Publications
| MASS SPECTROMETRY OF NUCLEIC ACIDS |
| S. C. Pomerantz and J. A. McCloskey. Detection of the common RNA nucleoside pseudouridine in mixtures of olingonucleotides by mass spectrometry. Anal. Chem., 77, 4687-4697 (2005). |
| T. Wagner, V. Nair, R. Guymon, S. C. Pomerantz, P. F. Crain, D. R. Davis and J. A. McCloskey. A novel method for sequence placement of modified nucleotides in mixtures of transfer RNA. Nucleic Acids Symp. Ser., 48, 263-264 (2004). |
| S. Zhou, D. Sitaramaiah, S. Pomerantz, P. F. Crain, and J. A. McCloskey. Tandem Mass Spectrometry for Structure Assignments of Wye Nucleosides from Transfer RNA. Nucleosides Nucleotides Nucleic Acids, 23, 41-50 (2004) Abstract |
| J. Rosenski and J.A. McCloskey. SOS: a simple user-interactive program for ab initio oligonucleotide sequencing by mass spectrometry. J. Am. Soc. Mass Spectrom., 13, 200-203 (2002). Abstract |
| F. Qiu and J. A. McCloskey. Selective detection of ribose-methylated nucleotides in RNA by a mass spectrometry based method. Nucleic Acids Res., 27, e20 (1999). Abstract |
| J. Rozenski and J. A. McCloskey. Determination of nearest neighbors in nucleic acids by mass spectrometry. Anal. Chem., 71, 1454-1459 (1999). Abstract |
| J. A. McCloskey, A. B. Whitehill, J. Rozenski, F. Qiu and P. F. Crain. New techniques for the rapid characterization of oligonucleotides by mass spectrometry. Nucleosides Nucleotides, 18, 1549-1553 (1999). Abstract |
| P. F. Crain and J. A. McCloskey. Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Current Opinion Biotechnol., 9, 25-34 (1998). Abstract |
| J. Gregson and J. A. McCloskey. Collision-induced dissociation of protonated guanine. Int. J. Mass Spectrom. Ion Processes, 165/166, 475-485 (1997). Abstract |
| S. C. Pomerantz, J. A. McCloskey, T. Tarasow and B. E. Eaton. Deconvolution of combinatorial oligonucleotide libraries by electrospray ionization tandem mass spectrometry. J. Am. Chem. Soc., 119, 3861-3867 (1997). Abstract |
| J. J. Dalluge, T. Hashizume and J.A. McCloskey. Quantitative measurement of dihydrouridine in RNA using isotope dilution liquid chromatography-mass spectrometry (LC/MS). Nucleic Acids Res., 24, 3242-3245 (1996). Abstract |
| M.L. Bartlett, J.A. McCloskey, S. Manalili and R. H. Griffey. The effect of backbone charge on the collision-induced dissociation of oligonucleotides. J. Mass Spectrom., 31, 1277-1283 (1996). Abstract |
| J. Ni, S. C. Pomerantz, J. Rozenski, Y. Zhang and J. A. McCloskey. Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem., 68, 1989-1999 (1996). Abstract |
| STRUCTURE AND FUNCTION OF POSTANSCRIPTIONALLY MODIFIED NUCLEOTIDES FROM RNA |
| A. Sauerwald, D. Sitaramaiah, J. A. McCloskey, D. Söll, and P. F. Crain. N6-Acetyladenosine: a new modified nucleoside from Methanopyrus kandleri tRNA. FEBS Lett. 579, 2807-2810 (2005). |
| M. Del Campo, C. Recinos, G. Yanez, S. C. Pomerantz, R. Guymon, P. F. Crain, J. A. McCloskey and J. Ofengand. Number, position and significance of the pseudourdines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans. RNA, 11, 210-219 (2005). |
| C. Polycarpo, A. Ambrogelly, A. Berube, S. M. Winbush, P. F. Crain, J. A. McCloskey, J. L. Wood and D. Söll. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA (2004), in press. Abstract |
| J. Salazar, A. Ambrogelly, P. F. Crain, J. A. McCloskey, and D. Söll. A truncated aminoacyl-tRNA synthetase modifies RNA. Proc. Natl. Acad. Sci. USA, 101, 7536-7541 (2004). Abstract |
| S. Zhou, D. Sitaramaiah, K. R. Noon, R. Guymon, T. Hashizume, and J. A. McCloskey. Structures of two new "minimalist" Modified Nucleosides from Archaeal tRNA. Bioorg. Chem., 32, 82-91 (2004).Abstract |
| K. R. Noon, R. Guymon, P. F. Crain, J. A. McCloskey, M. Thomm, J. Lim, R. Cavicchioli. Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature [Topt], 23oC) and Stetteria hydrogenophila (Topt 95oC). J. Bacteriol., 185, 5483-5490 (2003).
