@article{sohail_pirzada_guenther_barbieri_sit_menegatti_crook_opperman_khan_2023, title={Cellulose Acetate-Stabilized Pickering Emulsions: Preparation, Rheology, and Incorporation of Agricultural Active Ingredients}, volume={11}, ISSN={["2168-0485"]}, url={https://doi.org/10.1021/acssuschemeng.3c02428}, DOI={10.1021/acssuschemeng.3c02428}, abstractNote={We report the use of cellulose acetate (CA) nanoparticles (NPs) to produce oil in water Pickering emulsions. The CA NP can emulsify various oils and form stable emulsions at concentrations as low as 0.5 wt %. Rheological and microscopic analyses show evidence of interconnected NP aggregate networks between droplets. Yield stress measurements display evidence of “double” yielding. We postulate that the presence of the NP aggregates provides a secondary network between droplet clusters resulting in such behavior. We demonstrate the suitability of the emulsions as agriculture formulations by incorporating an agrochemical, abamectin (Abm), and a plant-growth-promoting microbe (PGPM) in the emulsions. Release assays exhibit sustained Abm release, promising higher efficacy at lower usage volumes. Incorporation of nonsporulating PGPM Pseudomonas simiae in the emulsions shows significantly higher microbe viability compared to controls after 70 days of storage. By demonstrating the application of CA NPs as a sustainable Pickering emulsifier, this study introduces the use of CA as a platform technology for the delivery of diverse agriculture cargos. A comprehensive evaluation of the system is articulated in a fundamental microstructure analysis and a demonstration of practical on-site attributes, including shelf-life stability and functional performance, verified through bioassays and plant growth studies.}, number={42}, journal={ACS SUSTAINABLE CHEMISTRY & ENGINEERING}, author={Sohail, Mariam and Pirzada, Tahira and Guenther, Richard and Barbieri, Eduardo and Sit, Tim and Menegatti, Stefano and Crook, Nathan and Opperman, Charles H. and Khan, Saad A.}, year={2023}, month={Sep}, pages={15178–15191} }
 @article{ochola_cortada_mwaura_tariku_christensen_ng'ang'a_hassanali_pirzada_khan_pal_et al._2022, title={Wrap-and-plant technology to manage sustainably potato cyst nematodes in East Africa}, volume={2}, ISSN={["2398-9629"]}, url={https://doi.org/10.1038/s41893-022-00852-5}, DOI={10.1038/s41893-022-00852-5}, abstractNote={Abstract}, journal={NATURE SUSTAINABILITY}, author={Ochola, Juliet and Cortada, Laura and Mwaura, Onesmus and Tariku, Meklit and Christensen, Shawn A. and Ng'ang'a, Margaret and Hassanali, Ahmed and Pirzada, Tahira and Khan, Saad and Pal, Lokendra and et al.}, year={2022}, month={Feb} }
 @article{sherman_guenther_reade_rochon_sit_smith_2020, title={Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes}, volume={94}, ISSN={["1098-5514"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85077664748&partnerID=MN8TOARS}, DOI={10.1128/JVI.01439-19}, abstractNote={
            Members of the
            Tombusviridae
            family have nearly identical shells, and yet they package genomes that range from 4.6 kb (monopartite) to 5.3 kb (bipartite) in size. To understand how this genome flexibility occurs within a rigidly conserved shell, we determined the high-resolution cryo-electron microscopy (cryo-EM) structures of cucumber leaf spot virus and red clover necrotic mosaic virus. In response to genomic size differences, it appears that the ssRNA binding (R) domain of the capsid diverged evolutionarily in order to recognize the different genomes. The next region, the “arm,” seems to have also coevolved with the R domain to allow particle assembly via interactions at the icosahedral 3-fold axes. In addition, there are differences at the icosahedral 3-fold axes with regard to metal binding that are likely important for transmission and the viral life cycle.
          }, number={2}, journal={JOURNAL OF VIROLOGY}, publisher={American Society for Microbiology}, author={Sherman, Michael B. and Guenther, Richard and Reade, Ron and Rochon, D'Ann and Sit, Tim and Smith, Thomas J.}, editor={Parrish, Colin R.Editor}, year={2020}, month={Jan} }
 @article{guenther_lommel_opperman_sit_2018, title={Plant Virus-Based Nanoparticles for the Delivery of Agronomic Compounds as a Suspension Concentrate}, volume={1776}, ISBN={["978-1-4939-7806-9"]}, ISSN={["1940-6029"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85048246738&partnerID=MN8TOARS}, DOI={10.1007/978-1-4939-7808-3_13}, abstractNote={Nanoparticle formulations of agrichemicals may enhance their performance while simultaneously mitigating any adverse environmental effects. Red clover necrotic mosaic virus (RCNMV) is a soil-transmitted plant virus with many inherent attributes that allow it to function as a plant virus-based nanoparticle (PVN) when loaded with biologically active ingredients. Here we describe how to formulate a PVN loaded with the nematicide abamectin (Abm) beginning with the propagation of the virus through the formulation, deactivation, and characterization of the finished product.}, journal={VIRUS-DERIVED NANOPARTICLES FOR ADVANCED TECHNOLOGIES: METHODS AND PROTOCOLS}, publisher={Springer New York}, author={Guenther, Richard H. and Lommel, Steven A. and Opperman, Charles H. and Sit, Tim L.}, year={2018}, pages={203–214} }
 @article{cao_guenther_sit_lommel_opperman_willoughby_2016, title={Development of abamectin loaded lignocellulosic matrices for the controlled release of nematicide for crop protection}, volume={23}, ISSN={["1572-882X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84955651797&partnerID=MN8TOARS}, DOI={10.1007/s10570-015-0817-6}, number={1}, journal={CELLULOSE}, publisher={Springer Science and Business Media LLC}, author={Cao, Jing and Guenther, Richard H. and Sit, Tim L. and Lommel, Steven A. and Opperman, Charles H. and Willoughby, Julie A.}, year={2016}, month={Feb}, pages={673–687} }
