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the effect of the β-aryl group on the ketene-formingelimination was assessed.Key Words : Elimination, E2 and E1cb Mechanism, β–Aryl Group effectIntroductionExtensive studies of the structure-reactivity relationshipsin the ketene-forming elimination reactions have led to thequalitative understanding of the relationship between thereactant structure and the mechanism.

value increased with a stronger electron-withdrawing 5-thienyl substituent, the Hammett plots arelinear except for X = MeO, and Yukawa-Tsuno plots are linear with ρ = 0.79-1.32 and r = 0.28-0.93,respectively. The ρ value increased and r value decreased with a stronger nucleophile, indicating an increase inthe electron density at the C=O bond and a decrease in the resonance demand. These results have beeninterpreted with enhanced N-C bond formation in the transition state with the reactivity increase. Key Words : Aminolysis, Bronsted-type plot, Hammett plot, Yukawa-Tsuno plot IntroductionExtensive studies of the structure-reactivity relationshipsin the acyl transfer reactions from XC

Elimination reactions of (E)-2,4-(NO2)2C6H2CH=NOC6H3-2-X-4-NO2 (1a-e) promoted by R3N/R3NH + in 70 mol % MeCN(aq) have been studied kinetically. The reactions are second-order and exhibit Bronsted β = 0.800.84 and |βlg| = 0.39-0.42, respectively. For all leaving groups and bases employed in this study, the β and |βlg| values remained almost the same. The results can be described by a negligible pxy interaction coefficient, pxy = ∂β/pKlg = ∂βlg/pKBH ≈ 0, which describes the interaction between the base catalyst and the leaving group. The negligible pxy interaction coefficient is consistent with the (E1cb)irr mechanism. Change of the base-solvent system from R3N/MeCN to R3N/R3NH + -70 mol % MeCN(aq) changed the reaction mechanism from E2 to (E1cb)irr. Noteworthy was the relative insensitivity of the transition state structure to the reaction mechanism change.

The transition state was shifted toward theE1cb corner by an electron-withdrawing β-aryl substituentand toward the E1 intermediate and the product by astronger base in the reaction coordinate diagram. On theother hand, when the leaving group was changed from 2,4-dinitrophenoxide to picrate, the ρ value decreased but the βvalue increased. The results are in conflict with the predic-tion of the reaction coordinate diagram because both ρ and βvalues should be decreased with a better leaving group. Theunusual changes in the transition-state structure noted withthe leaving group variation have been interpreted as result-ing from a large difference in the anion-stabilizing ability ofthe leaving groups. However, the validity of this interpreta-tion remains to be verified. To determine whether a change in mechanism could berealized by introducing an even more electron-withdrawingβ-aryl substituent, we have now studied the reactions of ( E)-2,4-dinitrobenzaldehyde O-aryloxime with R

Nitrile-forming eliminations from (1) promoted by in 70 mol % MeCN(aq) have been studied kinetically. When X = , the reactions exhibited second-order kinetics as well as Brnsted = 0.63 and = 0.34-0.46, and an E2 mechanism is evident. As the leaving group was made poorer (X = H, Cl, and ), Brnsted value increased from 0.63 to 0.85-0.89 without much change in the value E2, indicating that structure of the transition state changed to an E1cb-like with extensive bond cleavage, significant negative charge development at the -carbon, and limited -OAr bond cleavage.

A combination of a strong electron-withdrawing β-aryl group and anion-solvating protic solvent was required for the mecha-nistic change.We were interested in learning if a change to the E1cB mechanism could be realized in aprotic solvent by making the β-aryl group even more electron-withdrawing. To explore such possibility, we have now studied the reactions of (

dicating a higher sensitivity of ACaCL to the solvent polarity. This can be attributed to the polar amide group between the re-ceptor and fluorophore in ACaCL that can be better solvated by the polar solvent in the excited state, thereby enhancing the intramolecular charge transfer (ICT).When Ca

One of thesesequences, an 18-mer containing four guanine-tracts, 5'-GGGAGGGGCGGGUCUGGG-3' is associated with the 5'-UTR of the oncogenic N-ras sequence. According to a cell-free translation system coupled to a reporter gene assay, theN-ras G-quadruplex can inhibit gene expression at thetranslational level.

