Nonenzymatic template-directed synthesis on hairpin oligonucleotides. 2. Templates containing cytidine and guanosine residues

We have prepared hairpin oligonucleotides in which a 5'-terminal single-stranded segment contains cytidylate (C) and guanylate (G) residues. When these hairpin substrates are incubated with a mixture of cytidine 5'-phosphoro(2-methly)imidazolide (2-MeImpC) and guanosine 5'-phosphoro(2-methyl)imidazolide (2-MeImpG), the 5'-terminal segment acts as a template to facilitate sequence-specific addition of G and C residues to the 3'-terminus of the hairpin. If an isolated G residue is present at the 3'-end of the template strand, it is copied regiospecifically in the presence of 2-MeImpC and 2-MeImpG to give a product containing an isolated C residue linked to its G neighbors by 3'-5'-internucleotide bonds. However, if only 2-MeImpC is present in the reaction mixture, very little reaction occurs. Thus, the presence of 2-MeImpG catalyzes the incorporation of C. If the template strand contains a short sequence of G residues, it is copied in the presence of a mixture of 2-MeImpC and 2-MeImpG. If only 2-MeImpC is present in the reaction mixture, efficient synthesis occurs to give a final product containing one fewer C residue than the number of G residues in the template.     

Synthesis of oligonucleotides with a 2'-cap at the 3'-terminus via reversed phosphoramidites

[reaction: see text] A method is presented for the synthesis of single compounds or small combinatorial libraries of oligonucleotides with 2'-acylamido-2'-deoxyuridine residues at the 3'-terminus. Selection experiments identified the residue of anthraquinone-2-carboxylic acid as a "molecular cap" that increases the UV melting point of the duplex (5'-ACGCGU-3')(2) by up to 28 degrees C compared to the unmodified control duplex.     

A 2'-acylamido cap that increases the stability of oligonucleotide duplexes

[structure: see text]. Reported here is the synthesis of oligonucleotides containing a 2'-acylamido-2'-deoxyuridine residue at their 3'-terminus. Compared to control sequences bearing a thymidine residue, the quinolone-capped duplexes give higher UV melting points. In the case of (5'-ACGCGU-NA-2')2, where NA denotes a nalidixic acid residue, the melting point increase is up to 22 degrees C over that of (ACGCGT)2.     

Optimizing the stacking moiety and linker of 2'-acylamido caps of DNA duplexes with 3'-terminal adenine residues

Reported here is the synthesis of oligodeoxynucleotides with a 3'-terminal 2'-acylamido-2'-deoxyadenosine residue. The route to these oligonucleotides employs an N,O-Alloc-protected 5'-phosphoramidite of 2'-amino-2'-deoxyadenosine that was prepared in 11 steps from arabinoadenosine. Small combinatorial libraries of oligonucleotides were generated via acylation with a mixture of linker amino acids and subsequent acylation of their amino groups. Mass spectrometrically monitored nuclease selection assays led to oligonucleotides whose 2'-substituent increases the thermal stability of the DNA duplexes. A linker with three methylene groups between a perylene stacking moiety and the amido group gives a UV-melting point increase of up to 27.9 degrees C for the DNA sequence (TGCGCA*)2, where A* denotes the 2'-acylamidoadenosine residue. The same acylamido group improves mismatch discrimination at the terminal position with a melting point depression of >or=7 degrees C for any of the three mismatches in the target sequence of the octamer 5'-AGGTTGAA-3'. These results demonstrate how even a very weakly base-pairing nucleotide at the 3'-terminus of a DNA probe strand can be enforced to engage in strong and highly sequence-selective base-pairing interactions.     

