Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization

A polymerase ribozyme has been generated that uses nucleoside triphosphates to elongate an RNA primer by the successive addition of nucleotides complementary to an RNA template. Its polymerization is accurate, with an average error rate less than 3%, and it is general in terms of the sequence and the length of the primer and template RNAs. To begin to understand how the substrate contacts contribute to this accurate and general activity, we investigated which primer and template 2'-hydroxyl groups are involved in substrate recognition. We identified eight positions where 2'-deoxy substitutions can influence polymerization kinetics. All eight are within five nucleotides of the primer 3' terminus. Some, but not all, of the 2'-deoxy effects appear to be sequence dependent. These results begin to build a picture of how the polymerase ribozyme recognizes its substrates.     

Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical

In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.     

Negative-ion mass spectrometry of substituted adenine bases and adenosine nucleosides

The negative-ion chemical ionization (ammonia, 5 Pa source pressure) mass spectra of a series of substituted adenine bases, adenosine nucleosides, and the trimethylsilyl derivatives of the nucleosides are described. Selected ions from these spectra were subject to collisionally activated dissociation with mass-analysed ion kinetic energy (CAD/MIKE) analysis of the products and the spectra assessed for information content. In addition to observing strong peaks due to quasimolecular ions and heterocyclic-base ions, it proved possible to differentiate between 2'-, 3'- and 5'-deoxy and between 2'- and 3'-O-methyl isomers. The negative-ion chemical ionization spectra of four methyladenines are essentially identical, but could be clearly distinguished from each other by CAD/MIKE analysis.     

Deoxy Derivatives of L-like 5'-Noraristeromycin

Several base variations of 2'- and 3'-deoxy derivatives of (+)-4'-deoxy-5'-noraristeromycin have been prepared from enantiomerically pure precursors following standard purine nucleoside construction. These carbocyclic nucleosides were evaluated against hepatitis B virus (HBV) and found to be inactive. No cytotoxicity to the cell line was observed.     

Photochemistry of 4'-benzophenone-substituted nucleoside derivatives as models for ribonucleotide reductases: competing generation of 3'-radicals and photoenols

Ribonucleotide reductases (RNRs) catalyze the 2'-reduction of ribonucleotides, thus providing 2'-deoxyribonucleotides, the monomers for DNA-biosynthesis. The current mechanistic hypothesis for the catalysis effected by this class of enzymes involves a sequence of radical reactions. A 3'-hydrogen abstraction, effected by a radical at the enzyme's active site, is believed to initiate the catalytic cycle. As models for this substrate-enzyme interaction, the photochemically induced intramolecular hydrogen abstraction in a series of 4'-benzophenone-substituted nucleoside analogues was studied. Model compounds with hydroxy-, methoxy-, mesyloxy-groups or a cyclic carbonate in 2'- and 3'-positions were investigated. Depending on the substitution pattern, two different types of photoproducts were observed: Those which result from photoenol formation (gamma-H-abstraction) and those which result from abstraction of the 3'-H-atom (delta-H-abstraction). Photoenol formation was further supported by H/D-exchange experiments. Thus, the 3'-H-abstraction postulated as the initial step in RNR action was successfully modeled by photolysis of 4'-benzophenone-substituted nucleoside analogues. The regioselectivity of the photochemical H-abstraction and thus of the product distribution as a function of the 2'- and 3'-substituents was rationalized on the basis of a conformational analysis of the four model systems, utilizing molecular mechanics simulations.     

Nonenzymatic, template-directed ligation of oligoribonucleotides is highly regioselective for the formation of 3'-5' phosphodiester bonds

We have found that nonenzymatic, template-directed ligation reactions of oligoribonucleotides display high selectivity for the formation of 3'-5' rather than 2'-5' phosphodiester bonds. Formation of the 3'-5'-linked product is favored regardless of the metal ion catalyst or the leaving group, and for several different ligation junction sequences. The degree of selectivity depends on the leaving group: the ratio of 3'-5'- to 2'-5'-linked products was 10-15:1 when the 5'-phosphate was activated as the imidazolide, and 60-80:1 when the 5'-phosphate was activated by the formation of a 5'-triphosphate. Comparison of oligonucleotide ligation reactions with previously characterized single nucleotide primer extension reactions suggests that the strong preference for 3'-5'-linkages in oligonucleotide ligation is primarily due to occurence of ligation within the context of an extended Watston-Crick duplex. The ability of RNA to correctly self-assemble by template-directed ligation is an intrinsic consequence of its chemical structure and need not be imposed by an external catalyst (i.e., an enzyme polymerase); RNA therefore provides a reasonable structural basis for a self-replicating system in a prebiological world.     