The polymerization reaction of 4-[(n-butylsulfinyl)methyl]-4'-(chloromethyl)benzene (1a) with t-BuONa in CH 2 Cl 2 /monomethylformamide (MMF) (4/6) was studied kinetically. The reaction proceeds in two steps; the formation of a p-quinodimethane intermediate (M) followed by the polymerization of M. Results of kinetic studies and H-D exchange experiments reveal that the 1,6-elimination proceeds by the (Elcb)i rr mechanism. The rate of the disappearance of M was increased by the carbanion and S 2 O 8 2- , inhibited by TEMPO and unaltered by the addition of HCl. From these results, a free radical polymerization mechanism is proposed.

To identify RNA motifs interacting with the stem-loop RNA which plays an important role in the synthesis of gag-pol fusion protein of HIV-1, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was performed. RNA aptamers binding to the stem-loop sequence at the gag-pol junction of HIV-1 RNA were selected from a 30-mer random sequence library through 13 rounds of selection. Some of resulting RNA aptamers contained the consensus sequences AAGGGA and GUUGAU. The stem-loop RNA ligand interacted with synthetic RNA fragment containing two conserved sequence motifs AAGGGA and GUUGAU but did not bind to DNA oligonucleotides having the sequences identical to the RNA fragment. These results suggest that a specific tertiary interaction rather than Watson-Crick base-pairing is involved in the complex formation between RNA aptamer and the stem-loop RNA.

Ketene-forming eliminations from C4H3(S)CH2C(0)0-C6H3-2-X-4-N02 (1) promoted by R 2 NH in MeCN have been studied kinetically. The reactions are second-order and exhibit Bronsted β=0.51-0.62 and lβlgl= 0.47-0.53. Hence, an E2 mechanism is evident. The Bronsted β increased from 0.33 to 0.53 and |βlg| remained nearly the same by the change of the base-solvent from Bz(i-Pr)NH/Bz(i-Pr)NH 2 + in 70 mol% MeCN(aq) to Bz(i-Pr)NH-MeCN, indicating a change to a more symmetrical transition state with similar extents of Cβ-H and C α -OAr bond cleavage. When the /?-aryl group was changed from thienyl to phenyl in MeCN, the /? value increased from 0.53 to 0.73 and lβ lg l decreased from 0.53 to 0.43. This indicates that the transition state became skewed toward more Cβ-H bond breaking with less C α -OAr bond cleavage. Noteworthy is the greater double bond stabilizing ability of the thienyl group in the ketene-forming transition state.

The Kin.46 kinase ribozyme was previously selected from a random-sequence RNA library that was loosely based on the sequence of a known ATP aptamer, based on its ability to catalyze transfer of the thiophosphate from ATPgS to its own 5' hydroxyl end. The reaction requires an oligonucleotide effector that is complementary to the 3' end of the ribozyme and that served as reverse transcription primer during the amplification steps of the original selection for activity (Fig. 1). Omitting the oligonucleotide reduces the observed catalytic rate constant (kobs) by 10 3 to 10-fold, indicating that the oligo acts as an allosteric effector that is necessary for full catalytic activity. The activator helix is separated from the substrate-binding internal guide sequence by a 5nt “linker” that appears to form long-range baseparing interaction with nucleotides within the catalytic core (S. Rhee, unpublished results). Binding of small ligands, such as metal ions and ATP, can also potentially influence the folded structure of the RNA. Divalent metal ions are well known for their abilities to stabilize nucleic acid secondary and tertiary structures, and for their potential catalytic roles in ribozyme-catalyzed reactions. For example, we recently found that topologically rearranged versions of Kin.46 exhibit markedly altered Mg dependence. Similarly, nucleotide binding by aptamers nucleates formation of the folded structure and induces order in the NTP binding pocket (adaptive binding). ATP recognition by Kin.46 is clearly distinct from ATP recognition by the original aptamer; key nucleotides required for ATP recognition are mutated in Kin.46, and the values of Km ATPgS and Km ATP for Kin.46 (~3 mM) are >10 times higher than Kd ATP for the aptamer (~1 μM). In this work, fluorescence emission from cy5-labeled ribozymes was monitored in order to investigate conformational dynamics as a function of ATP concentration and Mg ion. Truncated versions of Kin.46 ribozyme were obtained by internal cleavage or deletions (Fig. 1). Ribozyme130 was derived from the Kin.46 by just cleaving the most right-side loop, ribozyme119 was obtained by deletion of the loop and