 @article{cao_guenther_sit_opperman_lommel_willoughby_2014, title={Loading and Release Mechanism of Red Clover Necrotic Mosaic Virus Derived Plant Viral Nanoparticles for Drug Delivery of Doxorubicin}, volume={10}, ISSN={["1613-6829"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84919761332&partnerID=MN8TOARS}, DOI={10.1002/smll.201400558}, abstractNote={Loading and release mechanisms of Red clover necrotic mosaicvirus (RCNMV) derived plant viral nanoparticle (PVN) are shown for controlled delivery of the anticancer drug, doxorubicin (Dox). Previous studies demonstrate that RCNMV's structure and unique response to divalent cation depletion and re‐addition enables Dox infusion to the viral capsid through a pore formation mechanism. However, by controlling the net charge of RCNMV outer surface and accessibility of RCNMV interior cavity, tunable release of PVN is possible via manipulation of the Dox loading capacity and binding locations (external surface‐binding or internal capsid‐encapsulation) with the RCNMV capsid. Bimodal release kinetics is achieved via a rapid release of surface‐Dox followed by a slow release of encapsulated Dox. Moreover, the rate of Dox release and the amount of released Dox increases with an increase in environmental pH or a decrease in concentration of divalent cations. This pH‐responsive Dox release from PVN is controlled by Fickian diffusion kinetics where the release rate is dependent on the location of the bound or loaded active molecule. In summary, controllable release of Dox‐loaded PVNs is imparted by 1) formulation conditions and 2) driven by the capsid's pH‐ and ion‐ responsive functions in a given environment.}, number={24}, journal={SMALL}, publisher={Wiley}, author={Cao, Jing and Guenther, Richard H. and Sit, Tim L. and Opperman, Charles H. and Lommel, Steven A. and Willoughby, Julie A.}, year={2014}, month={Dec}, pages={5126–5136} }
 @article{martin_he_meilleur_guenther_sit_lommel_heller_2013, title={New insight into the structure of RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering}, volume={158}, ISSN={["0304-8608"]}, url={http://europepmc.org/abstract/med/23483344}, DOI={10.1007/s00705-013-1650-6}, number={8}, journal={ARCHIVES OF VIROLOGY}, publisher={Springer Science and Business Media LLC}, author={Martin, Stanton L. and He, Lilin and Meilleur, Flora and Guenther, Richard H. and Sit, Tim L. and Lommel, Steven A. and Heller, William T.}, year={2013}, month={Aug}, pages={1661–1669} }
 @article{honarbakhsh_guenther_willoughby_lommel_pourdeyhimi_2013, title={Polymeric Systems Incorporating Plant Viral Nanoparticles for Tailored Release of Therapeutics}, volume={2}, ISSN={["2192-2659"]}, DOI={10.1002/adhm.201200434}, abstractNote={Abstract}, number={7}, journal={ADVANCED HEALTHCARE MATERIALS}, author={Honarbakhsh, Sara and Guenther, Richard H. and Willoughby, Julie A. and Lommel, Steven A. and Pourdeyhimi, Behnam}, year={2013}, month={Jul}, pages={1001–1007} }
 @article{graham_barley-maloney_stark_kaur_stolarchuk_sproat_leszczynska_malkiewicz_safwat_mucha_et al._2012, title={Functional Recognition of the Modified Human tRNA (Lys3) (UUU) Anticodon Domain by HIV's Nucleocapsid Protein and a Peptide Mimic (vol 410, pg 698, year 2011)}, volume={420}, number={3}, journal={Journal of Molecular Biology}, author={Graham, W. D. and Barley-Maloney, L. and Stark, C. J. and Kaur, A. and Stolarchuk, C. and Sproat, B. and Leszczynska, G. and Malkiewicz, A. and Safwat, N. and Mucha, P. and et al.}, year={2012}, pages={259–259} }
 @article{graham_barley-maloney_stark_kaur_stolyarchuk_sproat_leszczynska_malkiewicz_safwat_mucha_et al._2011, title={Functional recognition of the modified human tRNA(UUU)(Lys3) anticodon domain by HIV's nucleocapsid protein and a peptide mimic}, volume={410}, number={4}, journal={Journal of Molecular Biology}, author={Graham, W. D. and Barley-Maloney, L. and Stark, C. J. and Kaur, A. and Stolyarchuk, K. and Sproat, B. and Leszczynska, G. and Malkiewicz, A. and Safwat, N. and Mucha, P. and et al.}, year={2011}, pages={698–715} }
 @article{martin_guenther_sit_swartz_meilleur_lommel_rose_section_2010, title={Crystallization and preliminary X-ray diffraction analysis of red clover necrotic mosaic virus}, volume={66}, ISSN={["2053-230X"]}, url={http://europepmc.org/abstract/med/21045294}, DOI={10.1107/s1744309110032483}, abstractNote={Red clover necrotic mosaic virus (RCNMV) is a species that belongs to the Tombusviridae family of plant viruses with a T = 3 icosahedral capsid. RCNMV virions were purified and were crystallized for X-ray analysis using the hanging-drop vapor-diffusion method. Self-rotation functions and systematic absences identified the space group as I23, with two virions in the unit cell. The crystals diffracted to better than 4 Å resolution but were very radiation-sensitive, causing rapid decay of the high-resolution reflections. The data were processed to 6 Å in the analysis presented here.}, number={Pt 11}, journal={ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS}, author={Martin, S.L. and Guenther, R.H. and Sit, T.L. and Swartz, P.D. and Meilleur, Flora and Lommel, S.A. and Rose, Robert and Section, F.}, year={2010}, month={Nov}, pages={1458–1462} }
 @article{bilbille_vendeix_guenther_malkiewicz_ariza_vilarrasa_agris_2009, title={The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs}, volume={37}, ISSN={["0305-1048"]}, DOI={10.1093/nar/gkp187}, abstractNote={Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.}, number={10}, journal={NUCLEIC ACIDS RESEARCH}, author={Bilbille, Yann and Vendeix, Franck A. P. and Guenther, Richard and Malkiewicz, Andrzej and Ariza, Xavier and Vilarrasa, Jaume and Agris, Paul F.}, year={2009}, month={Jun}, pages={3342–3353} }