Metal ion complexes of antivirally active nucleotide analogues. Conclusions regarding their biological action

Acyclic nucleoside phosphonates (ANPs), i.e., analogues of (2'-deoxy)nucleoside 5'-monophosphates, have been studied during the past 15 years for their potential as antiviral drugs. One of these compounds, 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA; Adefovir) was recently approved in the form of its bis(pivaloyloxymethyl)ester (Adefovir dipivoxil) for use in hepatitis B therapy, a disease evoked by a DNA virus. Diphosphorylated PMEA(2-), i.e., PMEApp(4-), is initially recognized by nucleic acid polymerases as an excellent substrate, but after insertion in the growing nucleic acid chain, this is terminated due to the lack of a 3'-hydroxy group. Based on the metal ion-binding properties of PMEApp(4-) it can be explained why the ether oxygen in the aliphatic chain, R-CH(2)-O-CH(2)-PO(3)pp(4-), is compulsory for a useful biological activity. Consequently, this critical review presents an overview on the coordination chemistry of various ANPs and correlates this to their biological properties.     

Addition of difluorocarbene to 4',5'-unsaturated nucleosides: synthesis and deoxygenation reactions of difluorospirocyclopropane nucleosides

Synthetic routes to 4'-(2,2-difluorospirocyclopropane) analogues of adenosine, cytidine, and uridine are described. Treatment of 2',3'-O-isopropylidene-4',5'-unsaturated compounds derived from adenosine and uridine with difluorocarbene (generated from PhHgCF3 and NaI) gave diastereomeric mixtures of the 2,2-difluorospirocyclopropane adducts. Stereoselectivity resulting from hindrance by the isopropylidene group favored addition at the beta face. Removal of base and sugar protecting groups gave new difluorospirocyclopropane nucleoside analogues. The protected uridine analogue was converted into its cytidine counterpart via a 4-(1,2,4-triazol-1-yl) intermediate. Stannyl radical-mediated deoxygenation of the 3'-O-TBS-2'-thionocarbamate derivatives gave the 2'-deoxy products of direct hydrogen transfer. In contrast, identical treatment of the 2'-O-TBS-3'-thionocarbamate isomers resulted in opening of the vicinal difluorocyclopropane ring upon generation of a C3' radical followed by homoallylic hydrogen transfer to give 4'-(1,1-difluoroethyl)-3',4'-unsaturated nucleoside derivatives. Structural aspects and biological effect considerations are discussed.     

烷基修饰寡聚脱氧核苷酸磷酸残基的化学合成及稳定性研究

分别采用格氏试剂和三氯化磷三步取代法合成了4个新的烷基修饰磷酸残基的亚磷酸酰胺单体, 其结构经1H NMR和31P NMR表征. 利用这些单体合成模型序列5'-dTTTx TT-3', 考察了单体及寡聚核苷酸序列在DNA/RNA合成条件下的稳定性, 提出了固相合成含有烷基修饰磷酸残基的寡聚核苷酸序列裂解及脱保护条件.     

Reversed Assembly of Dyes in an RNA Duplex Compared with Those in DNA

We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4′‐methylthioazobenzene, and thiazole orange) on D ‐threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3′‐side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5′‐side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H‐aggregates) even on an A‐type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA–thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA–dye conjugates are potentially useful probes for real‐time monitoring of RNA interference (RNAi) mechanisms.     

