@article{gryko_gryko_sierzputowska-gracz_piatek_jurczak_2004, title={Factors influencing the course of the macrocyclization of alpha,omega-diamines with esters of alpha,omega-dicarboxylic acids}, volume={87}, ISSN={["1522-2675"]}, DOI={10.1002/hlca.200490004}, abstractNote={Abstract}, number={1}, journal={HELVETICA CHIMICA ACTA}, author={Gryko, D and Gryko, DT and Sierzputowska-Gracz, H and Piatek, P and Jurczak, J}, year={2004}, pages={156–166} }
 @article{crouse_sierzputowska-gracz_mikkelsen_wollum_2002, title={Monitoring phosphorus mineralization from poultry manure using phosphatase assays and phosphorus-31 nuclear magnetic resonance spectroscopy}, volume={33}, ISSN={["0010-3624"]}, DOI={10.1081/CSS-120003882}, abstractNote={Phosphatase enzymes are responsible for mineralization of organic-phosphorus (P) compounds in soil where they hydrolyze the organic phosphate esters to inorganic phosphate. One way to monitor the mineralization process in soils receiving poultry manure is by assessing the activity of phosphatase in a soil amended with poultry manure relative to a soil that is not amended. In a laboratory incubation, soil phosphomonoesterase activity and soil phosphodiesterase activity were measured 0, 1, 2, 4, 8, 12, 16, and 20 weeks after soil incorporation of poultry litter. Two soils, both Fine-loamy siliceous, thermic Typic Kandiudults, were used in the study. Both soils differed in their previous management. The first soil was from a conventionally tilled field that received annual poultry litter applications for 18 consecutive years. The second soil was from an adjacent recently cleared woodland that had no history of manure application. In the previously non-manured soil, soil phosphodiesterase activity following poultry litter addition increased from 4 to 66 μg p-nitrophenol g soil−1 hour−1 by the second week. However, in the same soil, after 8 weeks, phosphodiesterase activity resulting from poultry litter applications was not evident. There was a net increase in phosphomonoesterase activity from week 0 to 20 in the previously manured and previously non-manured soils that were amended with poultry litter. A simultaneous study was conducted to measure the relative concentration of organic P forms during the mineralization process using 31P nuclear magnetic resonance. Subsamples from the poultry manure-amended soil were extracted with 0.25 M NaOH+0.05 M EDTA following 0, 1, 2, 4, 8, 12, 16, and 20 weeks after manure addition and incorporation. The concentration of organic P compounds decreased from the time of poultry litter incorporation until week 20 whereas orthophosphate concentration increased during this period.}, number={7-8}, journal={COMMUNICATIONS IN SOIL SCIENCE AND PLANT ANALYSIS}, author={Crouse, DA and Sierzputowska-Gracz, H and Mikkelsen, RL and Wollum, AG}, year={2002}, pages={1205–1217} }
 @article{ke_sierzputowska-gracz_gdaniec_theil_2000, title={Internal loop/bulge and hairpin loop of the iron-responsive element of ferritin mRNA contribute to maximal iron regulatory protein 2 binding and translational regulation in the iso-iron-responsive element/iso-iron regulatory protein family}, volume={39}, ISSN={["0006-2960"]}, DOI={10.1021/bi9924765}, abstractNote={Iron-responsive elements (IREs), a natural group of mRNA-specific sequences, bind iron regulatory proteins (IRPs) differentially and fold into hairpins [with a hexaloop (HL) CAGUGX] with helical distortions: an internal loop/bulge (IL/B) (UGC/C) or C-bulge. C-bulge iso-IREs bind IRP2 more poorly, as oligomers (n = 28-30), and have a weaker signal response in vivo. Two trans-loop GC base pairs occur in the ferritin IRE (IL/B and HL) but only one in C-bulge iso-IREs (HL); metal ions and protons perturb the IL/B [Gdaniec et al. (1998) Biochemistry 37, 1505-1512]. IRE function (translation) and physical properties (T(m) and accessibility to nucleases) are now compared for IL/B and C-bulge IREs and for HL mutants. Conversion of the IL/B into a C-bulge by a single deletion in the IL/B or by substituting the HL CG base pair with UA both derepressed ferritin synthesis 4-fold in rabbit reticulocyte lysates (IRP1 + IRP2), confirming differences in IRP2 binding observed for the oligomers. Since the engineered C-bulge IRE was more helical near the IL/B [Cu(phen)(2) resistant] and more stable (T(m) increased) and the HL mutant was less helical near the IL/B (ribonuclease T1 sensitive) and less stable (T(m) decreased), both CG trans-loop base pairs contribute to maximum IRP2 binding and translational regulation. The (1)H NMR spectrum of the Mg-IRE complex revealed, in contrast to the localized IL/B effects of Co(III) hexaammine observed previously, perturbation of the IL/B plus HL and interloop helix. The lower stability and greater helix distortion in the ferritin IL/B-IRE compared to the C-bulge iso-IREs create a combinatorial set of RNA/protein interactions that control protein synthesis rates with a range of signal sensitivities.}, number={20}, journal={BIOCHEMISTRY}, author={Ke, YH and Sierzputowska-Gracz, H and Gdaniec, Z and Theil, EC}, year={2000}, month={May}, pages={6235–6242} }
 @article{collins_kim_holton_sierzputowska-gracz_stejskal_2000, title={NMR quantum computation with indirectly coupled gates}, volume={62}, ISSN={1050-2947 1094-1622}, url={http://dx.doi.org/10.1103/PhysRevA.62.022304}, DOI={10.1103/physreva.62.022304}, abstractNote={An NMR realization of a two-qubit quantum gate which processes quantum information indirectly via couplings to a spectator qubit is presented in the context of the Deutsch-Jozsa algorithm. This enables a successful comprehensive NMR implementation of the Deutsch-Jozsa algorithm for functions with three argument bits and demonstrates a technique essential for multi-qubit quantum computation.}, number={2}, journal={Physical Review A}, publisher={American Physical Society (APS)}, author={Collins, David and Kim, K. W. and Holton, W. C. and Sierzputowska-Gracz, H. and Stejskal, E. O.}, year={2000}, month={Jul} }
 @article{crouse_sierzputowska-gracz_mikkelsen_2000, title={Optimization of sample pH and temperature for phosphorus-31 nuclear magnetic resonance spectroscopy of poultry manure extracts}, volume={31}, ISSN={["0010-3624"]}, DOI={10.1080/00103620009370432}, abstractNote={Abstract Organic phosphorus (P) compounds can be characterized using nuclear magnetic resonance (NMR) spectroscopy provided conditions are suitable for detecting the NMR signal. The objective of the research was to optimize pH and temperature conditions for turkey manure extracts prior to analysis of organic P compounds using NMR. Samples of turkey manure were extracted with 0.25 MNaOH + 0.05 MEDTA. The extracts were lyophilized and resolubilized in distilled H2O before analysis on a General Electric GN500 NMR spectrometer. Initial 31P NMR experiments were run to determine the optimal instrumental parameters for 31P studies. Samples were titrated to seventeen pH values ranging from 4.0 to 13.2. Samples adjusted to pH 10.0 had the greatest spectral resolution. A seven‐by‐three factorial experiment was used to investigate the effect of seven temperatures (5,10,20,30,40,50, and 60°C) on three separate samples at pH 6.5,9.0, or 10.0. Spectra resolution was greatest at pH 10.0 and 20°C.}, number={1-2}, journal={COMMUNICATIONS IN SOIL SCIENCE AND PLANT ANALYSIS}, author={Crouse, DA and Sierzputowska-Gracz, H and Mikkelsen, RL}, year={2000}, pages={229–240} }