D-glucose-derived polymer intermediates as templates for the synthesis of ultrastable and redispersible gold colloids

A two-stage hydrothermal process was developed for the synthesis of highly dispersed Au colloids. In the first stage, a novel glucose-derived polymer template was prepared by the hydrothermal treatment of glucose at 160 degrees C. This template was then further used in the next step to synthesize highly dispersed gold (Au) colloids by hydrothermal treatment with HAuCl(4.) The templates treated at 160 degrees C with changing reaction times had different templating effects toward Au species. The 3-h treated template was able tightly adhere to the Au colloids. As a result, an unusual stability was observed for the prepared Au particles that could be repeatedly precipitated and redispersed with the template in H(2)O and were also stable against heating (below 160 degrees C) and aging. Meanwhile, the 5-h and 7-h treated templates had much poorer templating effects to Au species, leading to severe aggregation of the Au colloids immobilized on them. The various templating effects were correlated to the different structural features of the templates. Compared to the 5- or 7-h treated templates that were deeply carbonized, the 3-h treated template was only slightly carbonized, thus possessing a lot of functional and hydrophilic O-containing groups that could bind to Au species. These differences in templating ability were also observed in the Au samples prepared by the sonication-assisted method. The highly dispersed Au colloids immobilized on the 3-h treated template were tested for CO oxidation, and a good catalytic activity and stability for CO oxidation was observed.     

Kinetic analysis of an efficient DNA-dependent TNA polymerase

alpha-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives and potential progenitors of present-day beta-d-2'-deoxyribofuranosyl nucleoside triphosphates (dNTPs). Therminator DNA polymerase, a variant of the 9 degrees N DNA polymerase, is an efficient DNA-directed threosyl nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and dNTPs from a DNA primer-template complex and carried out parallel experiments with a chimeric DNA-TNA primer-DNA template containing five TNA residues at the primer 3'-terminus. Remarkably, no drop in the rate of TNA incorporation was observed in comparing the DNA-TNA primer to the all-DNA primer, suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl(2). These results indicate that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective catalyst of TNA polymerization despite changes in the geometry of the reactants.     

Pore size tailoring in large-pore SBA-15 silica synthesized in the presence of hexane

Large-pore SBA-15 silicas were synthesized using poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) block copolymer Pluronic P123 as a template and hexane as a micelle expander. The reaction was initially carried out at 15 degrees C, followed by the heating of the synthesis gel at temperatures from 40 to 130 degrees C. Small-angle X-ray scattering data indicate that highly ordered two-dimensional hexagonal material (SBA-15 structure) formed at 15 degrees C and was preserved even after 5 days of heating at 130 degrees C. The unit-cell parameter for as-synthesized SBA-15 silicas was about 16.5 nm and increased only slightly after the heat treatment, whereas the unit-cell parameter after calcination was appreciably larger (16 vs 14 nm) for materials that were subjected to the thermal treatment. The pore size distribution of SBA-15 formed at 15 degrees C was narrow and centered at approximately 9.5 nm, which is close to the upper limit of pore diameters typically reported for SBA-15. The presence of constrictions in the pores of this material was evident. The heat treatment led to the elimination of the constrictions and to the pore diameter increase to 15 nm or more, tailored by the selection of appropriate treatment temperature and time. The pore size increase was the fastest during the first day of treatment, but it continued for at least 5 days. The pore size distribution broadened as the time of the treatment increased beyond 1 day. The pore size increase appears to be primarily related to the decrease in the degree of shrinkage during the calcination (removal of the template) and the decrease in the pore wall thickness.     

Tuning the reaction site for enzyme-free primer-extension reactions through small molecule substituents

The replication of genetic information relies on the template-directed extension of DNA primers catalyzed by polymerases. The active sites of polymerases accept four different substrates and ensure fidelity and processivity for each of them. Because of the pivotal role of catalyzed primer extension for life, it is important to better understand this reaction on a molecular level. Here we present results from primer-extension reactions performed with chemical systems that show high reactivity in the absence of polymerases. Small molecular caps linked to the 5'-terminus of templates are shown to enhance the rate and selectivity of primer extension driven by 2-methylimidazolides as activated monomers for any of the four different templating bases (A, C, G, and T). The most consistent effect is provided by a stilbene carboxamide residue, rather than larger aromatic or aliphatic substituents. Up to 20-fold rate enhancements were achieved for the reactions at the terminus of the template. The preference for a medium size cap can be explained by competing interactions with both the oligonucleotides and the incoming deoxynucleotide. The data also show that there is no particularly intractable problem in combining promiscuity with fidelity. Exploratory experiments involving a longer template and a downstream-binding strand with a 5'-cap show up to 38-fold rate acceleration over the same reaction templated by a single overhanging nucleotide.     