 @article{loo_guenther_lommel_franzen_2008, title={Infusion of dye molecules into Red clover necrotic mosaic virus}, ISSN={["1359-7345"]}, DOI={10.1039/b714748a}, abstractNote={The Red clover necrotic mosaic virus capsid is utilized to package and release molecules through reversible depletion and re-addition of divalent cations.}, number={1}, journal={CHEMICAL COMMUNICATIONS}, author={Loo, LiNa and Guenther, Richard H. and Lommel, Steven A. and Franzen, Stefan}, year={2008}, pages={88–90} }
 @article{loo_guenther_basnayake_lommel_franzen_2006, title={Controlled encapsidation of gold nanoparticles by a viral protein shell}, volume={128}, ISSN={["0002-7863"]}, DOI={10.1021/ja057332u}, abstractNote={Icosahedral virus capsids demonstrate a high degree of selectivity in packaging cognate nucleic acid components during assembly. This packaging specificity, when integrated as part of a nanotechnological protocol, has the potential to encapsidate a wide array of foreign materials for delivery of therapeutics or biosensors into target cells. Red clover necrotic mosaic virus (RCNMV) exclusively packages two genomic ssRNAs initiated by a specific protein:RNA interaction between the RCNMV coat protein (CP) and the viral RNA origin of assembly (OAS) element. In the present work, an oligonucleotide mimic of the RCNMV OAS sequences is attached to Au nanoparticles as a recognition signal to initiate the virion-like assembly by RCNMV CP. Covalent linkage of the OAS to Au functions as a trigger for specific encapsidation and demonstrates that foreign cargo can be packaged into RCNMV virions.}, number={14}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Loo, L and Guenther, RH and Basnayake, VR and Lommel, SA and Franzen, S}, year={2006}, month={Apr}, pages={4502–4503} }
 @article{sherman_guenther_tama_sit_brooks_mikhailov_orlova_baker_lommel_2006, title={Removal of divalent cations induces structural transitions in Red clover necrotic mosaic virus, revealing a potential mechanism for RNA release}, volume={80}, ISSN={["1098-5514"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33750318283&partnerID=MN8TOARS}, DOI={10.1128/JVI.01137-06}, abstractNote={ABSTRACT}, number={21}, journal={JOURNAL OF VIROLOGY}, publisher={American Society for Microbiology}, author={Sherman, Michael B. and Guenther, Richard H. and Tama, Florence and Sit, Tim L. and Brooks, Charles L. and Mikhailov, Albert M. and Orlova, Elena V. and Baker, Timothy S. and Lommel, Steven A.}, year={2006}, month={Nov}, pages={10395–10406} }
 @article{guenther_sit_gracz_dolan_townsend_liu_newman_agris_lommel_2004, title={Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus}, volume={32}, ISSN={["1362-4962"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-3042761419&partnerID=MN8TOARS}, DOI={10.1093/nar/gkh585}, abstractNote={The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.}, number={9}, journal={NUCLEIC ACIDS RESEARCH}, publisher={Oxford University Press (OUP)}, author={Guenther, RH and Sit, TL and Gracz, HS and Dolan, MA and Townsend, HL and Liu, GH and Newman, WH and Agris, PF and Lommel, SA}, year={2004}, month={May}, pages={2819–2828} }
 @article{stuart_koshlap_guenther_agris_2003, title={Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe)}, volume={334}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2003.09.058}, abstractNote={Post-transcriptional modifications contribute chemistry and structure to RNAs. Modifications of tRNA at nucleoside 37, 3'-adjacent to the anticodon, are particularly interesting because they facilitate codon recognition and negate translational frame-shifting. To assess if the functional contribution of a position 37-modified nucleoside defines a specific structure or restricts conformational flexibility, structures of the yeast tRNA(Phe) anticodon stem and loop (ASL(Phe)) with naturally occurring modified nucleosides differing only at position 37, ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)), and ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)), were determined by NMR spectroscopy and restrained molecular dynamics. The ASL structures had similarly resolved stems (RMSD approximately 0.6A) of five canonical base-pairs in standard A-form RNA. The "NOE walk" was evident on the 5' and 3' sides of the stems of both RNAs, and extended to the adjacent loop nucleosides. The NOESY cross-peaks involving U(33) H2' and characteristic of tRNA's anticodon domain U-turn were present but weak, whereas those involving the U(33) H1' proton were absent from the spectra of both ASLs. However, ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) exhibited the downfield shifted 31P resonance of U(33)pGm(34) indicative of U-turns; ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) did not. An unusual "backwards" NOE between Gm(34) and A(35) (Gm(34)/H8 to A(35)/H1') was observed in both molecules. The RNAs exhibited a protonated A(+)(38) resulting in the final structures having C(32).A(+)(38) intra-loop base-pairs, with that of ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) being especially well defined. A single family of low-energy structures of ASL(Phe)-(Cm(32),Gm(34), m(1)G(37),m(5)C(40)) (loop RMSD 0.98A) exhibited a significantly restricted conformational space for the anticodon loop in comparison to that of ASL(Phe)-(Cm(32),Gm(34),m(5)C(40)) (loop RMSD 2.58A). In addition, the ASL(Phe)-(Cm(32),Gm(34),m(1)G(37),m(5)C(40)) average structure had a greater degree of similarity to that of the yeast tRNA(Phe) crystal structure. A comparison of the resulting structures indicates that modification of position 37 affects the accuracy of decoding and the maintenance of the mRNA reading frame by restricting anticodon loop conformational space.}, number={5}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Stuart, JW and Koshlap, KM and Guenther, R and Agris, PF}, year={2003}, month={Dec}, pages={901–918} }