 @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{gdaniec_sierzputowska-gracz_theil_1999, title={Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy (vol 37, pg 1505, 1998)}, volume={38}, ISSN={["0006-2960"]}, DOI={10.1021/bi9950746}, abstractNote={The ferritin IRE, a highly conserved (96 -99% in vertebrates) mRNA translation regulatory element in animal mRNA, was studied by molecular modeling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg 2+. IRE isoforms in other mRNAs regulate mRNA translation or stability; all IREs bind IRPs (iron regulatory proteins). A G ‚C base pair, conserved in ferritin IREs, spans an internal loop/bulge in the middle of an A-helix and, combined with a dynamic G‚U base pair, formed a pocket suitable for Co(III) hexammine binding. On the basis of the effects of Co(III) hexammine on the 1H NMR spectrum and results of automatic docking into the IRE model, the IRE bound Co(III) hexammine at the pocket in the major groove; Mg 2+ may bind to the IRE at the same site on the basis of an analogy to Co(III) hexammine and on the Mg 2+ inhibition of Cu(phen)2 cleavage at the site. Distortion of the IRE helix by the internal loop/bulge near a conserved unpaired C required for IRP binding and adjacent to an IRP cross-linking site suggests a role for the pocket in ferritin IRE/IRP interactions. RNA sequences in the noncoding region of mRNAs can regulate mRNA function. The predicted secondary structure is a hairpin distorted by a bulge, bulge loop, or internal loop. Specificity of the three-dimensional structure of RNA regulatory elements is recognized by proteins as in the Tat/ TAR and Rev/RRE interactions of the HIV virus ( 1-3). Bulge loops and internal loops in RNA induce bends or distortions in helixes, creating specific three-dimensional structures and, often, metal binding sites ( 4). Little is known about the three-dimensional structure of natural regulatory elements in eukaryotic mRNAs. The IRE (iron responsive element) family of isoelements is a particularly well characterized control element in normal animal mRNAs encoding proteins of iron metabolism. IREs are hairpins of 9 or 10 base pairs, interrupted by a bulge loop of 1-4 nucleotides with a conserved C residue and with a terminal hexaloop, CAGUGX (reviewed most recently in refs 5-8). The metal complex Cu(phen) 2 binds at the internal bulge/loop ( 9, 10). All IREs recognize a family of RNA binding proteins, the IRPs (iron regulatory proteins); some IREs recognize other proteins as well, such as initiation factors (11, 12, 14). Single-copy IREs in the 5 ′-untranslated regions of mRNAs regulate ribosome binding, while pentuple-copy IREs in the 3 ′-untranslated regions are part of a rapid turnover element regulating mRNA stability; each type of IRE is highly conserved (96 -99%) which contrasts with the lower sequence conservation (35 -45%) between translation and rapid turnover IREs ( 8). The ferritin IRE is the best characterized IRE in terms of structure and function. Assurance of the biological relevance of IRE studies with synthetic RNA, used here and in other types of experiments, has been uniquely provided by earlier investigations using natural ferritin mRNA [poly(A +) RNA]1 to study IRE structure, the IRP binding site and IRE function in regulating protein synthesis ( 9-11, 14-16); ferritin poly(A+) RNA showed function and/or chemical and enzymatic reactivity similar to those of the synthetic RNAs. The ferritin IRE is the most efficient of the translational regulatory IREs (13), possibly because of a conserved internal loop/bulge involving UGC/C rather than the bulge C of other IREs. Previous NMR studies have focused on the role of the ferritin IRE terminal hexaloop ( 17, 18). In this study, a model of the complete IRE 30-mer is developed, assisted by NMR data from15Nand13C-labeled RNA and cobalt(III) hexammine/RNA complexes; the model is consistent with previous chemical and enzymatic studies. Co(III) hexammine significantly shifted proton NMR resonances of G7 