In vitro selection was used to isolate Mg 2 + -dependent self-cleaving ribozymes with cis-cleavage activity from a pre-tRNA library having 40-mer random sequences attached to 5'-end of E. coli tRNA P h c . After 8 rounds ofSELEX (Systematic Evolution of Ligands by Exponential Enrichment), RNA molecules which can self-cleave at the high concentration of Mg 2 + were isolated. The selected ribozymes can carry out the self-cleavage reaction in the presence of 100 mM Mg 2 + but not in 10 mM Mg 2 + . The cleavage sites of the ribozymes are located at +3 and +4 of tRNA P h e , compared with +1 position of 5'-end cleavage site of pre-tRNA by RNase P. New RNA constructs deprived of its D stem-loop, anticodon stem-loop, variable loop and T stem-loop, respectively showed the cleavage specificity identical to a ribozyme having the intact tRNA structure. Also, the new ribozyme fused with both a ribozyme and tRNA L e u showed the cleavage activities at the various sites within its sequences, different from two sites of position +3 and +4 observed in the ribozyme with tRNA P h c . Our results suggest that the selected ribozyme is not structural-specific for tRNA.

Elimination reactions of have been studied under various conditions. When X was moderately electron-withdrawing, Y = H, and base-solvent was NH-MeCN, the reaction proceeded by the E2 mechanism via an E1cb-like transition state. Concave downward curve was noted in the Hammett plots. When X = 4-, Y = Cl, , and the base-solvent was in 70 mol % MeCN(aq), the reaction proceeded by the E2 mechanism. The mechanism changed to a competing E2 and E1cb when X = 4- and Y = H, MeO, and to the E1cb when X = 2,4-(, and Y = . From these results, a plausible pathway of the change of the mechanism from E2 to the E1cb extreme is proposed.

Recently, the development and use of single precursors for metal organic chemical vapor deposition (MOCVD) has been extensively focused on application to electronic devices. However, systematic design and synthesis of organic ligands appropriate for preparation of metal complexes with relevant chemical and physical properties, such as stability, volatility, and resistance to air and moisture have not received much attention. Generalization to prepare organic ligands for MOCVD precursors is especially important because the large scale synthesis of the metal complexes exclusively depends on the potential usefulness of the ligands. It is desirable for metal complexes to be in monomeric forms because mononuclear complexes generally show high vapor pressures and low sublimation or boiling temperatures. To do so, the coordinated atom of ligands should be crowded in its own environment with some substituents by keeping the coordinated atoms from bonding to another metal through bridging configuration. Therefore, pendant groups should be introduced into organic ligands. Some research results have been reported on the synthesis and application of organic ligands containing pendant groups. Herrmann reported his pioneering works on the synthesis of donor-functionalized alcohols and their application as bidentate ligands for the preparation of metal complexes. A variety of donor-functionalized alcohols which contain two alkyls on the α–carbon of the hydroxyl group were prepared and used to give metal complexes such as M(mmp)4 (mmp = 1-methoxy-2-methyl-2-propanolate; M = Zr, Hf), M(mmp)3 (M = Cr, Bi), 9 M(dmamp)3 (dmamp = 1-dimethylamino-2-methyl-2-propanolate; M = Y, Lu), Cu(dmamp)2. 12 The ligands in the complexes have pendant groups capable of coordinating to metals as bidentate ligands. Some of trifunctional alcohols have been used for the preparation and homoleptic complexes of alkaline-earth elements as well as transition metals. For larger cations such as Ba and Sr, it is necessary to introduce a neutral ancillary ligand possessing a sufficient number of donor sites or to incorporate a donor-functionalized feature into the anionic ligand to satisfy the multiple coordination requirement. Chi reported the successful preparation of alkalineearth metal complexes using a multi-donor site monoalcohol. Herein we disclose the synthesis and characterization of novel alcohols, which have pendant groups to stabilize the metal compounds by coordinating to the metal center in the formation of metal complexes. New alkoxyalcohols were prepared by the nucleophilic addition ring opening reaction between alkoxide anions and a highly reactive alkene oxide (epoxide).