 @article{yarian_townsend_czestkowski_sochacka_malkiewicz_guenther_miskiewicz_agris_2002, title={Accurate translation of the genetic code depends on tRNA modified nucleosides}, volume={277}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.M200253200}, abstractNote={Transfer RNA molecules translate the genetic code by recognizing cognate mRNA codons during protein synthesis. The anticodon wobble at position 34 and the nucleotide immediately 3′ to the anticodon triplet at position 37 display a large diversity of modified nucleosides in the tRNAs of all organisms. We show that tRNA species translating 2-fold degenerate codons require a modified U34 to enable recognition of their cognate codons ending in A or G but restrict reading of noncognate or near-cognate codons ending in U and C that specify a different amino acid. In particular, the nucleoside modifications 2-thiouridine at position 34 (s2U34), 5-methylaminomethyluridine at position 34 (mnm5U34), and 6-threonylcarbamoyladenosine at position 37 (t6A37) were essential for Watson-Crick (AAA) and wobble (AAG) cognate codon recognition by tRNA UUU Lys at the ribosomal aminoacyl and peptidyl sites but did not enable the recognition of the asparagine codons (AAU and AAC). We conclude that modified nucleosides evolved to modulate an anticodon domain structure necessary for many tRNA species to accurately translate the genetic code.}, number={19}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Yarian, C and Townsend, H and Czestkowski, W and Sochacka, E and Malkiewicz, AJ and Guenther, R and Miskiewicz, A and Agris, PF}, year={2002}, month={May}, pages={16391–16395} }
 @article{nobles_yarian_liu_guenther_agris_2002, title={Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding}, volume={30}, ISSN={["0305-1048"]}, DOI={10.1093/nar/gkf595}, abstractNote={Transfer RNA structure involves complex folding interactions of the TPsiC domain with the D domain. However, the role of the highly conserved nucleoside modifications in the TPsiC domain, rT54, Psi55 and m5C49, in tertiary folding is not understood. To determine whether these modified nucleosides have a role in tRNA folding, the association of variously modified yeast tRNA(Phe) T-half molecules (nucleosides 40-72) with the corresponding unmodified D-half molecule (nucleosides 1-30) was detected and quantified using a native polyacrylamide gel mobility shift assay. Mg2+ was required for formation and maintenance of all complexes. The modified T-half folding interactions with the D-half resulted in K(d)s (rT54 = 6 +/- 2, m5C49 = 11 +/- 2, Psi55 = 14 +/- 5, and rT54,Psi55 = 11 +/- 3 microM) significantly lower than that of the unmodified T-half (40 +/- 10 microM). However, the global folds of the unmodified and modified complexes were comparable to each other and to that of an unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by lead cleavage patterns at U17 and nucleoside substitutions disrupting the Levitt base pair. Thus, conserved modifications of tRNA's TPsiC domain enhanced the affinity between the two half-molecules without altering the global conformation indicating an enhanced stability to the complex and/or an altered folding pathway.}, number={21}, journal={NUCLEIC ACIDS RESEARCH}, author={Nobles, KN and Yarian, CS and Liu, G and Guenther, RH and Agris, PF}, year={2002}, month={Nov}, pages={4751–4760} }
 @article{mucha_szyk_rekowski_guenther_agris_2002, title={Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay}, volume={8}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838202020319}, abstractNote={A sensitive capillary electrophoresis mobility shift assay (CEMSA) to analyze RNA/peptide interactions has been developed. Capillary electrophoresis (CE) has been adapted for investigating the interaction between variously methylated 17-nt analogs of the yeast tRNAPhe anticodon stem and loop domain (ASL(Phe)) and 15-amino-acid peptides selected from a random phage display library (RPL). A peptide-concentration-dependent formation of RNA/peptide complex was clearly visible during CEMSA. In the presence of peptide, the UV-monitored CE peak for ASLPhe with three of the five naturally occurring modifications (2'-O-methylcytidine (Cm32), 2'-O-methylguanine (Gm34) and 5-methylcytidine (m5C40) shifted from 18.16 to 20.90 min. The mobility shift was observed only for methylated RNA. The negative effects of diffusion, electroosmotic flow and adhesion of molecules to the capillary internal wall were suppressed by using a buffer containing a sieving polymer and a polyacrylamide-coated capillary. Under these conditions, well-shaped peaks and resolution of RNA free and bound to peptide were achieved. Peptide tF2, the most populated ligand in the RPL, specifically bound triply methylated ASLPhe in a methylated nucleoside-dependent manner. CE was found to be an efficient and sensitive method for the qualitative analysis of RNA-peptide interaction and should be generally applicable to the study of RNA-peptide (protein) interactions.}, number={5}, journal={RNA}, author={Mucha, P and Szyk, A and Rekowski, P and Guenther, R and Agris, PF}, year={2002}, month={May}, pages={698–704} }
 @article{stuart_gdaniec_guenther_marszalek_sochacka_malkiewicz_agris_2000, title={Functional anticodon architecture of human tRNA(Lys3) includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t(6)A}, volume={39}, ISSN={["0006-2960"]}, DOI={10.1021/bi0013039}, abstractNote={The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding.}, number={44}, journal={BIOCHEMISTRY}, author={Stuart, JW and Gdaniec, Z and Guenther, R and Marszalek, M and Sochacka, E and Malkiewicz, A and Agris, PF}, year={2000}, month={Nov}, pages={13396–13404} }
