“Integration Host Factor Binds DNA Holliday Junctions,” S.H. Lin, D. Zhao, V. Deng, V.K. Birdsall, S Ho, O. Buzovetsky, C. M. Etson and I. Mukerji, Int. J. Mol. Sci. 2023, 24(1), 580;

“Förster Resonance Energy Transfer Mapping: A New Methodology to Elucidate Global Structural Features,” J. Northrop, D. Oliver and I. Mukerji, Journal of Visualized Experiments, 2022 (181), e63433, doi:10.3791/63433

“SUMO Fosters Assembly of the MutSγ Complex to Facilitate Meiotic Crossing Over,” W. He, G. F. Verhees, N. Bhagwat, Y. Yang, D. S. Kulkarni, Z. Lombardo, S. Lahiri, P. Roy, J. Zhuo, B. Dang, A. Snyder, S. Shastry, M. Moezpoor, L. Alocozy, K. G. Lee, D. Painter, I. Mukerji and N. Hunter, Developmental Cell, 2021, 56(14) P2073-2088.E3. DOI:

“Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics” Li, Yan; Lombardo, Zane; Joshi, Meera; Hingorani, Manju M.; Mukerji, Ishita. 2019. Int. J. Mol. Sci. 20, no. 17: 4271.

“Alignment of the protein substrate hairpin along the SecA two-helix finger primes protein transport in Escherichia coli,” Q. Zhang, S. Lahiri, T. Banerjee, Z. Sun, D. Oliver and I. Mukerji Proc. Natl. Acad. Sci USA 2017, 114 (35) 9343-9348. doi: 10.1073/pnas.1702201114

“The Stories Tryptophans Tell: Exploring Protein Dynamics of Heptosyltransferase I from Escherichia coli,” J. M. Cote, C. A. Ramirez-Mondragon, Z. S. Siegel, D. J. Czyzyk, J. Gao, Y. Y. Sham, I. Mukerji and E. A. Taylor Biochemistry, 2017, 56 (6), 886-895. DOI: 10.1021/acs.biochem.6b00850

“Photophysical Characterization of Enhanced 6-Methylisoxanthopterin Fluorescence in Duplex DNA,” A. Moreno, J. L. Knee and I. Mukerji J. Phys. Chem. B, 2016, 120 (48), 12232-12248. DOI: 10.1021/acs.jcpb.6b07369

“Probing the Ion Binding Site in a DNA Holliday Junction using Förster Resonance Energy Transfer (FRET),” Litke, J.L.; Li, Y.; Nocka, L.M.; Mukerji, I.  J. Mol. Sci.2016, 17, 366, doi: 10.3390/ijms17030366

“Conserved SecA Signal Peptide-binding Site Revealed by Engineered Protein Chimeras and Förster Resonance Energy Transfer,” Q. Zhang, Y. Li, R. Olson, I. Mukerji and D. Oliver Biochemistry, 2016, 55(9), pp 1291–1300, DOI:1021/acs.biochem.5b01115

“Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments,” Wang, L. M. Nocka, B. Z. Wiemann, D. M. Hinckley, I. Mukerji and F. W. Starr (2016) Scientific Reports 6, 22863. doi:10.1038/srep22863

“Fabrication and Experimental Analysis of Axially Oriented Nanofibers,” A.N. Aphale, K. Mahakalkar, I.G. Macwan, I. Mukerji, P.J. Cox, M. Mahapatra, P. Singh, P.M. Ajayan, and P.K. Patra, (2015) Nanosci. Nanotech. 15, 1-9. doi:10.1166/jnn.2015.10827

“Defining the solution-state dimer structure of Escherichia coli SecA using Förster resonance energy transfer,” S. M. Auclair, D. B. Oliver, and I. Mukerji, (2013) Biochemistry, Publication Date (Web): March 13, 2013, DOI: 1021/bi301217t

“Resonance Raman Spectroscopy,” Mukerji, Ishita (December 2012). In: eLS 2012, John Wiley & Sons Ltd: Chichester [DOI: 10.1002/9780470015902.a0003113.pub2]

“Analysis of high affinity binding of PKR to dsRNA,” B. Husain, I. Mukerji and J. L. Cole (2012) Biochemistry, 51 (44), pp 8764–8770. DOI: 10.1021/bi301226h