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.     

Folding of a miniprotein with mixed fold

Using the 28 residue betabetaalpha protein FSD-EY as a target system, we examine correction terms for the ECEPP/3 force field. We find an increased probability of formation of the native state at low temperatures resulting from a reduced propensity to form alpha helices and increased formation of beta sheets. Our analysis of the observed folding events suggests that the C-terminal helix of FSD-EY is much more stable than the N-terminal beta hairpin and forms first. The hydrophobic groups of the helix provide a template which promotes the formation of the beta hairpin that is never observed to form without the helix.     

Pyrosequencing trade mark technology at elevated temperature

To date, the Pyrosequencing trade mark technology has been performed at 28 degrees C due to the low thermostability of the firefly luciferase. In this study, firefly luciferase was stabilized in the presence of glycine betaine, allowing DNA sequencing at 37 degrees C. By increasing the temperature to 37 degrees C, false signals due to primer-dimers and loop-structures were decreased significantly. In addition, a combination of (i) replacing the natural dGTP with 7'deaza-dGTP in the polymerase chain reaction (PCR), (ii) 1.6 M glycine betaine, and (iii) an increase of the temperature to 37 degrees C enabled us to sequence a DNA template with the initial sequence 3'-ATGGCCCGGGGGGGAGCTCCA em leader 5'. Furthermore, we describe a method to analyze if a primer forms a primer-dimer with extendable 3'-ends.     

A novel catechol-based universal support for oligonucleotide synthesis

A novel universal support for deoxyribo- and ribonucleic acid synthesis has been developed. The support, constructed from 1,4-dimethoxycatechol, represents an improvement over existing universal supports because of its ability to cleave and deprotect under mild conditions in standard reagents. Because no nonvolatile additives are required for cleavage and deprotection, the synthesized oligonucleotides do not require purification prior to use in biochemical assays. Using reverse phase HPLC and electrospray mass spectroscopy, it was determined that oligonucleotides synthesized on the universal support (UL1) 3'-dephosphorylate quickly (9 h in 28-30% ammonium hydroxide (NH4OH) at 55 degrees C, 2 h in 28-30% NH4OH at 80 degrees C, or <1 h in ammonium hydroxide/methylamine (1:1) (AMA) at 80 degrees C). Oligonucleotides used as primers for the polymerase chain reaction (PCR) assay were found to perform identically to control primers, demonstrating full biological compatibility. In addition, a method was developed for sintering the universal support directly into a filter plug which can be pressure fit into the synthesis column of a commercial synthesizer. The universal support plugs allow the synthesis of high-quality oligonucleotides at least 120 nucleotides in length, with purity comparable to non-universal commercial supports and approximately 50% lower reagent consumption. The universal support plugs are routinely used to synthesize deoxyribo-, ribo-, 3'-modified, 5'-modified, and thioated oligonucleotides. The flexibility of the universal support and the efficiency of 3'-dephosphorylation are expected to increase the use of universal supports in oligonucleotide synthesis.     

Catalytic enantioselective desymmetrization of meso-N-acylaziridines with TMSCN

A catalytic enantioselective desymmetrization of meso-N-p-nitrobenzoylaziridines with TMSCN was developed using a chiral gadolinium catalyst generated from Gd(OiPr)3 and d-glucose-derived ligand 1. In this reaction, the addition of a catalytic amount of trifluoroacetic acid (TFA) improved enantioselectivity. High enantioselectivity was obtained from a range of meso-aziridines at 0-60 degrees C. The product could be easily transformed into beta-amino acids. Thus, the developed catalytic enantioselective desymmetrization reaction allowed for efficient catalytic synthesis of chiral cyclic beta-amino acids. The incorporation of TFA into the catalyst complex was observed using ESI-MS. Generation of this new complex might be the origin of the improved enantioselectivity.     