 @article{sengupta_vainauskas_yarian_sochacka_malkiewicz_guenther_koshlap_agris_2000, title={Modified constructs of the tRNA T Psi C domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases}, volume={28}, ISSN={["0305-1048"]}, DOI={10.1093/nar/28.6.1374}, abstractNote={The TPsiC stem and loop (TSL) of tRNA contains highly conserved nucleoside modifications, m(5)C(49), T(54), Psi(55)and m(1)A(58). U(54)is methylated to m(5)U (T) by m(5)U(54)methyltransferase (RUMT); A(58)is methylated to m(1)A by m(1)A(58)tRNA methyltransferase (RAMT). RUMT recognizes and methylates a minimal TSL heptadecamer and RAMT has previously been reported to recognize and methylate the 3'-half of the tRNA molecule. We report that RAMT can recognize and methylate a TSL heptadecamer. To better understand the sensitivity of RAMT and RUMT to TSL conformation, we have designed and synthesized variously modified TSL constructs with altered local conformations and stabilities. TSLs were synthesized with natural modifications (T(54)and Psi(55)), naturally occurring modifications at unnatural positions (m(5)C(60)), altered sugar puckers (dU(54)and/or dU(55)) or with disrupted U-turn interactions (m(1)Psi(55)or m(1)m(3)Psi(55)). The unmodified heptadecamer TSL was a substrate of both RAMT and RUMT. The presence of T(54)increased thermal stability of the TSL and dramatically reduced RAMT activity toward the substrate. Local conformation around U(54)was found to be an important determinant for the activities of both RAMT and RUMT.}, number={6}, journal={NUCLEIC ACIDS RESEARCH}, author={Sengupta, R and Vainauskas, S and Yarian, C and Sochacka, E and Malkiewicz, A and Guenther, RH and Koshlap, KM and Agris, PF}, year={2000}, month={Mar}, pages={1374–1380} }
 @article{yarian_marszalek_sochacka_malkiewicz_guenther_miskiewicz_agris_2000, title={Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNA(UUU)(Lys) species}, volume={39}, ISSN={["0006-2960"]}, DOI={10.1021/bi001302g}, abstractNote={Nucleoside modifications are important to the structure of all tRNAs and are critical to the function of some tRNA species. The transcript of human tRNA(Lys3)(UUU) with a UUU anticodon, and the corresponding anticodon stem and loop domain (ASL(Lys3)(UUU)), are unable to bind to poly-A programmed ribosomes. To determine if specific anticodon domain modified nucleosides of tRNA(Lys) species would restore ribosomal binding and also affect thermal stability, we chemically synthesized ASL(Lys) heptadecamers and site-specifically incorporated the anticodon domain modified nucleosides pseudouridine (Psi(39)), 5-methylaminomethyluridine (mnm(5)U(34)) and N6-threonylcarbamoyl-adenosine (t(6)A(37)). Incorporation of t(6)A(37) and mnm(5)U(34) contributed structure to the anticodon loop, apparent by increases in DeltaS, and significantly enhanced the ability of ASL(Lys3)(UUU) to bind poly-A programmed ribosomes. Neither ASL(Lys3)(UUU)-t(6)A(37) nor ASL(Lys3)(UUU)-mnm(5)U(34) bound AAG programmed ribosomes. Only the presence of both t(6)A(37) and mnm(5)U(34) enabled ASL(Lys3)(UUU) to bind AAG programmed ribosomes, as well as increased its affinity for poly-A programmed ribosomes to the level of native Escherichia coli tRNA(Lys). The completely unmodified anticodon stem and loop of human tRNA(Lys1,2)(CUU) with a wobble position-34 C bound AAG, but did not wobble to AAA, even when the ASL was modified with t(6)A(37). The data suggest that tRNA(Lys)(UUU) species require anticodon domain modifications in the loop to impart an ordered structure to the anticodon for ribosomal binding to AAA and require a combination of modified nucleosides to bind AAG.}, number={44}, journal={BIOCHEMISTRY}, author={Yarian, C and Marszalek, M and Sochacka, E and Malkiewicz, A and Guenther, R and Miskiewicz, A and Agris, PF}, year={2000}, month={Nov}, pages={13390–13395} }
 @article{ashraf_guenther_ansari_malkiewicz_sochacka_agris_2000, title={Role of modified nucleosides of yeast tRNA(Phe) in ribosomal binding}, volume={33}, ISSN={["1559-0283"]}, DOI={10.1385/CBB:33:3:241}, abstractNote={Naturally occurring nucleoside modifications are an intrinsic feature of transfer RNA (tRNA), and have been implicated in the efficiency, as well as accuracy-of codon recognition. The structural and functional contributions of the modified nucleosides in the yeast tRNA(Phe) anticodon domain were examined. Modified nucleosides were site-selectively incorporated, individually and in combinations, into the heptadecamer anticodon stem and loop domain, (ASL(Phe)). The stem modification, 5-methylcytidine, improved RNA thermal stability, but had a deleterious effect on ribosomal binding. In contrast, the loop modification, 1-methylguanosine, enhanced ribosome binding, but dramatically decreased thermal stability. With multiple modifications present, the global ASL stability was mostly the result of the individual contributions to the stem plus that to the loop. The effect of modification on ribosomal binding was not predictable from thermodynamic contributions or location in the stem or loop. With 4/5 modifications in the ASL, ribosomal binding was comparable to that of the unmodified ASL. Therefore, modifications of the yeast tRNA(Phe) anticodon domain may have more to do with accuracy of codon reading than with affinity of this tRNA for the ribosomal P-site. In addition, we have used the approach of site-selective incorporation of specific nucleoside modifications to identify 2'O-methylation of guanosine at wobble position 34 (Gm34) as being responsible for the characteristically enhanced chemical reactivity of C1400 in Escherichia coli 16S rRNA upon ribosomal footprinting of yeast tRNA(Phe). Thus, effective ribosome binding of tRNA(Phe) is a combination of anticodon stem stability and the correct architecture and dynamics of the anticodon loop. Correct tRNA binding to the ribosomal P-site probably includes interaction of Gm34 with 16S rRNA C1400.}, number={3}, journal={CELL BIOCHEMISTRY AND BIOPHYSICS}, author={Ashraf, SS and Guenther, RH and Ansari, G and Malkiewicz, A and Sochacka, E and Agris, PF}, year={2000}, pages={241–252} }
