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1. Roy, S.; Majee, P.; Sudhakar, S.; Mishra, S.; Kalia, J.; Pradeepkumar, P.I.;* Srivatsan, S. G.* Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes. Chem. Sci. 2024, DOI:10.1039/d4sc01755b.

2. Khatik, S. Y.; Roy, S.; Srivatsan, S. G.* Synthesis and enzymatic incorporation of a dual-app nucleotide probe that reports antibiotics-induced conformational change in the bacterial ribosomal decoding site RNA. ACS Chem. Biol. 2024, 19, 687-695.

3. Pandey, A.; Roy, S.; Srivatsan, S. G.* Probing the competition between duplex, G-quadruplex and i-motif structures of the oncogenic c-Myc DNA promoter region. Chem. Asian J. 2023, e202300510.

4. Khatik, S. Y.; Sudhakar, S.; Mishra, S.; Kalia, J.; Pradeepkumar, P.I.; Srivatsan, S. G.* Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy.  Chem. Sci. 2023, 14, 5627-5637.

5. Khatik, S. Y.; Srivatsan, S. G.* Environment-sensitive nucleoside probe unravels the complex structural dynamics of i-motif DNAs. Bioconjugate Chem. 2022, 33, 1515-1526.

6. Ghosh, P.; Kropp, H. M.; Betz, K.; Ludmann, S.; Diederichs, K.; Marx, A.;* Srivatsan, S. G.* Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J. Am. Chem. Soc. 2022, 144, 10556-10569.

7. Walunj, M. B.; Srivatsan, S. G.* Heterocycle-modified 2′-deoxyguanosine nucleolipid analogs stabilize guanosine gels and self-assemble to form green fluorescent gels. Chemistry - An Asian Journal 2021, 17, e202101163.

8. Manna, S.; Sontakke, V. A.; Srivatsan, S. G.* Incorporation and utility of a responsive ribonucleoside analogue in probing the conformation of a viral RNA motif by fluorescence and 19F NMR spectroscopy. ChemBioChem 2021, 23, e202100601.

9. Walunj, M. B.; Dutta, S.; Srivatsan, S. G.* Architectures of nucleolipid assemblies and their applications in Molecular architectonics and Nanoarchitectonics. Springer Nature, 2021, 307-334.

10. Walunj, M. B.; Srivatsan, S. G.* Nucleic acid conformation influences postsynthetic Suzuki–Miyaura labeling of oligonucleotides. Bioconjugate Chem. 2020, 31, 2513-2521.

11. George, J. T.; Srivatsan, S. G.* Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem. Commun. 2020, 56, 12307-12318.

12. George, J. T.; Srivatsan, S. G.* Responsive fluorescent nucleotides serve as efficient substrates to probe terminal uridylyl transferase. Chem. Commun. 2020, 56, 12307-12318.

13. 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.

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

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

16. 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.

17. 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.

18. 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.

19. 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.

20. 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.

21. 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.

22. 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.

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

24. 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.

25. 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.

26. 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).

27. 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.

28. 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.

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

30. 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.

31.  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.

32.  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.

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

34.  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.

35.  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.

36.  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.

37.  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.

38.  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.

39.  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.

40.  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.

41.  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.

42.  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.

43.  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.

44.  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).

45.  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.

46.  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.

47.  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, 1097−1112.

48.  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, 501−503. Selected as a Hot Article for Chem. Commun: see http://blogs.rsc.org/cc/2011/12/06/simple-detection-of-rna-depurination-by-rips/

49.  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, 498−500. 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.

50.  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, 12820−12827.

51.  Pawar, M. G.; Srivatsan, S. G. Synthesis, Photophysical Charaterization, and Enzymatic Incorporation of a Microenvironment-Sensitive Fluorescent Uridine Analog. Org. Lett., 2011, 13, 1114−1117.

52.  Srivatsan, S. G.; Sawant, A. A. Fluorescent Ribonucleoside Analogues as Probes for Investigating RNA Structure and Function. Pure Appl. Chem., 2011, 1, 213−232.

53.  Srivatsan, S. G. and Tor, Y.: Enzymatic Incorporation of Emissive Pyrimidine Ribonucleotides. Chemistry Asian J., 2009, 4, 419−427.

54.  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.

55.  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.

56.  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.

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

58.  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.

59.  Srivatsan, S. G. and Tor, Y.: Using an emissive uridine analogue for assembling fluorescent HIV-1 TAR constructs. Tetrahedron 2007, 63, 3601−3607.

60.  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.

61.  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.

62.  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.

63.  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, 1559−1562.

64.  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, 740−741.

65.  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, 340−344.

66.  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.

67.  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.

68.  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, 237−241.

69.  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, 299−303.

70.  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, 5162−5173.

71.  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.

72. 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, o378−o380.

73. 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, 240−241.

74.  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, 95−99.

75.  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.

76.  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.

77.  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

78. Srivatsan, S. G. and Famulok, M. Functional nucleic acids in high-throughput screening and drug discovery. Combinatorial Chemistry & High Throughput Screening 2007, 10, 698−705.

79. Srivatsan, S. G. Modeling prebiotic catalysis with nucleic acid-like polymers and its implications for the proposed RNA world. Pure Appl. Chem., 2004, 76, 2085−2099.

80. 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, 129−150.