and G27 in the internal loop/bulge region and docked in a pocket caused by distortion of the major groove in the middle of the IRE. The same region is also hypersensitive to cleavage by hydroxyl radical ( 16) and displays Mg† The work was supported in part by NIH Grant DK-20251. * Corresponding author at Department of Biochemistry, North Carolina State University, Raleigh, NC 27695-7622. Phone: 919-5155805. Fax: 919-515-5805. E-mail: Theil@bchserver.bch.ncsu.edu. ‡ Polish Academy of Sciences. § Department of Biochemistry, North Carolina State University. | Department of Chemistry, North Carolina State University. 1 Poly(A+) RNA from a natural cell rich in ferritin mRNA [the embryonic red cell in which∼10% of the mRNA is ferritin mRNA (11)] was used with immunoprecipitation to examine control of ferritin synthesis ( 11, 14, 15) or with specific primers to examine IRE structure in the RNA after reaction with structure probes or IRP binding ( 9, 16). 1505 Biochemistry1998,37, 1505-1512 S0006-2960(97)01981-8 CCC: $15.00 © 1998 American Chemical Society Published on Web 01/23/1998 sensitive changes in cleavage by Cu(phen) 2 (9 , indicating solvent accessibility and suggesting that hydrated Mg 2+ binds at the site. In the IRE model, G7/U6 in the internal loop/ bulge and G18/U19 which cross-link to the IRP ( 21) are 22 Å apart, in contrast to only 18 Å in an IRE model without the interhelical pocket, which may relate to correct positioning in the IRP binding site. MATERIALS AND METHODS RNA Synthesis . The 30-mer representing the frog ferritin IRE (Figure 1) was synthesized using the double-stranded T7 polymerase site and the complement of the 30-mer as a template, as previously described ( 17); vertebrate ferritin IREs are highly conserved ( 5-8) (96-99%), but the frog ferritin IRE is the only one which has been studied in natural [poly(A+)] mRNA as well as in synthetic mRNAs and RNA oligomers. The use of full-length double-stranded template increased the yield∼1.5-2-fold; reaction volumes were 24 90 mL. Cloned T7 polymerase was isolated as described by Studier et al. ( 22). RNA was purified by electrophoresis in urea/acrylamide gels as before ( 17), electroreluted, and concentrated by alcohol precipitation. To study the effect of pH on the detection of the G ‚U base pair (Figure 2C), commercially prepared (Cybersyn) RNA was used, but was purified by gel electrophoresis and dialyzed extensively against water before use. RNA enriched in13C and15N was prepared using 13C/15N nucleotide triphosphates (NTPs) as described for the synthesis of RNA with natural abundance levels of the isotopes ( 19, 20). The13Cand15N-enriched NTPs were prepared using crude rRNA fromMethylophilus methyltrophus provided by the NIH Research Resource for Heavy Atoms at Los Alamos National Laboratory. The crude rRNA was digested with DNAse, extracted with phenol and chloroform/isoamyl alcohol (24:1), and precipitated with alcohol followed by digestion to nucleotides with nuclease P1 ( 23) and conversion to NTPs using nucleoside monophosphate kinase, guanylate kinase, pyruvate kinase, myokinase, phosphoenolpyruvate, and ATP as described by Nikonowicz et al. ( 24). After concentration, lyophilization, and alcohol precipitation, the crude NTPs were dissolved in col d 1 M triethylamine/borate buffer (TEAB) at pH 9.5 and desalted on an Affigel 601 (Biorad) column equilibrated i n 1 M TEAB buffer at 5°C (25); the NTPs were eluted with cold distilled water acidified to pH 4-5 with CO2, lyophilized, dissolved in water, filtered through a washed Centricon 10 filter, and stored at pH 8.1 and-20 °C until use. NMR Spectroscopy.RNA (0.5-1.0 mM in 10 mM sodium phosphate buffer and 0.1 mM EDTA at pH 6.8) was heated at 85°C and slowly cooled in the NMR tube. Spectra were acquired on a Bruker DRX 500 MHz spectrometer. Spectra