Synthesis, gene silencing, and molecular modeling studies of 4'-C-aminomethyl-2'-O-methyl modified small interfering RNAs

The linear syntheses of 4'-C-aminomethyl-2'-O-methyl uridine and cytidine nucleoside phosphoramidites were achieved using glucose as the starting material. The modified RNA building blocks were incorporated into small interfering RNAs (siRNAs) by employing solid phase RNA synthesis. Thermal melting studies showed that the modified siRNA duplexes exhibited slightly lower T(m) (～1 °C/modification) compared to the unmodified duplex. Molecular dynamics simulations revealed that the 4'-C-aminomethyl-2'-O-methyl modified nucleotides adopt South-type conformation in a siRNA duplex, thereby altering the stacking and hydrogen-bonding interactions. These modified siRNAs were also evaluated for their gene silencing efficiency in HeLa cells using a luciferase-based reporter assay. The results indicate that the modifications are well tolerated in various positions of the passenger strand and at the 3' end of the guide strand but are less tolerated in the seed region of the guide strand. The modified siRNAs exhibited prolonged stability in human serum compared to unmodified siRNA. This work has implications for the use of 4'-C-aminomethyl-2'-O-methyl modified nucleotides to overcome some of the challenges associated with the therapeutic utilities of siRNAs.     

Four unit linking groups IV. Liquid crystals of positive dielectric anisotropy

Three separate series of new materials of weak to strongly positive dielectric anisotropy have been prepared. Each series contains four sub-sets of materials each incorporating a different four unit linking group (i.e., C₄H₈, C₄H₆, C₃H₆O and C₃H₄O) and the same series of end groups (i.e. F, CN and OCF₃) in various substitution patterns. The synthesis and liquid crystal transition temperatures of these novel substances are described and compared with those of the corresponding materials incorporating standard central linkages (i.e.-, C₂H₄, CH₂O, COO). The effect of an additional trans carbon-carbon double bond in the terminal alkyl chain and in the central linking unit has also been studied.     

Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages

We previously used in vitro selection to identify several classes of deoxyribozymes that mediate RNA ligation by attack of a hydroxyl group at a 5'-triphosphate. In these reactions, the nucleophilic hydroxyl group is located at an internal 2'-position of an RNA substrate, leading to 2',5'-branched RNA. To obtain deoxyribozymes that instead create linear 3'-5'-linked (native) RNA, here we strategically modified the selection approach by embedding the nascent ligation junction within an RNA:DNA duplex region. This approach should favor formation of linear rather than branched RNA because the two RNA termini are spatially constrained by Watson-Crick base pairing during the ligation reaction. Furthermore, because native 3'-5' linkages are more stable in a duplex than isomeric non-native 2'-5' linkages, this strategy is predicted to favor the formation of 3'-5' linkages. All of the new deoxyribozymes indeed create only linear 3'-5' RNA, confirming the effectiveness of the rational design. The new deoxyribozymes ligate RNA with k(obs) values up to 0.5 h(-1) at 37 degrees C and 40 mM Mg2+, pH 9.0, with up to 41% yield at 3 h incubation. They require several specific RNA nucleotides on either side of the ligation junction, which may limit their practical generality. These RNA ligase deoxyribozymes are the first that create native 3'-5' RNA linkages, which to date have been highly elusive via other selection approaches.     

The 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleosides in the solid-phase synthesis of oligoribonucleotides

Emerging RNA-based technologies for controlling gene expression have triggered a high demand for synthetic oligoribonucleotides and have motivated the development of ribonucleoside phosphoramidites that would exhibit coupling kinetics and coupling efficiencies comparable to those of deoxyribonucleoside phosphoramidites. To fulfill these needs, the novel 4-(N-dichloroacetyl-N-methylamino)benzyloxymethyl group for 2'-hydroxyl protection of ribonucleoside phosphoramidites 9a-d has been implemented (Schemes 1 and 2). The solid-phase synthesis of AUCCGUAGCUAACGUCAUGG was then carried out employing 9a-d as 0.2 M solutions in dry MeCN and 5-benzylthio-1H-tetrazole as an activator. The coupling efficiency of 9a-d averaged 99% within a coupling time of 180 s. Following removal of all base-sensitive protecting groups, cleavage of the remaining 2'-[4-(N-methylamino)benzyl] acetals from the RNA oligonucleotide was effected in buffered 0.1 M AcOH (pH 3.8) within 30 min at 90 degrees C. RP-HPLC and PAGE analyses of the fully deprotected AUCCGUAGCUAACGUCAUGG were comparable to those of a commercial RNA oligonucleotide sharing an identical sequence. Enzymatic digestion of the RNA oligomer catalyzed by bovine spleen phosphodiesterase and bacterial alkaline phosphatase revealed no significant amounts of RNA fragments containing (2'-->5')-internucleotidic phosphodiester linkages or noteworthy nucleobase modifications.     