 @article{sochacka_czerwinska_guenther_cain_agris_malkiewicz_2000, title={Synthesis and properties of uniquely modified oligoribonucleotides: Yeast tRNA(Phe) fragments with 6-methyluridine and 5,6-dimethyluridine at site-specific positions}, volume={19}, ISSN={["1525-7770"]}, DOI={10.1080/15257770008035004}, abstractNote={Abstract The phosphoramidites of 6-methyluridine and 5,6-dimethyluridine were synthesized and the modified uridines site-selectively incorporated into heptadecamers corresponding in sequence to the yeast tRNAPhe anticodon and TΦC domains. The oligoribonucleotides were characterized by NMR, MALDI-TOF MS and UV-monitored thermal denaturations. The 6-methylated uridines retained the syn conformation at the polymer level and in each sequence location destabilized the RNAs compared to that of the unmodified RNA. The decrease in RNA duplex stability is predictable. However, loss of stability when the modified uridine is in a loop is sequence context dependent, and can not, at this time, be predicted from the location in the loop.}, number={3}, journal={NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS}, author={Sochacka, E and Czerwinska, G and Guenther, R and Cain, R and Agris, PF and Malkiewicz, A}, year={2000}, pages={515–531} }
 @article{koshlap_guenther_sochacka_malkiewicz_agris_1999, title={A distinctive RNA fold: The solution structure of an analogue of the yeast tRNA(Phe) T psi C domain}, volume={38}, ISSN={["0006-2960"]}, DOI={10.1021/bi990118w}, abstractNote={The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spectroscopy and restrained molecular dynamics. The molecule contained the highly conserved modification ribothymidine at its naturally occurring position. The ribothymidine-modified T Psi C stem-loop is the product of the m5U54-tRNA methyltransferase, but is not a substrate for the m1A58-tRNA methyltransferase. Site-specific substitutions and 15N labels were used to confirm the assignment of NOESY cross-peaks critical in defining the global fold of the molecule. The structure is unusual in that the loop folds far over into the major groove of the curved stem. This conformation is stabilized by both stacking interactions and hydrogen bond formation. Furthermore, this conformation appears to be unique among RNA hairpins of similar size. There is, however, a considerable resemblance to the analogous domain in the crystal structure of the full-length yeast tRNAPhe. We believe, therefore, that the structure we have determined may represent an intermediate in the folding pathway during the maturation of tRNA.}, number={27}, journal={BIOCHEMISTRY}, author={Koshlap, KM and Guenther, R and Sochacka, E and Malkiewicz, A and Agris, PF}, year={1999}, month={Jul}, pages={8647–8656} }
 @article{agris_marchbank_newman_guenther_ingram_swallow_mucha_szyk_rekowski_peletskaya_et al._1999, title={Experimental models of protein-RNA interaction: Isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries}, volume={18}, ISSN={["0277-8033"]}, DOI={10.1023/A:1020688609121}, abstractNote={Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNA(Phe) (tRNA(ACPhe)) were selected from a random-sequence, 15-amino acid bacteriophage display library. An experimental system, including an affinity selection method, was designed to identify primary RNA-binding peptide sequences without bias to known amino acid sequences and without incorporating nonspecific binding of the anionic RNA backbone. Nitrocellulose binding assays were used to evaluate the binding of RNA by peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bacteriophage were determined from the foreign insert DNA sequences, and peptides corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs (Kd approximately 0.1-5.0 microM) were analyzed successfully using fluorescence and circular dichroism spectroscopies. These methodologies demonstrate the feasibility of rapidly identifying, isolating, and initiating the analyses of small peptides that bind to RNAs in an effort to define better the chemistry, structure, and function of protein-RNA complexes.}, number={4}, journal={JOURNAL OF PROTEIN CHEMISTRY}, author={Agris, PF and Marchbank, MT and Newman, W and Guenther, R and Ingram, P and Swallow, J and Mucha, P and Szyk, A and Rekowski, P and Peletskaya, E and et al.}, year={1999}, month={May}, pages={425–435} }
 @article{hardin_sneeden_lemon_brown_guenther_sierzputowska-gracz_1999, title={Folding of pyrimidine-enriched RNA fragments from the vicinity of the internal ribosomal entry site of Hepatitis A virus}, volume={27}, ISSN={["1362-4962"]}, DOI={10.1093/nar/27.2.665}, abstractNote={Two RNA fragments from the region just upstream of the internal ribosome entry site of Hepatitis A virus (HAV) were studied, a 35mer (HAV-35), 5'U4C3U3C3U4C3U3C2UAU2C3U33(4), and a 23mer (HAV-23), 5(4)U4C3U3C3U4C3U33(4). Secondary structural predictions and nuclease digestion patterns obtained with genomic RNAs suggested that they link two stable Watson-Crick (WC) hairpins in the genomic RNA and do not form conventional WC secondary structure, but do fold to form a condensed, stacked 'domain'. To obtain more information, folding of HAV-23 and -35 RNA fragments was characterized using 1H nuclear magnetic resonance, in H2O as a function