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Light-Wahl KJ, Springer DL, Winger BE, Edmonds CG, Camp DG, Thrall BD, Smith RD: Observation of a small oligonucleotide duplex by electrospray ionization massspectrometry. J Am Chem Soc (1993) 115:803-804.
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Cui M, Heldsinger A, Lemrow SM, Loo JA, SannesLowery KA, Sharmeen L, Czarnik AW: 14204-14212. ESI-MS and other methods are used to study the binding of three ligands which bind HIV-1 TAR RNA. It is demonstrated that ESI-MS can be used to study the differential binding of ligands to TAR variants (eg, a construct in which the hexanucleotide loop is replaced with a polyethylene glycol linker).
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Mei HY, Cui M, Heldsinger A, Lemrow SM, Loo JA, SannesLowery KA, Sharmeen L, Czarnik AW: Inhibitors of proteinRNA complexation that target the RNA: Specific recognition of human immunodeficiency virus type 1 TAR RNA by small organic molecules. Biochemistry (1998) 37:14204-14212. ESI-MS and other methods are used to study the binding of three ligands which bind HIV-1 TAR RNA. It is demonstrated that ESI-MS can be used to study the differential binding of ligands to TAR variants (eg, a construct in which the hexanucleotide loop is replaced with a polyethylene glycol linker).
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Sannes-Lowery KA, Mei H-Y, Loo JA: Studying aminoglycoside antibiotic binding to HIV-1 TAR RNA by electrospray ionization mass spectrometry. Int J Mass Spectrom (1999) 193:115-122.
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Sannes-Lowery KA, Crooke ST, Ecker DJ, Sasmor H, Manalili S, Griffey RH: 3436-3440. It is shown that ESI-MS can be used as an affinity screen between compound collections and RNA constructs of similar (or identical) mass by using a neutral mass tag on one or more of the RNA targets. The neutral mass tag shifts the signal of the target, and associated complexes, to a unique region of the mass spectrum in which mass ambiguities are minimized.
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Hofstadler SA, Sannes-Lowery KA, Crooke ST, Ecker DJ, Sasmor H, Manalili S, Griffey RH: Multiplexed screening of neutral mass tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: A paradigm for high-throughput affinity screening. Anal Chem (1999) 71:3436-3440. It is shown that ESI-MS can be used as an affinity screen between compound collections and RNA constructs of similar (or identical) mass by using a neutral mass tag on one or more of the RNA targets. The neutral mass tag shifts the signal of the target, and associated complexes, to a unique region of the mass spectrum in which mass ambiguities are minimized.
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Hofstadler, S.A.1
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24
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Targeted site-specific gas-phase cleavage of oligoribonucleotides
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Greig MJ, An H, Sasmor H, Manalili S: 474-475. Incorporation of deoxynucleotides into a chimeric oligoribonucleotide is shown to generate a series of labile sites where collisionally activated dissociation is favored. Binding of ligands at the labile sites affords protection from collisionally activated dissociation in MS-MS experiments. This mass spectrometry-based protection assay can be used to establish the binding sites for RNA binding ligands without the need for additional chemical reagents or radiolabeling of the RNA.
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Griffey RH, Greig MJ, An H, Sasmor H, Manalili S: Targeted site-specific gas-phase cleavage of oligoribonucleotides. Application in mass spectrometry-based identification of ligand binding sites. J Am Chem Soc (1999)121:474-475. Incorporation of deoxynucleotides into a chimeric oligoribonucleotide is shown to generate a series of labile sites where collisionally activated dissociation is favored. Binding of ligands at the labile sites affords protection from collisionally activated dissociation in MS-MS experiments. This mass spectrometry-based protection assay can be used to establish the binding sites for RNA binding ligands without the need for additional chemical reagents or radiolabeling of the RNA.
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Application in Mass Spectrometry-based Identification of Ligand Binding Sites. J Am Chem Soc
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Determinants of aminoglycoside-blnding specificity for rRNA by using mass spectrometry
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Hofstadler SA, Sannes-Lowery KA, Ecker DJ, Crooke ST: 10129-10133. ESI-FTICR MS is used to characterize the binding of three classes of aminoglycoside antibiotics to the 16S and 18S rRNA Asites. In addition to determining binding affinities, the locations of the binding sites on the RNAs were identified from a protection pattern generated by fragmenting the aminoglycoside/RNA complex. Specific base substitutions were introduced in the RNA models and their impact on binding affinity and selectivity were measured.
