@article{noah_shapkina_nanda_huggins_wollenzien_2003, title={Conformational change in the 16S rRNA in the Escherichia coli 70S ribosome induced by P/P- and P/E-site tRNA(Phe) binding}, volume={42}, ISSN={["0006-2960"]}, DOI={10.1021/bi035369q}, abstractNote={The effects of P/P- and P/E-site tRNA(Phe) binding on the 16S rRNA structure in the Escherichia coli 70S ribosome were investigated using UV cross-linking. The identity and frequency of 16S rRNA intramolecular cross-links were determined in the presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an mRNA analogue containing a single Phe codon. For N-acetyl-Phe-tRNA(Phe) with either poly(U) or the mRNA analogue, the frequency of an intramolecular cross-link C967 x C1400 in the 16S rRNA was decreased in proportion to the binding stoichiometry of the tRNA. A proportional effect was true also for deacyl-tRNA(Phe) with poly(U), but the decrease in the C967 x C1400 frequency was less than the tRNA binding stoichiometry with the mRNA analogue. The inhibition of the C967 x C1400 cross-link was similar in buffers with, or without, polyamines. The exclusive participation of C967 with C1400 in the cross-link was confirmed by RNA sequencing. One intermolecular cross-link, 16S rRNA (C1400) to tRNA(Phe)(U33), was made with either poly(U) or the mRNA analogue. These results indicate a limited structural change in the small subunit around C967 and C1400 during tRNA P-site binding sensitive to the type of mRNA that is used. The absence of the C967 x C1400 cross-link in 70S ribosome complexes with tRNA is consistent with the 30S and 70S crystal structures, which contain tRNA or tRNA analogues; the occurrence of the cross-link indicates an alternative arrangement in this region in empty ribosomes.}, number={49}, journal={BIOCHEMISTRY}, author={Noah, JW and Shapkina, TG and Nanda, K and Huggins, W and Wollenzien, P}, year={2003}, month={Dec}, pages={14386–14396} }
 @article{noah_shapkina_wollenzien_2000, title={UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry}, volume={28}, ISSN={["1362-4962"]}, DOI={10.1093/nar/28.19.3785}, abstractNote={Sixteen long-range crosslinks are induced in Escherichia coli 16S rRNA by far-UV irradiation. Crosslinking patterns in two other organisms, Bacillus subtilis and Thermus aquaticus, were investigated to determine if the number and location of crosslinks in E.coli occur because of unusually photoreactive nucleotides at particular locations in the rRNA sequence. Thirteen long-range crosslinks in B.subtilis and 15 long-range crosslinks in T.aquaticus were detected by gel electrophoresis and 10 crosslinks in each organism were identified completely by reverse transcription analysis. Of the 10 identified crosslinks in B.subtilis, eight correspond exactly to E.coli crosslinks and two crosslinks are formed close to sites of crosslinks in E.coli. Of the 10 identified crosslinks in T.aquaticus, five correspond exactly to E.coli crosslinks, three are formed close to E.coli crosslinking sites, one crosslink corresponds to a UV laser irradiation-induced crosslink in E.coli and the last is not seen in E.coli. The overall similarity of crosslink positions in the three organisms suggests that the crosslinks arise from tertiary interactions that are highly conserved but with differences in detail in some regions.}, number={19}, journal={NUCLEIC ACIDS RESEARCH}, author={Noah, JW and Shapkina, T and Wollenzien, P}, year={2000}, month={Oct}, pages={3785–3792} }
 @article{noah_dolan_babin_wollenzien_1999, title={Effects of tetracycline and spectinomycin on the tertiary structure of ribosomal RNA in the Escherichia coli 30 S ribosomal subunit}, volume={274}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.274.23.16576}, abstractNote={Structural analysis of the 16 S rRNA in the 30 S subunit and 70 S ribosome in the presence of ribosome-specific antibiotics was performed to determine whether they produced rRNA structural changes that might provide further insight to their action. An UV cross-linking procedure that determines the pattern and frequency of intramolecular 16 S RNA cross-links was used to detect differences reflecting structural changes. Tetracycline and spectinomycin have specific effects detected by this assay. The presence of tetracycline inhibits the cross-link C967×C1400 completely, increases the frequency of cross-link C1402×1501 twofold, and decreases the cross-link G894×U244 by one-half without affecting other cross-links. Spectinomycin reduces the frequency of the cross-link C934×U1345 by 60% without affecting cross-linking at other sites. The structural changes occur at concentrations at which the antibiotics exert their inhibitory effects. For spectinomycin, the apparent binding site and the affected cross-linking site are distant in the secondary structure but are close in tertiary structure in several recent models, indicating a localized effect. For tetracycline, the apparent binding sites are significantly separated in both the secondary and the three-dimensional structures, suggesting a more regional effect.}, number={23}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Noah, JW and Dolan, MA and Babin, P and Wollenzien, P}, year={1999}, month={Jun}, pages={16576–16581} }
 @article{noah_wollenzien_1998, title={Dependence of the 16S rRNA decoding region structure on Mg2+, subunit association, and temperature}, volume={37}, ISSN={["0006-2960"]}, DOI={10.1021/bi981148m}, abstractNote={The effects of Mg2+ concentration, subunit association, and temperature on the structure of 16S rRNA in the Escherichia coli ribosome were investigated using UV cross-linking and gel electrophoresis analysis. Mg2+ concentrations between 1 and 20 mM and temperatures between 5 and 55 degreesC had little effect on the frequency of 12 of the 14 cross-links in 30S subunits and modest effects on the same cross-links in 70S ribosomes. In contrast, two cross-links, C967 x C1400 and C1402 x C1501, involving rRNA in the decoding region are present in 30S subunits only above 3 mM Mg2+, increase in frequency at higher Mg2+ concentration, and are both more frequent when 50S subunits are included in the reactions. In 70S ribosomes, the cross-link C1402 x C1501 increases but the cross-link C967 x C1400 decreases at higher Mg2+ concentrations. One cross-link, C1397 x U1495, is detected only in 70S ribosomes and decreases in frequency as Mg2+ concentration is increased. An additional cross-link, A1093 x C1182, decreases upon subunit association. The cross-link frequency differences indicate that the arrangement of the decoding region of the 16S rRNA, but not in the rest of the subunit, is readily altered by Mg2+ ions and subunit association.}, number={44}, journal={BIOCHEMISTRY}, author={Noah, JW and Wollenzien, P}, year={1998}, month={Nov}, pages={15442–15448} }
 @article{wilms_noah_zhong_wollenzien_1997, title={Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30s ribosomal subunits}, volume={3}, number={6}, journal={RNA}, author={Wilms, C. and Noah, J. W. and Zhong, D. G. and Wollenzien, P. L.}, year={1997}, pages={602–612} }
 @article{wilms_noah_zhong_wollenzien_1997, title={Exact determination of UV-induced crosslinks in 16S ribosomal RNA in 30s ribosomal subunits: Erratum}, volume={3}, number={8}, journal={RNA}, author={Wilms, C. and Noah, J. W. and Zhong, D. and Wollenzien, P.}, year={1997}, pages={945} }