“Applying 6-MI Enhanced Fluorescence to Examine Protein-DNA Interactions in the Picomolar Range,” A. T. Moreno, J. L. Knee and I. Mukerji, (2012) Biochemistry 51, 6847-6859. DOI: 1021/bi300466d

“Molecular Dynamics Structure Prediction of a Novel Protein-DNA Complex: Two HU Proteins with a DNA Four-Way Junction,” G. Wheatley, S. N. Pieniazek, I. Vitoc, I. Mukerji and D. L. Beveridge (2012) Innovations in Biomolecular Modeling and Simulations: Volume 2, 2012, 2, 111-128 DOI:10.1039/9781849735056-00111

“Getting Places Together: How to Find and Keep a Good Mentor,” S. Cavagnero and I. Mukerji, Biophysical Society Newsletter, April 2012.

“Molecular Dynamics of a DNA Holliday Junction: The Inverted Repeat Sequence d(CCGGTACCGG)4,” E. G. Wheatley, S. N. Pieniazek, I. Mukerji and D. L. Beveridge (2012) Biophys. J. 102(3), 552-560. doi: 10.1016/j.bpj.2011.11.4023

“Nitric oxide reduces sickle hemoglobin polymerization: Potential role of nitric oxide-induced charge alteration in depolymerization,” Ikuta, T., Thatte, H. S., Tang, J. X., Mukerji, I., Knee, K., Bridges, K. R., Wang, S., Montero-Huerta, P., Joshi, R. M., Head, C.A., (2011) Biochem. Biophys. 510, 53-61. DOI:

C. I. Vitoc and I. Mukerji, “HU Binding to a DNA Four-Way Junction Probed by Förster Resonance Energy Transfer,”(2011) Biochemistry 50 1432–1441.  DOI:  10.1021/bi1007589

Y. Wang, S. Petty, K. Knee, D. Goulet, I. Mukerji and J. A. King, “Formation of amyloid fibrils in vitro from partially unfolded intermediates of Human γC-Crystallin,” (2010) Investigative Ophthalmology and Visual Science 51 672-678. doi: 10.1167/iovs.09-3987

Auclair, S. M., Moses, J. P., Musial-Siwek, M. Kendall, D. A., Mukerji, I. and Oliver, D. B. “Mapping of the Signal Peptide-binding Domain of Escherichia coli SecA Using Förster Resonance Energy Transfer,” Biochemistry 49: 782-792. (2010) DOI: 10.1021/bi901446r

“UV Resonance Raman Characterization of Diphenylalanine-Graphene Nanotubes,” A. Bhattacharya, A. Cheng, S. Bhosale, A. Aphale, I. Macwan, P. K. Patra and I. Mukerji (2012) Spectroscopy 27 (11), 2-7. Featured on the cover.

K. M. Knee and I. Mukerji, J. , “Real Time Monitoring of Hb S Fiber Formation with UV Resonance Raman Spectroscopy,” (2009) Biochemistry 48, 9903–9911.  DOI:  10.1021/bi901352m.

Tumpa Sarkar, Anton Petrov, Jason R. Vitko, Stephen C. Harvey, Ishita Mukerji and Nicholas V. Hud, “Integration Host Factor (IHF) Dictates the Structure of Polyamine-DNA Condensates: Implications for the Role of IHF in the Compaction of Bacterial Chromatin,” Biochemistry 48 667-75. DOI:  10.1021/bi8019965 (2009)

K. M. Knee, S. Dixit, C. E. Aitken, S. Pomonarev, , D. L. Beveridge and I. Mukerji “Spectroscopic and Molecular Dynamics Evidence for a Sequential Mechanism for the DNA B to A transition,” Biophysical J., BioFAST: March 7, 2008. doi:10.1529/biophysj.107.117606. (2008)

K. M. Knee, C. K. Roden, M. R. Flory and I. Mukerji, “The Role of β93 Cys in the inhibition of Hb S Fiber Formation,” Biophysical Chem., 187: 181-193. doi:10.1016/j.bpc.2007.02.002 (2007)

Jason Vitko, Iulian Rujan, Lagu Androga, Ishita Mukerji, Philip H. Bolton, “Molecular Beacon-Equilibrium Cyclization Detection of DNA-Protein Complexes,” Biophysical J. 93: 3210-3217. doi:10.1529/biophysj.106.097642. (2007)