Double addition of grignard reagents to N-glycosyl nitrones: a new tool for the construction of enantiopure azaheterocycles

[Reaction: see text] C-Phenyl-N-erythrosylnitrone 3 behaves as a C1,C1' bis-electrophile, undergoing a double addition of Grignard reagents in a domino fashion to afford acyclic hydroxylamines 4. The reaction proceeds at 0 degrees C with variable degrees of diastereoselectivity, from moderate to good, mainly depending on the organomagnesium reagent used. The usefulness of compounds 4 has been exemplified with the synthesis of pyrroloazepine 12 through a ring closing metathesis key step.     

A synthetic approach to diverse 3-acyltetramic acids via O- to C-acyl rearrangement and application to the total synthesis of penicillenol series

For the efficient approach to medicinally important α-branched 3-acyltetramic acids, the key reaction of O- to C- acyl rearrangement using α-amino-acid-derived 4-O-acyltetramic acids was extensively examined in the presence of various metal salts. Use of CaCl(2) or NaI dramatically changed the results in the reaction efficiency and rapidly brought about the desired α-branched 3-acyltetramic acids in markedly improved yields. We also discuss an epimerization at C5 stereocenter under the rearrangement conditions as well as the tolerance for structural variation at C3 and C5. In addition to the preceding success in the total synthesis of new cytotoxic tetramic acid, penicillenol A(1), this methodology could be also applied to the first total synthesis of penicillenol A(2).     

Synthesis and Solution Conformation of β‐Hairpin Mimetics Utilizing a Template Derived from (2S,3R,4R)‐Diaminoproline

A novel template was synthesized for stabilizing β‐hairpin conformations in cyclic peptide mimetics. The template is a diketopiperazine derived formally from L ‐aspartic acid and (2S,3R,4R)‐diaminoproline, the latter being available by an efficient synthetic route from vitamin C. The template was incorporated by solid‐phase peptide synthesis into a cyclic loop mimetic containing the sequence (‐Ala‐Asn‐Pro‐Asn‐Ala‐Ala‐template‐). This mimetic was shown by NMR to adopt a stable β‐hairpin conformation in (D₆)DMSO solution. The template may prove to be generally useful for creating small‐molecule mimetics of hairpin loops on proteins of diverse function.     

Combinatorial Biomimetic Chemistry: Parallel Synthesis of a Small Library of β‐Hairpin Mimetics Based on Loop III from Human Platelet‐Derived Growth Factor B

Combinatorial diversity in hypervariable β‐hairpin loops is exploited by the immune system to select binding sites on antibodies for a wide variety of different protein antigens. In a first step towards mimicking this strategy in vitro, for the selection of novel protein ligands, an approach is described here for the parallel synthesis of small libraries of conformationally defined β‐hairpin protein epitope mimetics. Starting from a protruding hairpin loop in platelet‐derived growth factor B (PDGF‐B), 8 and 12 residues were first transplanted from the protein to a D ‐Pro‐L ‐Pro template, to afford the cyclic peptide‐loop mimetics 1 and 2 , respectively. NMR and MD studies in aqueous solution show that both mimetics populate conformations which closely mimic the β‐hairpin in the crystal structure of the native protein (Fig. 5). Based on 1 as a scaffold, a library of 24 mimetics was synthesized in which the four residues at the tip of the loop (VRKK) were held constant, and flanking residues at positions 1, 2, 7, and 8 in the hairpin were varied (Fig. 7). The library was prepared by parallel synthesis in a two‐stage solid‐phase assembly/solution‐phase cyclization process. The products were analyzed by MS, NMR, and CD. 2D‐NOESY revealed for most library members characteristic long‐range NOEs that show that the hairpin conformation is stably maintained. The results suggest that this approach may be useful for the synthesis of much larger libraries of peptide and protein mimetics based on a β‐hairpin scaffold.     