of pH and temperature, circular dichroism as a function of NaCl concentration, pH and temperature, and square-wave voltammetry as a function of pH. The results indicate that these oligo-nucleotides form intramolecular structures that contain transient U*U base pairs at pH 7 and moderate ionic strength (100 mM NaCl). This folded structure becomes destabilized and loses the U*U base pairs above and below neutral pH, especially at ionic strengths above 0.1. All of the cytidine protons exchange relatively rapidly with solvent protons (exchange lifetimes shorter than 1 ms), so the structure contains few if any C*CH+base pairs at neutral pH, but can apparently form them at pH values below 6. We present a series of possible models in which chain folding draws the strand termini closer together, possibly serving to pull the attached WC hairpin domains together and providing a functional advantage by nucleating reversible formation of a more viable RNA substrate.}, number={2}, journal={NUCLEIC ACIDS RESEARCH}, author={Hardin, CC and Sneeden, JL and Lemon, SM and Brown, BA and Guenther, RH and Sierzputowska-Gracz, H}, year={1999}, month={Jan}, pages={665–673} }
 @article{ashraf_guenther_agris_1999, title={Orientation of the tRNA anticodon in the ribosomal P-site: Quantitative footprinting with U-33-modified, anticodon stem and loop domains}, volume={5}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838299990933}, abstractNote={Binding of transfer RNA (tRNA) to the ribosome involves crucial tRNA-ribosomal RNA (rRNA) interactions. To better understand these interactions, U33-substituted yeast tRNA(Phe) anticodon stem and loop domains (ASLs) were used as probes of anticodon orientation on the ribosome. Orientation of the anticodon in the ribosomal P-site was assessed with a quantitative chemical footprinting method in which protection constants (Kp) quantify protection afforded to individual 16S rRNA P-site nucleosides by tRNA or synthetic ASLs. Chemical footprints of native yeast tRNA(Phe), ASL-U33, as well as ASLs containing 3-methyluridine, cytidine, or deoxyuridine at position 33 (ASL-m3U33, ASL-C33, and ASL-dU33, respectively) were compared. Yeast tRNAPhe and the ASL-U33 protected individual 16S rRNA P-site nucleosides differentially. Ribosomal binding of yeast tRNA(Phe) enhanced protection of C1400, but the ASL-U33 and U33-substituted ASLs did not. Two residues, G926 and G1338 with KpS approximately 50-60 nM, were afforded significantly greater protection by both yeast tRNA(Phe) and the ASL-U33 than other residues, such as A532, A794, C795, and A1339 (KpS approximately 100-200 nM). In contrast, protections of G926 and G1338 were greatly and differentially reduced in quantitative footprints of U33-substituted ASLs as compared with that of the ASL-U33. ASL-m3U33 and ASL-C33 protected G530, A532, A794, C795, and A1339 as well as the ASL-U33. However, protection of G926 and G1338 (KpS between 70 and 340 nM) was significantly reduced in comparison to that of the ASL-U33 (43 and 61 nM, respectively). Though protections of all P-site nucleosides by ASL-dU33 were reduced as compared to that of the ASL-U33, a proportionally greater reduction of G926 and G1338 protections was observed (KpS = 242 and 347 nM, respectively). Thus, G926 and G1338 are important to efficient P-site binding of tRNA. More importantly, when tRNA is bound in the ribosomal P-site, G926 and G1338 of 16S rRNA and the invariant U33 of tRNA are positioned close to each other.}, number={9}, journal={RNA}, author={Ashraf, SS and Guenther, R and Agris, PF}, year={1999}, month={Sep}, pages={1191–1199} }
 @article{ashraf_sochacka_cain_guenther_malkiewicz_agris_1999, title={Single atom modification (O -> S) of tRNA confers ribosome binding}, volume={5}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838299981529}, abstractNote={Escherichia coli tRNALysSUU, as well as human tRNALys3SUU, has 2-thiouridine derivatives at wobble position 34 (s2U*34). Unlike the native tRNALysSUU, the full-length, unmodified transcript of human tRNALys3UUU and the unmodified tRNALys3UUU anticodon stem/loop (ASLLys3UUU) did not bind AAA- or AAG-programmed ribosomes. In contrast, the completely unmodified yeast tRNAPhe anticodon stem/loop (ASLPheGAA) had an affinity (Kd = 136+/-49 nM) similar to that of native yeast tRNAPheGmAA (Kd = 103+/-19 nM). We have found that the single, site-specific substitution of s2U34 for U34 to produce the modified ASLLysSUU was sufficient to restore ribosomal binding. The modified ASLLysSUU bound the ribosome with an affinity (Kd = 176+/-62 nM) comparable to that of native tRNALysSUU (Kd = 70+/-7 nM). Furthermore, in binding to the ribosome, the modified ASLLys3SUU produced the same 16S P-site tRNA footprint as did native E. coli tRNALysSUU, yeast tRNAPheGmAA, and the unmodified ASLPheGAA. The unmodified ASLLys3UUU had no footprint at all. Investigations of thermal stability and structure monitored by UV spectroscopy and NMR showed that the dynamic conformation of the loop of modified ASLLys3SUU was different from that of the unmodified ASLLysUUU, whereas the stems were isomorphous. Based on these and other data, we conclude that s2U34 in tRNALysSUU and in other s2U34-containing tRNAs is critical for generating an anticodon conformation that leads to effective codon interaction in all organisms. This is the first example of a single atom substitution (U34-->s2U34) that confers the property of ribosomal binding on an otherwise inactive tRNA.}, number={2}, journal={RNA}, author={Ashraf, SS and Sochacka, E and Cain, R and Guenther, R and Malkiewicz, A and Agris, PF}, year={1999}, month={Feb}, pages={188–194} }