Bongrae ChoDepartment of Applied Chemistry, Cheongju University, Cheongju 360-764, Korea. E-mail: brcho@cju.ac.krReceived March 14, 2013, Accepted March 27, 2013Key Words : Sequence motif, G-rich sequence RNA, 5'-UTR, RNA aptamer, SELEXGuanine-rich tracts are observed in terminal segments ofeukaryotic genomes.

The effects of amine donors (a:NH 2 , b:NMe 2 , c:NMePh, d:NPh 2 ) and conjugation length on the molecular hyperpolarizabilities of a series of dipolar molecules have been theoretically investigated by using CPHF/6-31G method. The first hyperpolarizabilities (β) of p-nitrobenzene derivatives increase with the donor in the order, NH 2 < NMe 2 < NMePh < NPh 2 , whereas slightly different order is observed in more conjugated derivatives, i.e., NH 2 < NPh 2 < NΜe 2 < NMePh. The result has been attributed to the extent of charge transfer and torsion angle. Moreover, the results show that "non-traditional" π-conjugation effect exists in small compounds and decreases as the conjugation length between donor and acceptor increases.

The G-quadruplexes play a biological role in DNA telomere ends,the purine-rich DNA strands of the oncogenic promoterelements such as c-myc and c-kit, and RNA 5'-untranslatedregion (UTR) in close to translational start sites. Telomereslocated at the ends of eukaryotic chromosomes are com-posed of the tandem DNA repeats of guanine-rich sequencesand essential for chromosome stability. They appear to playa critical role in cellular aging and cancer.

1,3,5-Tricyano-2,4,6-tris[2-(thiophen-2-yl)vinyl]benzene derivatives have been synthesized as a new type of octupolar nonlinear optical molecules and their linear and nonlinear optical properties were determined. The λ m a x values increased with the conjugation length and as the conjugation bridge was changed from phenyl to thienyl group. For phenyl and thiophene derivatives, the β value increased with conjugation length. In contrast, the b values of the thiophene derivatives were much smaller than the corresponding phenyl derivatives.

E-mail: brcho@cju.ac.krReceived June 27, 2011, Accepted August 9, 2011Key Words : G-rich RNA, RNA aptamer, RNase T1, Nuclease S1, RNase V1 RNA structure has sometimes been analyzed by thebiophysical method of NMR (nuclear magnetic resonance),which has not been popular because the RNA with smallsize only is available and a large amount of RNA is requiredfor the structural analysis with NMR.

Secondary structure models of Kin.46 ribozyme and the tethered ribozyme derived from Kin.46 (15-nt tether shown). Paired elements P1 through P4, connecting loop L3, and joining elements J1/2, J2/3, J3/2, J2/1 and J1/4 are indicated. The tethered ribozyme is built from the two strands, outer strand and inner strand. Thick line in the tethered ribozyme indicates 13-nt DNA oligonucleotide com-plementary to the 15-nt tether.

Secondary structures of two ribozyme versions derived from the Kin.46 self-thiophosphorylating ribozyme by the internal truncations. (A) A ribozyme119 derivative has 4 strands; a 7-mer, a upper (up) strand, a lower (lw) strand and an activating oligomer (AO)with 18 nucleotide. (B) A ribozyme103 derivative also has four diffe-rent strands but the length of a up strand and an lw strand is short. Only RNA portions at the RNA-RNA double strand region in a up strand were substituted for DNA portions.

The Kin.46 kinase ribozyme was selected for the transfer of the thiophosphate from ATP- γ-S to its own 5’ hydroxyl end in the presence of oligo-nucleotide effector which is complementary to its 3’ primer binding sequence (PBS) used in the ampli-fication steps during the original selection for acti-vity.

Ribozyme119 derivatives from the Kin.46 self-thiopho-sphorylating ribozyme by internal deletions has 3 strands; a left high (LH) strand, a lower (lw) strand and an activating oligomer (AO) with 18 nucleotide (A), and has 4 strands; a 7-mer, an upper (up) strand, a lower (lw) strand and an activating oligomer (AO) with 18 nucleotide (B). For a lw strand, dyes (Cy3 and Cy5) were incorporatedto the 5’-end during transcription with the class II promoter using AMP-dye-AMP as a primer. Dye-labeled AO was purchased.

