Articles in journals

• Madison, K. E., Abdelmeguid, M., Jones-Foster, E. N., and Nakai, H.. "A new role for translation initiation factor 2 in maintaining genome integrity.." PLoS Genetics 8.4 (2012): e1002648.
• Madison, K. E., Abdelmeguid, M., Kirtland, S., North, S. H., and Nakai, H.. "The role of alarmone (p)ppGpp in the PriA-PriC restart pathway.." (in preparation) (2011).
• Marshall-Batty, K. R., and Nakai, H.. "Trans-targeting of protease substrates by conformationally activating a regulable ClpX-recognition motif." Mol. Microbiol. 67 (2008): 920-933.
• Marshall-Batty, K. R., and H. Nakai. "Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility." J. Biol. Chem. 238 (2008): 9060-9070.
• North, S. H., Kirtland, S. E., and Nakai, H.. "Translation factor IF2 at the interface of transposition and replication by the PriA-PriC pathway." Mol. Microbiol. 66 (2007): 1566-78.
• Nakai, H., & North, SH. "Host factors that promote transposome disassembly and the PriA-PriC pathway for restart primosome assembly." Mol. Microbiol. 56.6 (2005): 1601-16.
• Chen, H. W., North, S. H., and Nakai, H.. "Properties of the PriA helicase domain and its role in binding PriA to specific DNA structures." J. Biol. Chem. 279 (2004): 38503-38512.
• Defenbaugh, D. A., and Nakai, H.. "A context-dependent ClpX recognition determinant located at the C terminus of phage Mu repressor ." J. Biol. Chem. 278 (2004): 52333-52339.
• Marshall-Batty, K. R., and Nakai, H. . "Trans-targeting of phage Mu repressor is promoted by conformational changes that expose its ClpX recognition determinant." J. Biol. Chem. 278 (2003): 1612-1617.
• Mukhopadhyay, B. Marshall-Batty, K. R., Kim, B. D., O’Handley, D.. "Modulation of phage Mu repressor DNA binding and degradation by distinct determinants in its C-terminal domain ." Mol. Microbiol. 47 (2003): 171-182.
• O’Handley, D., and Nakai, H. . "Derepression of bacteriophage Mu transposition functions by truncated froms of the immunity repressor." J. Mol. Biol. 322 (2002): 311-324.
• Jones, J. M., and Nakai, H. . "Escherichia coli PriA helicase: Fork binding orients the helicase to unwind the lagging strand side of arrested replication forks." J. Mol. Biol. 312 (2001): 935-947.
• Rai, S. S., O’Handley, D., and Nakai, H. . "Conformational dynamics of a transposition repressor in modulating DNA binding." J. Mol. Biol. 312 (2001): 311-322.
• Nakai, H., Doseeva, V., and Jones, J. M. . "Hand-off from recombinase to replisome: Insights from transposition." Proc. Natl. Acad. Sci. USA 98 (2001): 8247-8254.
• Jones, J. M., and Nakai, H.. "PriA and phage T4 gp59: factors that promote DNA replication on forked DNA substrates." Mol. Microbiol. 36 (2000): 519-527.
• Jones, J. M., and Nakai, H. . "Duplex opening by primosome protein PriA for replisome assembly on a recombination intermediate." J. Mol. Biol. 289 (1999): 503-515.
• Jones, J. M., and Nakai, H. . "The ?X174-type primosome promotes replisome assembly at the site of recombination in bacteriophage Mu transposition." EMBO J. 16 (1997): 6886-6895.
• Welty, D. J., Jones, J. M., and Nakai, H.. "Communication of ClpXP protease sensitivity to bacteriophage Mu repressor isoforms." J. Mol. Biol. 272 (1997): 31-41.
• Kruklitis, R., Welty, D. J., and Nakai, H.. ". ClpX protein of Escherichia coli activates bacteriophage Mu transposase in the strand transfer complex for initiation of Mu DNA synthesis." EMBO J. 15 (1996): 935-944.
• Nakai, H., and Kruklitis, R.. "Disassembly of the bacteriophage Mu transposase for the initiation of Mu DNA replication." J. Biol. Chem. 270 (1995): 19591-19598.
• Kruklitis, R., and Nakai, H. . "Participation of bacteriophage Mu A protein and host factors in the initiation of Mu DNA synthesis in vitro." J. Biol. Chem. 269 (1994): 16469-16477.
• Nakai, H. . "Amplification of bacteriophage Mu DNA by rolling circle DNA replication in vitro." J. Biol. Chem. 268 (1993): 23997-24004.

Articles in books

• North, S. H., and Nakai, H. . "Potential mechanisms for linking phage Mu transposition with cell physiology.." The Bacterial Chromosome. Ed. N. P. Higgins. Washington, DC: ASM Press, 2005: 499-512