 @article{yarian_basti_cain_ansari_guenther_sochacka_czerwinska_malkiewicz_agris_1999, title={Structural and functional roles of the N1-and N3-protons of Psi at tRNA's position 39}, volume={27}, ISSN={["1362-4962"]}, DOI={10.1093/nar/27.17.3543}, abstractNote={Pseudouridine at position 39 (Psi(39)) of tRNA's anticodon stem and loop domain (ASL) is highly conserved. To determine the physicochemical contributions of Psi(39)to the ASL and to relate these properties to tRNA function in translation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)and Psi(39). Psi(39)increased the thermal stability of the ASL (Delta T (m)= 1.3 +/- 0.5 degrees C), but did not significantly affect ribosomal binding ( K (d)= 229 +/- 29 nM) compared to that of the unmodified ASL (K (d)= 197 +/- 58 nM). The ASL-Psi(39)P-site fingerprint on the 30S ribosomal subunit was similar to that of the unmodified ASL. The stability, ribosome binding and fingerprint of the ASL with m(1)Psi(39)were comparable to that of the ASL with Psi(39). Thus, the contribution of Psi(39)to ASL stability is not related to N1-H hydrogen bonding, but probably is due to the nucleoside's ability to improve base stacking compared to U. In contrast, substitutions of m(3)Psi(39), the isosteric m(3)U(39)and m(1)m(3)Psi(39)destabilized the ASL by disrupting the A(31)-U(39)base pair in the stem, as confirmed by NMR. N3-methylations of both U and Psi dramatically decreased ribosomal binding ( K (d)= 1060 +/- 189 to 1283 +/- 258 nM). Thus, canonical base pairing of Psi(39)to A(31)through N3-H is important to structure, stability and ribosome binding, whereas the increased stability and the N1-proton afforded by modification of U(39)to Psi(39)may have biological roles other than tRNA's binding to the ribosomal P-site.}, number={17}, journal={NUCLEIC ACIDS RESEARCH}, author={Yarian, CS and Basti, MM and Cain, RJ and Ansari, G and Guenther, RH and Sochacka, E and Czerwinska, G and Malkiewicz, A and Agris, PF}, year={1999}, month={Sep}, pages={3543–3549} }
 @article{ashraf_ansari_guenther_sochacka_malkiewicz_agris_1999, title={The uridine in "U-turn": Contributions to tRNA-ribosomal binding}, volume={5}, ISSN={["1469-9001"]}, DOI={10.1017/S1355838299981931}, abstractNote={"U-turns" represent an important class of structural motifs in the RNA world, wherein a uridine is involved in an abrupt change in the direction of the polynucleotide backbone. In the crystal structure of yeast tRNAPhe, the invariant uridine at position 33 (U33), adjacent to the anticodon, stabilizes the exemplar U-turn with three non-Watson-Crick interactions: hydrogen bonding of the 2'-OH to N7 of A35 and the N3-H to A36-phosphate, and stacking between C32 and A35-phosphate. The functional importance of each noncanonical interaction was determined by assaying the ribosomal binding affinities of tRNAPhe anticodon stem and loop domains (ASLs) with substitutions at U33. An unsubstituted ASL bound 30S ribosomal subunits with an affinity (Kd = 140+/-50 nM) comparable to that of native yeast tRNAPhe (Kd = 100+/-20 nM). However, the binding affinities of ASLs with dU-33 (no 2'-OH) and C-33 (no N3-H) were significantly reduced (2,930+/-140 nM and 2,190+/-300 nM, respectively). Surprisingly, the ASL with N3-methyluridine-33 (no N3-H) bound ribosomes with a high affinity (Kd = 220+/-20 nM). In contrast, ASLs constructed with position 33 uridine analogs in nonstacking, nonnative, and constrained conformations, dihydrouridine (C2'-endo), 6-methyluridine (syn) and 2'O-methyluridine (C3'-endo) had almost undetectable binding. The inability of ASLs with 6-methyluridine-33 and 2'O-methyluridine-33 to bind ribosomes was not attributable to any thermal instability of the RNAs. These results demonstrate that proton donations by the N3-H and 2'OH groups of U33 are not absolutely required for ribosomal binding. Rather, the results suggest that the overall uridine conformation, including a dynamic (C3'-endo > C2'-endo) sugar pucker, anti conformation, and ability of uracil to stack between C32 and A35-phosphate, are the contributing factors to a functional U-turn.}, number={4}, journal={RNA}, author={Ashraf, SS and Ansari, G and Guenther, R and Sochacka, E and Malkiewicz, A and Agris, PF}, year={1999}, month={Apr}, pages={503–511} }
 @article{agris_guenther_sochacka_newman_czerwinska_liu_ye_malkiewicz_1999, title={Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs}, volume={46}, number={1}, journal={Acta Biochimica Polonica}, author={Agris, P. F. and Guenther, R. and Sochacka, E. and Newman, W. and Czerwinska, G. and Liu, G. H. and Ye, W. P. and Malkiewicz, A.}, year={1999}, pages={163–172} }
 @article{guenther_forrest_newman_malkiewicz_agris_1998, title={Modified RNAs as potential drug targets}, volume={45}, number={1}, journal={Acta Biochimica Polonica}, author={Guenther, R. and Forrest, B. and Newman, W. and Malkiewicz, A. and Agris, P. F.}, year={1998}, pages={13–18} }
 @inproceedings{ashraf_guenther_ye_lee_malkiewicz_agris_1997, title={Ribosomal binding of modified tRNA anticodons related to thermal stability}, volume={36}, booktitle={Symposium on RNA Biology II. RNA: Tool and Target (1997: North Carolina Biotechnology Center) Research Triangle Park, North Carolina, USA, October 17-19, 1997  (Nucleic acids symposium series; no. 36)}, publisher={Oxford: Oxford University Press}, author={Ashraf, S. S. and Guenther, R. and Ye, W. and Lee, Y. and Malkiewicz, A. and Agris, P. F.}, year={1997}, pages={58–60} }
 @article{agris_guenther_ingram_basti_stuart_sochacka_malkiewicz_1997, title={Unconventional structure of tRNA(Lys)SUU anticodon explains tRNA's role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1}, volume={3}, number={4}, journal={RNA}, author={Agris, P. F. and Guenther, R. H. and Ingram, P. C. and Basti, M. M. and Stuart, J. W. and Sochacka, E. and Malkiewicz, A.}, year={1997}, pages={420–428} }