Enzymes and chemical which have mainlybeen used for probing RNA structure in solution, are double-strand-specific RNase V1, single-strand-specific nucleaseS1, RNase T1 which has a specificity for a guanine in singlestrand region, and kethoxal (3-ethoxy-1,1-dihydroxy-2-butanone), which modify the N1 and N2 of guanine in thesingle strand. Hydroxyl radical (·OH) has also been used forthe structural analysis of RNA. Exposed nucleotides aredamaged by hydroxyl radical while nucleotides involved intertiary contacts are protected from damage, making it afavorable approach for establishing exterior/interior relationsfor RNA.

ion from the ribose 4' carbon leads to strand scission. The cleavage reaction of the kinase ribozyme with hydroxyl radical was quenched with thiourea and the products were analyzed by PAGE. Hydroxyl radical cleavage reaction was performed both in the absence and the presence of ATP (Fig. 3). Sequence C88GGGG92 was cleaved more strongly in the presence of ATP than at the absence of ATP, suggesting that this sequence which is conserved in ATP aptamers and close to catalytic core, is exposed by ATP in the secondary structure model of kinase ribozyme molecule. In conclusion, the structure of kinase ribozyme was analyzed in solution with probes such as RNase T1, RNase V1, kethoxal and hydroxyl radical generated from Fe/ EDTA/H2O2. The result suggested that 1) helices P2 and P3 are stabilized in the presence of ATP, 2) nucleotides in loop J3/2 are exposed in the presence of ATP, and 3) single strand region L3, which does not play an important role in the activity of this kinase ribozyme, is also exposed in the secondary structure model. Experimental Section Preparation of RNA. The kinase ribozyme strand was synthesized by run-off in vitro transcription with T7 RNA polymerase from the DNA template to which the T7 promoter was annealed. The resulting RNA was treated with CIP (calf intestinal alkaline phosphatase) to remove 5' end Figure 2. RNase T1 cleavage sites of ribozyme labeled at the 5'end, following kethoxal modification. Kethoxal modification reaction was performed at the 50 mM Mg concentration in the absence and presence of 10 mM ATP. The cleaved guanines which are in double strand, are indicated by arrows. A and P indicate the absence and the presence of ATP, respectively. Notations are as described in the legend to Figure 1. Figure 3. Hydroxyl radical cleavage sites of ribozyme labeled at the 5'-end. The cleavage reaction was performed at the 50 mM Mg concentration in the absence and the presence of 10 mM ATP. The strong cleavages were occurred in the presence of 10 mM ATP, compare with the absence of ATP and their cleavage sites were denoted by bar. A and P indicate absence and presence of ATP, respectively. Notations are as described in the legend to Figure 1. Figure 4. Schematic representation of possible secondary structure of kinase ribozyme. Open arrows indicate the sites cleaved by RNase T1 at the absence of ATP, and stars and filled arrows indicate guanines (in the double) not modified with kethoxal and the sites cleaved by hydroxyl radical in the presence of ATP, respectively. 788 Bull. Korean Chem. Soc. 2006, Vol. 27, No. 5 Notes phosphate and then labeled at the 5' end using [γ-P]ATP and T4 polynucleotide kinase. Enzymatic cleavage reaction. 5'-terminal radiolabeled kinase ribozyme strand and activating DNA oligomer were heated in KCl/Pipes buffer (200 mM KCl in 150 mM PipesKOH, pH 7.0) at 90 C for 2 min and allowed to cool to RT (~21 C). These were adjusted to a final concentration of 50 mM MgCl2. Then 0.1-1 unit of nuclease S1 or 0.001-0.01 unit of RNase V1 or 0.1-1 unit of RNase T1 was added to the above mixture and then the reaction mixture was incubated for 20 min at RT. The cleavage products were recovered by ethanol precipitation and separated on a 12% polyacylamide gel in 90 mM Tris-borate (pH 8.3) and 2.5 mM EDTA containing 7 M urea. Kethoxal modification and RNase T1 cleavage reaction. 5'-end labeled RNA and activating DNA oligomer were renatured as above. The renatured mixture was adjusted to a final concentration of 10 mM (or 0 mM) ATP in the presence of 50 mM MgCl2. 1 uL of kethoxal was dissolve in 10 uL of 100% ethanol and 10 uL of 70% ethanol and 1-2 uL of dissolved kethoxal solution was added to the renatured mixture, which was incubated for 20-25 min at RT. The modified products were recovered by ethanol precipitation and then digested with RNase T1 for 15 min in the presence of 7 M urea. The cleavage mixtures were subject to a denaturing 12% polyacylamide gel electrophoresis. Fe2+/EDTA/H2O2 cleavage reaction. 5'-end labeled RNA and activating DNA oligomer were renatured as above. The renatured mixture was adjusted to a final concentration of 10 mM (or 0 mM) ATP in the presence of 50 mM MgCl2. 1 uL of 0.4 mM Fe(NH4)2(SO4)2·6H2O (freshly prepared), 1 uL of 0.8 mM EDTA, pH 8.0, 1 uL of 0.3% H2O2 and 1 uL of 1 mM DTT were added to the mixture and the reaction mixture was incubated for 5-10 min at RT. The reaction was quenched by adding thiourea to 1.3 mM and the cleavage products were recovered by ethanol precipitation and separated on a 12% polyacylamide gel containing 7 M urea. Acknowledgement. I appreciate Dr. Donald H. Burke (Department of Molecular Microbiology & Immunology and Biochemistry, University of Missouri) for his helpful discussion.