T. Sarkar, C. I. Vitoc, I. Mukerji and N. V. Hud, “Bacterial Protein HU Dictates the Morphology of DNA Condensate Produced by Crowding Agents and Polyamines,” Nucleic Acids Research, 35: 951-961 (2007). DOI: 10.1093/nar/gkl1093

K. E. Augustyn, K. Wojtuszewski, M. E. Hawkins, J. R. Knutson and I. Mukerji “Examination of A-Tract Bending using a Fluorescent Adenosine Analogue,” Biochemistry, 45: 5039-5047 (2006). DOI: 10.1021/bi0518343

I. Mukerji, “Resonance Raman Spectroscopy”  in Encyclopedia of Life Sciences.  John Wiley and Sons, Ltd: Chichester. [doi: 10.1038/npg.els.0003113]

K. Wojtuszewski, I.Mukerji, “The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: Structural elements of specificity.” Protein Science 13, 2416-2428 (2004).

H. Arthanari, K. Wojtuszewski, I. Mukerji, P. H. Bolton, “Effects of HU binding on the equilibrium cyclization of mismatched, curved and normal DNA.” Biophys. J. 83(3), 1625-31 (2004).

K. Wojtuszewski,, I. Mukerji, “HU Binding to Bent DNA: A Fluorescence Resonance Energy Transfer and Anisotropy Study.” Biochemistry 42(10), 3096-3104 (2003).

I. Mukerji, A. P. Williams, “UV Resonance Raman and Circular Dichroism Studies of a DNA Duplex Containing an A3T3 Tract:  Evidence for a Premelting Transition and Three-Centered H-Bonds.” Biochemistry 41, 69-7 (2002).

K. Wojtuszewski, M.E. Hawkins, J.L. Cole, I. Mukerji, “Hu Binding to DNA: Evidence for Multiple Complexes and DNA Bending.” Biochemistry 40, 2588-2598 (2001).

H. Ding, I. Mukerji, D. Oliver, “Conformational Changes of E. coli Sec A probed by intrinsic tryptophan fluorescence.” Biochemistry 40, 1835-1844 (2001).

L. Sokolov, I. Mukerji, “Structure of Sickle Cell Hemoglobin Fibers probed with UV Resonance Raman Spectroscopy.” J. Phys. Chem. B. 104, 10835-10843 (2000).

M. Schmidt, H. Ding, V. Ramamurthy, I. Mukerji, D. Oliver, “Nucleotide-binding activity of SecA homodimer is conformationally regulated by temperature and altered by prlD and azi mutations.” J. Biol. Chem., 275, 15440-15448 (2000).

M. E. Yohe, K. M. Sheffield, I. Mukerji, “Solubility of Fluormethemoglobin S: Effect of Phosphate and Temperature on Polymerization.” Biophys. J. 78, 3218-3226 (2000).

M. E. Yohe, K. M. Sheffield, I. Mukerji, “Solubility of Fluormethemoglobin S: Effect of Phosphate and Temperature on Polymerization.” Biophys. J. 78, 3218-3226 (2000).

X. Hu, K. R. Rodgers, I. Mukerji, T. G. Spiro, “New Light on Allostery: Dynamic Resonance Raman Spectroscopy of Hemoglobin Kempsey.” Biochemistry 38, 3462-3467 (1999).

I. Mukerji, L. Sokolov, M.-R. Mihailescu, “A UV Resonance Raman Investigation of Poly (rI): Evidence for Cation Dependent Structural Perturbations.” Biopolymers 46, 475-487 (1998).

L. Sokolov, I. Mukerji, “Conformational Changes in FmetHbS Probed with UV Resonance Raman and Fluorescence Spectroscopic Methods.” J. Phys. Chem. B 102, 8314-8319 (1998).

S. S. Chan, R. H. Austin, I. Mukerji, T. G. Spiro, “Temperature Dependent UV Resonance Raman Spectroscopy of the Premelting State of dA-dT DNA.” Biophys. J. 72, 1512-1520 (1997).

I. Mukerji, M. C. Shiber, T. G. Spiro, J. R. Fresco, “A UV Resonance Raman Study of Tetrads Formed from Hairpin Dimers of d(A-G)10 at Neutral pH.” Nucleic Acids Research 24, 5013-5020 (1996).

