. G. and Famulok, M. Functional nucleic acids in high-throughput screening and drug discovery. Combinatorial Chemistry & High Throughput Screening 2007, 10, 698705.

69. Srivatsan, S. G. Modeling prebiotic catalysis with nucleic acid-like polymers and its implications for the proposed RNA world. Pure Appl. Chem., 2004, 76, 20852099.

70. Verma, S., Srivatsan, S. G. and Madhavaiah, C. Copper containing nuclease mimics: Synthetic models and biochemical applications: Artificial Nucleases 232 (Nucleic Acids and Molecular Biology Series), Ed. Zenkova, M. A., Springer-Verlag, Heidelberg, 2004, 13, 129150.