E-mail: brcho@cju.ac.krReceived September 6, 2012, Accepted September 26, 2012Key Words : Guanine-rich RNA, RNA aptamer, RNase T1, Nuclease S1, RNase V1 RNA structure has sometimes been analyzed by bio-physical method such as NMR (nuclear magnetic resonance),which has not been popular because the RNA with smallsize only is available and a large amount of RNA is requiredfor the structural analysis with NMR.

were added to AHg2 inHEPES buffer, one- and two-photon excited fluorescence in-tensity increased gradually without affecting the absorptionspectra, presumably because of the blocking of the photoinduced electron transfer (PeT) by the complexation with themetal ion. The fluorescence enahncement factors [FEF = (F− F

Enzymatic probing of RNA aptamer 13-1-15 labeled at the 5’-end. The RNA was partially digested with RNase T1 (A), RNase V1 (B) and nuclease S1 (C). The cleaved nucleotides are indicated by arrows. Region A7UA9 was protected from RNase V1 digestion by the hairpin RNA. Lane C, control; lane T, the denatured RNA treated with RNase T1; lane OH, partial alkaline ladder; lanes R and R+S-l, enzymatic cleavages in the absence of and the presence of stem-loop RNA, respectively.

RNase T1, RNase S1, RNase V1, RNA aptamer, Stem-loop RNARNA structure can be analyzed by biophysical or bio-chemical methods. X-ray crystallography or NMR (nuclearmagnetic resonance) involved in biophysical method has notbeen popular so far because it is not easy to make RNAcrystal for X-ray crystallography and the small size of RNAonly is available for the structural analysis with NMR.

Autokinase, ATP, FRET, TMRThe Kin.46 kinase ribozyme was selected for the transferof the thiophosphate from ATP γS to its own 5' hydroxyl end.The reaction requires an oligonucleotide effector that iscomplementary to the 3' primer binding sequence (PBS) ofthe ribozyme and this effector served as reverse transcriptionprimer during the amplification steps of the original selec-tion for activity (Fig. 1).

rRNA The eukaryotic ribosome consists of two subunits, 60Slarge and 40S small. The 60S large subunit contains 5SrRNA, 5.8S rRNA and 28S rRNA, and the 40S smallsubunit has 18S rRNA. Presently, the rRNAs are thought tobe directly involved in the ribosome function. There isextensive biochemical, genetic and phylogenetic evidencefor the functional role of ribosomal RNAs. This includes then i ( ng NA Ri d bin n, t io t mc RNA see NA i rR nof l on i at ip ic rt a pA, P and E sites), ribosomal subunit association, proofread-ing, factor binding, antibiotic interaction, termination andthe peptidyltransferase function.