Abstract |
| P.F. Crain, J.D. Alfonzo, J. Rozenski, S.T. Kapushoc, J.A. McCloskey and L. Simpson. Modification of the universally unmodified uridine-33 in a mitochondria-imported edited tRNA and the role of the anticodon arm structure on editing efficiency. RNA, 8, 752-761, (2002). Abstract |
| J. Kowalak, E. Bruenger, P. F. Crain and J. A. McCloskey. Identities and phylogenetic comparisons of posttranscriptional modifications in 16S ribosomal RNA from Haloferax volcanii. J. Biol. Chem., 275, 24484-24489 (2000). Abstract |
| K. R. Noon, E. Bruenger and J. A. McCloskey. Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus. J. Bacteriol., 180, 2883-2888 (1998). Abstract |
| J.J. Dalluge, T. Hamamoto, K. Horikoshi, R.Y. Morita, K.O. Stetter and J.A. McCloskey. Posttranscriptional modification of transfer RNA in psychrophilic bacteria. J. Bacteriol., 179, 1918-1923 (1997). Abstract |
| C. Ushida, T. Muramatsu, H. Mizushima, Y. Kuchino, T. Ueda, K. Watanabe, K.O. Stetter, P. F. Crain and J. A. McCloskey. Structural features of the initiator tRNA gene from Pyrodictium occultum and the thermal stability of its gene product, tRNAMiet. Biochemie, 78, 847-855 (1996). Abstract |
| J. A. Kowalak, E. Bruenger, T. Hashizume, J. M. Peltier, J. Ofengand and J. A. McCloskey. Structural characterization of U*-1915 in domain IV from E. coli 23S ribosomal RNA as 3-methylpseudouridine. Nucleic Acids Res. 24, 688-693 (1996). Abstract |
| J. A. Dalluge, T. Hashizume, A. E. Sopchik, J. A. McCloskey and D. R. Davis. Conformational flexibility in RNA: the role of dihydrouridine. Nucleic Acids Res. 24, 1073-1079 (1996). Abstract |
| J. A. Kowalak, E. Bruenger and J. A. McCloskey, Posttranscriptional modification of the central loop of domain V in E. coli 23S ribosomal RNA. J. Biol. Chem. 270, 17758-17764 (1995). Abstract |
| Bakin, J. A. Kowalak, J. A. McCloskey, and J. Ofengand. A single pseudouridine residue in E. coli 16S RNA is located at position 516. Nucleic Acids Res. 22, 3681-3684 (1994). Abstract |
| J. A. Kowalak, J. J. Dalluge, J. A. McCloskey and K. O. Stetter. Role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry 33, 7869-7876 (1994). Abstract |
| J. Moriya, T. Yokogawa, K. Wakita, T. Ueda, K. Nishikawa, P. F. Crain, T. Hashizume, S. C. Pomerantz, J. A. McCloskey, G. Kawai, N. Hayashi, S. Yokoyama and K. Watanabe. A novel nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria. Biochemistry 33, 2234-2239 (1994). Abstract |
| M. Gregson, P. F. Crain, C. G. Edmonds, R. Gupta, T. Hashizume, D. W.Phillipson and J. A. McCloskey. Structure of the archaeal transfer RNA nucleoside G* 15 (2-amino-4,7-dihydro-4-oxo-7-ß-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimidine-5-carboximidamide (archaeosine)). J. Biol. Chem. 268, 10076-10086 (1993). Abstract |
| EVOLUTIONARY RELATIONSHIPS OF NATURAL RNA MODIFICATIONS |
| J. A. McCloskey and J. Rozenski. The small subunit rRNA modification database. Nucleic Acids Res., 33 (2005), D135-D138. Abstract |
| J.A. McCloskey, D.E. Graham, S.Zhou, P.F. Crain, M. Ibba, J. Konisky, D. Söll and G.J. Olsen. Posttranscriptional modification in Archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res., Vol. 29, No. 22, 4699-4706, (2001). Abstract |
| J. Kowalak, E. Bruenger, P. F. Crain and J. A. McCloskey. Identities and phylogenetic comparisons of posttranscriptional modifications in 16S ribosomal RNA from Haloferax volcanii. J. Biol. Chem., 275, 24484-24489 (2000). Abstract |
| B. Felden, K. Hanawa, J. F. Atkins, H. Himeno, A. Muto, R. F. Gesteland, J. A. McCloskey and P. F. Crain. Presence and location of modified nucleotides in E. coli tmRNA: Structural mimicry with tRNA acceptor branches. EMBO J., 17, 3188-3196 (1998). Abstract |
| M. Watanabe, M. Matsuo, S. Tanaka, H. Akimoto, S. Asahi, S. Nishimura, J. R. Katze, T. Hashizume, P. F. Crain. J. A. McCloskey and N. Okada. Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacment on the tRNA polynucleotide chain. J. Biol. Chem., 272, 20146-20151 (1997). Abstract |
| P. A. Limbach, P. F. Crain, and J. A. McCloskey. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22, 2183-2196 (1994). Abstract |
|