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Griffey RH, Hofstadler SA, Sannes-Lowery KA, Ecker DJ, Crooke ST: Determinants of aminoglycoside-blnding specificity for rRNA by using mass spectrometry. Proc Natl AcadSci USA (1999) 96:10129-10133. ESI-FTICR MS is used to characterize the binding of three classes of aminoglycoside antibiotics to the 16S and 18S rRNA Asites. In addition to determining binding affinities, the locations of the binding sites on the RNAs were identified from a protection pattern generated by fragmenting the aminoglycoside/RNA complex. Specific base substitutions were introduced in the RNA models and their impact on binding affinity and selectivity were measured.
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Proc Natl AcadSci USA
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Griffey, R.H.1
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26
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Fourmy D, Recht Ml, Puglisi JD: Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 rRNA. J Mol B/o/(1998) 277:347-362.
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Drader JJ, Griffey RH, Hofstadler SA
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Sannes-Lowery KA, Drader JJ, Griffey RH, Hofstadler SA: Fourier transform Ion cyclotron resonance mass spectrometry as a high-throughput affinity screen to Identify RNA-binding ligands. Trends Anal Chem (2000) in press.
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Roepstorff P: 4427-4432.
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Choong 1C, Ellman JA: 2419-2424. A method for the identification of ligands to biological targets is reported in which ligands that bind with low affinity are connected by common chemical linkage groups through a set of flexible linkers to create components with enhanced binding affinity.
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Maly DJ, Choong 1C, Ellman JA: Combinatorial target-guided ligand assembly: Identification of potent subtype-selective c-Src Inhibitors. Proc Natl Acad Sei USA (2000) 97:2419-2424. A method for the identification of ligands to biological targets is reported in which ligands that bind with low affinity are connected by common chemical linkage groups through a set of flexible linkers to create components with enhanced binding affinity.
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Proc Natl Acad Sei USA
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Maly, D.J.1
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Hajduk PJ, Marcotte PA, Nettesheim DG, Meadows RP, Edalji R, Holzman TF, Fesik SW: 5828-5832. This work, and previous work by the same group, describes an NMR-based method for the identification of weakly bound chemical motifs. Compounds with higher target affinity are created by linking the binding motifs.
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Olejniczak ET, Hajduk PJ, Marcotte PA, Nettesheim DG, Meadows RP, Edalji R, Holzman TF, Fesik SW: Stromelysin inhibitors designed from weakly bound fragments: Effects of linking and cooperativity. J Am Chem Soc (1997) 119:5828-5832. This work, and previous work by the same group, describes an NMR-based method for the identification of weakly bound chemical motifs. Compounds with higher target affinity are created by linking the binding motifs.
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Detection and selective dissociation of intact ribosomes in a mass spectrometer
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Fucini P, Benjamin DR, Juenemann R, Nierhaus KH, Hartl FU, Dobson CM, Robinson CV: 5185-5190. Intact E coli ribosomes were studied using ESI-TOF instrumentation with a nano-electrospray ionization source. Individual ions with m/z in excess of 20,000 were detected and coadded to yield mass spectra of the intact 70S ribosome. A mass measurement of 852,187 + 3918 Da was obtained for the 30S subunit, in good agreement with the theoretical value of 846,681 Da calculated from the combined masses of the 21 small subunit proteins and the 165 RNA.
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Rostom AA, Fucini P, Benjamin DR, Juenemann R, Nierhaus KH, Hartl FU, Dobson CM, Robinson CV: Detection and selective dissociation of intact ribosomes in a mass spectrometer. Proc Natl Acad Sei USA (2000) 97:5185-5190. Intact E coli ribosomes were studied using ESI-TOF instrumentation with a nano-electrospray ionization source. Individual ions with m/z in excess of 20,000 were detected and coadded to yield mass spectra of the intact 70S ribosome. A mass measurement of 852,187 + 3918 Da was obtained for the 30S subunit, in good agreement with the theoretical value of 846,681 Da calculated from the combined masses of the 21 small subunit proteins and the 165 RNA.
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(2000)
Proc Natl Acad Sei USA
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Rostom, A.A.1
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