I. Mukerji, “Biochemical Spectroscopy.” Book Review, Biophys. J. 70, 2458-2459 (1996).

T. Jordan, I. Mukerji, T. G. Spiro, “UV Resonance Raman Spectroscopy of the Proline Peptide Bond.” J. Molec. Struct. 379, 51-64 (1996).

M. J. Latimer, V. J. DeRose, I. Mukerji, V. K. Yachandra, K. Sauer, M. P. Klein, “Evidence for the Proximity of Calcium to the Manganese Cluster of Photosystem II: Determination by X-ray Absorption Spectroscopy.” Biochemistry 34, 10898-10909 (1995).

V. Jayaraman, K. R. Rodgers, I. Mukerji, T. G. Spiro, “Hemoglobin Allostery: Resonance Raman Spectroscopy of Kinetic Intermediates.” Science 269, 1843-1848 (1995).

I. Mukerji, M. C. Shiber, T. G. Spiro, J. R. Fresco, “A UV Resonance Raman Study of d(A+-G)10, a Single-Stranded Helix without Stacked or Paired Bases.” Biochemistry 34, 14300-14303 (1995).

V. J. DeRose, M. J. Latimer, J.-L. Zimmermann, I. Mukerji, V. K. Yachandra, K. Sauer, M. P. Klein, “Fluoride Substitution in the Mn Cluster from Photosystem II: EPR and X-ray Absorption Spectroscopy Studies.” Chemical Physics 194, 443-459 (1994).

V. J. DeRose, I. Mukerji, M. J. Latimer, V. K. Yachandra, K. Sauer, M. P. Klein, “A Comparison of the Manganese Oxygen-Evolving Complex in Photosystem II of Spinach and Synechococcus sp. with Multinuclear Manganese Model Compounds by X-ray Absorption Spectroscopy.” J. Am. Chem. Soc. 116, 5239-5249 (1994).

I. Mukerji, J. C. Andrews, V. J. DeRose, M. J. Latimer, V. K. Yachandra, K. Sauer, M. P. Klein, “Orientation of the Oxygen Evolving Manganese Complex in a Photosystem II Membrane Preparation: An X-Ray Absorption Spectroscopy Study.” Biochemistry 33, 9712-9721 (1994).

I. Mukerji, T. G. Spiro, “Modeling the Hemoglobin Switchpoint with Cyanomet Valency Hybrids: Raman Spectroscopic Probes of Tertiary and Quaternary Structure.” Biochemistry 33, 13132-13139 (1994).

V. K. Yachandra, V. J. DeRose, M. J. Latimer, I. Mukerji, K. Sauer, M. P. Klein, “Where Plants Make Oxygen: A Structural Model for the Photosynthetic Oxygen Evolving Manganese Cluster.” Science 260, 675-679 (1993).

V. Jayaraman, K. R. Rodgers, I. Mukerji, T. G. Spiro, “R and T States of Fluoromethemoglobin Probed by UV Resonance Raman Spectroscopy.” Biochemistry 32, 4547-4551 (1993).

I. Mukerji, K. Sauer, “Energy Transfer Dynamics of an Isolated Light Harvesting Complex of Photosystem I from Spinach: Time-resolved Fluorescence Measurements at 295K and 77K.” Biochim. Biophys. Acta 1142, 311-320 (1993).

I. Mukerji, K. Sauer, “Optical Spectroscopy on a Photosystem I Antenna Complex.”  in Current Research in Photosynthesis (M. Baltscheffsky, ed.), Vol. II, Kluwer Academic Publishers, The Netherlands, pp. 321-324 (1990).

I. Mukerji, K. Sauer, “Temperature Dependent Steady-state and Picosecond Kinetic Fluorescence Measurements of a Photosystem I Preparation from Spinach,” in Photosynthesis (W.R. Briggs, ed.) A.R. Liss, New York, pp. 105-122 (1989).

H. G. Brittain, A. L. Wayda, I. Mukerji, “Luminescence Studies of Tris(bis(trimethylsilyl)amido)Terbium (III) and of its Adduct Complexes.” Inorganic Chem. 26, 2742-2746 (1987).

I. Mukerji, A.L. Wayda, G. Dabbagh, S.H. Bertz, “Alkylation of Epoxides with new Organoyttrium and Organolanthanoid Reagents,” Angew. Chem. Int. Ed. Engl. 25, 760-762 (1986).