@misc{agris_ashraf_2005, title={Antibacterial and antiviral agents and methods of screening for the same}, volume={6,962,785}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Agris, P. F. and Ashraf, S.}, year={2005} }
 @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} }
 @misc{agris_ashraf_1999, title={Antibacterial agents and methods of screening for the same}, volume={6,461,815}, number={1999 May 20}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Agris, P. F. and Ashraf, S.}, year={1999} }
 @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{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} }
 @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} }
 @misc{pliura_wiffen_ashraf_magnin_1996, title={Purification of hemoglobin by displacement chromatography}, volume={5,545,328}, number={1996 Aug. 13}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Pliura, D. H. and Wiffen, D. E. and Ashraf, S. and Magnin, A. A.}, year={1996} }
 @misc{pliura_wiffen_ashraf_magnin_1995, title={Displacement chromatography process}, volume={5,439,591}, number={1995 Aug. 8}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Pliura, D. H. and Wiffen, D. E. and Ashraf, S. and Magnin, A. A.}, year={1995} }