微波场中T型分子筛的合成及晶化研究

研究了微波场中T型分子筛的结晶过程。考察了微波加热体系中合成参数如合成时间、溶胶组成、反应压力和模板剂用量对分子筛晶化的影响。微波加热的主要优点是减少合成时间,无模板剂的溶胶在普通加热条件下的晶化时间需要120 h,而在微波场中则仅需要20～25 h。另一方面,由于微波的快速加热特性促进了稳定相钙十字沸石的生成,从而减小了次稳定相T型分子筛的结晶区间。在未添加模板剂条件时,100 ℃下微波水热合成T型分子筛的结晶区间为：20≤n_SiO2/n_Al2O3≤22和0.31≤ n_M2O/n_SiO2≤0.33(其中M₂O=Na₂O+K₂O, n_Na/n_K=3和n_M2O/n_SiO2=11.70)。在普通加热和微波加热合成体系中,添加模板剂均能扩大结晶区间,同时还可以进一步减少合成时间。     

Kinetics of template-directed pyrophosphate-linked dideoxyguanylate synthesis as a function of 2-MeImpdG and poly(C) concentration: insights into the mechanism.

Aqueous solutions of deoxyguanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpdG, yield primarily deoxyguanosine 5'-monophosphate, 5'dGMP, and pyrophosphate-linked dideoxyguanylate, dG5'ppdG, abbreviated G2p (see Chart 1). The initial rate of G2p formation, d[G2p]/dt in M h-1, determined at 23 degrees C, pH 7.8, 1.0 M NaCl and 0.2 M Mg2+ by timed high-performance liquid chromatography (HPLC) analysis, exhibits a second-order dependence on 2-MeImpdG concentration, [G]o, indicating a bimolecular mechanism of dimerization in the range 0.02 M < or = [G]o < or = 0.09 M. In the presence of polycytidylate, poly(C), G2p synthesis is accelerated and oligodeoxyguanylate products are formed by incorporation of 2-MeImpdG molecules. The kinetics of G2p formation as a function of both monomer and polymer concentration, expressed in C equivalents, were also determined under the above conditions and exhibited a complex behavior. Specifically, at a constant [poly(C)], values of d[G2p]/dt typically increased with [G]o with a parabolic upward curvature. At a constant [G]o, values of d[G2p]/dt increase with [poly(C)], but level off at the higher poly(C) concentrations. As [G]o increases this saturation occurs at a higher poly(C) concentration, a result opposite to expectation for a simple complexation of two reacting monomers with the catalyst prior to reaction. Nevertheless, these results are shown to be quantitatively consistent with a template-directed (TD) mechanism of dimerization where poly(C) acts as the template to bind 2-MeImpdG in a cooperative manner and lead, for the first time, to the formulation of principles that govern template-directed chemistry. Analysis of the kinetic data via a proposed TD cooperative model provides association constants for the affinity between polymer and monomer and the intrinsic reactivity of 2-MeImpdG toward pyrophosphate synthesis. To the best of our knowledge, poly(C)/2-MeImpdG is the first system that could serve as a textbook example of a TD reaction under conditions such that the template is fully saturated by monomers and under conditions that it is not.     

Effectiveness of the suzuki-miyaura cross-coupling reaction for solid-phase peptide modification

The Suzuki-Miyaura (SM) cross-coupling reaction has recently become one of the most efficient methods for C-C bond construction opening a wide range of opportunities in organic synthesis. This study focused on the evaluation of the use of the SM reaction to modify peptides using a solid-phase synthesis approach, an avenue that was still not investigated intensively. We used as a peptide model [Ala (1,2,3), Leu (8)]Enk linked to a polystyrene support on which it was previously assembled. The aromatic residues Tyr (4) and Phe (7) of [Ala (1,2,3), Leu (8)]Enk were respectively substituted with p-iodo-Phe, and an SM-related strategy was developed. Results indicated that the reaction conditions involving K 3PO 4 or Na 2CO 3 (base), DMF (solvent), Pd(PPh 3) 4 (catalyst), and temperatures ranging from 50 to 80 degrees C during 20 h were found as optimal. Finally applying those optimal conditions, a series of [Ala (1,2,3), Leu (8)]Enk analogs modified at Tyr (4) or Phe (7) positions was synthesized using diverse boronic acid derivatives.