in H2O were obtained either by the Watergate method (26) or by presaturation of the HDO signal fo r 2 s prior to applying an observation pulse or by using the jump -return water suppression and excitation maximum set to the imino resonances ( 27). Data for the two-dimensional (2D) NOESY experiment in 10% D2O/90% H2O were acquired at 12 °C using Watergate-water suppression [a 3 -9-19 pulse sequence with the gradients for water suppression with excitation maximum set to the imino resonances ( 26)]. The spectrum was 2048 × 256 complex data points with a sweep width of 12 000 Hz, a mixing time of 250 ms, a recycle delay of 1.7 s, and 256 scans per slice. Spectra were processed with FELIX 95.0 software (Biosym/Molecular Simulations, Inc.) using an exponential weighing function or shifted sinebell function to resolve overlapped imino protons. NOESY, DQF-COSY, and TOCSY experiments were recorded in 99.996% D 2O on a 500 MHz GE Omega spectrometer or a Bruker 500 MHz spectrometer. Data sets with 2048 complex points int2 and 512 complex points in t1 were acquired with 5000 Hz sweep widths in both dimensions and 128 scans per slice. NOESY spectra were acquired with mixing times of 120, 200, and 400 ms and a recycle delay o f 2 s at 12 and 20°C. The TOCSY spectrum was recorded with a 75 ms MLEV spin lock pulse and a recycle delay of 1.5 s. The DQF-COSY spectra were recorded with WALTZ decoupling of 31P during acquisition and a recycle delay of 1.6 s. The diagonal and cross-peaks of DQF-COSY spectra were phased with antiphase absorption line shape in both directions. All spectra were processed with combinations of exponential and sine-skewed functions and zero-filled to 2K× 2K data points using XWINNMR Bruker or Felix 95.0 software. Spectra with Co(III) hexammine and with varyious pHs were acquired on a Bruker DRX 500 MHz system. Imino proton spectra were obtained by the Watergate method ( 26). Typically, 2048 scans were collected. 1H spectra in 10% D2O/90% H2O were collected at 12°C in 16K point data sets consisting of 1024 scans each. Spectra of double-labeled RNA were obtained on a Varian Unity Plus 600 MHz NMR spectrometer at the University of Chicago, Biological Sciences Division NMR Facility, used in consultation with Dr. Klaas Hallenga. The 2D ( 1H-15N) HSQC experiments were carried out using gradie}, number={17}, journal={BIOCHEMISTRY}, author={Gdaniec, Z and Sierzputowska-Gracz, H and Theil, EC}, year={1999}, month={Apr}, pages={5676–5676} }
 @article{gorman_smith_hager_parkhurst_sierzputowska-gracz_haney_1999, title={Molecular structure-property relationships for electron-transfer rate attenuation in redox-active core dendrimers}, volume={121}, ISSN={["1520-5126"]}, DOI={10.1021/ja990875h}, abstractNote={Two series of redox-active, iron−sulfur core dendrimers of the general structure (nBu4N)2[Fe4S4(S-Dend)4] (Dend = dendrons of generations 1 through 4) were prepared. Heterogeneous electron-transfer rate constants indicated that the rigid series of dendrimers were more effective at attenuating the rate of electron transfer than were the flexible series of dendrimers. These results were rationalized using computationally derived models which indicated an offset and mobile iron−sulfur core in the flexible series of molecules and a more central and relatively immobile iron−sulfur core in the rigid series of molecules. Further consideration of these data indicated that, while the dendrimers containing rigid ligands had better encapsulated redox cores for a given molecular weight, these molecules had higher electron-transfer rates for a given molecular radius.}, number={43}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Gorman, CB and Smith, JC and Hager, MW and Parkhurst, BL and Sierzputowska-Gracz, H and Haney, CA}, year={1999}, month={Nov}, pages={9958–9966} }