Molecular recognition studies on supramolecular systems. 32. Molecular recognition of dyes by organoselenium-bridged bis(beta-cyclodextrin)s.

A series of novel bis(beta-cyclodextrin)s tethered with organoselenium linkers, i.e., 6,6'-(o-phenylene-diseleno)-bridged bis(beta-cyclodextrin) (2), 6,6'-[2,2'-diselenobis(benzoyloxy)]-bridged bis(beta-cyclodextrin) (3), and 6,6'-[2,2'-diselenobis[2-(benzoylamino)ethylamino]]-bridged bis(beta-cyclodextrin) (4), were synthesized from beta-cyclodextrin (1). The inclusion complexation behavior of 1-4 with some dyes, such as 8-anilinonaphthalenesulfonate (ANS), Brilliant Green, Crystal Violet, Tropaeolin OO, Auramine O, and Methyl Orange, was investigated in aqueous phosphate buffer solution (pH 7.20) at 25 degrees C by UV-vis, fluorescence, and circular dichroism spectrometry, as well as fluorescence lifetime measurements. The complex stability constants (Ks) and Gibbs free energy changes (delta Go) for the stoichiometric 1:1 inclusion complexation of 1-4 with the dyes were obtained by the spectrophotometric or spectropolarimetric titrations. The bis(beta-cyclodextrin)s 2-4 showed much higher affinities toward these guest dyes than native beta-cyclodextrin 1 with fairly good molecular selectivities. The cooperative binding abilities of these bis(beta-cyclodextrin)s are discussed from the viewpoints of size/shape-fit interaction, induced-fit concept, and multiple recognition mechanism.     

Planar Chiral Phosphoramidites with a Paracyclophane Scaffold: Synthesis,Gold(I) Complexes,and Enantioselective Cycloisomerization of Dienynes

The key structural feature of the new phosphoramidites is a paracyclophane scaffold in which two aryl rings are tethered by both a 1,8‐biphenylene unit and a O?P?O bridge. Suitable aryl substituents generate planar chirality. The corresponding gold(I) complexes promote the cycloisomerization of prochiral nitrogen‐tethered dienynes. These reactions afford bicyclo[4.1.0]heptene derivatives displaying three contiguous stereogenic centers, with very high diastereoselectivity and up to 95 % ee.     

Phosphoramidites as Synthons for Polynucleotide Synthesis

Abstract

Methods for the rapid synthesis of DNA and RNA are described. The procedures involve using nucleoside phosphoramidites as synthons and silica as a polymeric support. Additionally, a novel reaction involving nucleoside O-alkyl methylphosphonothioates is described.     

DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction

Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2’-deoxyribonucleosides ( 1 and 2 ) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.     

A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme

BACKGROUND: The group I intron is an RNA enzyme capable of efficiently catalyzing phosphoryl-transfer reactions. Functional groups that stabilize the chemical transition state of the cleavage reaction have been identified, but they are all located within either the 5'-exon (P1) helix or the guanosine cofactor, which are the substrates of the reaction. Functional groups within the ribozyme active site are also expected to assist in transition-state stabilization, and their role must be explored to understand the chemical basis of group I intron catalysis. RESULTS: Using nucleotide analog interference mapping and site-specific functional group substitution experiments, we demonstrate that the 2'-OH at A207, a highly conserved nucleotide in the ribozyme active site, specifically stabilizes the chemical transition state by approximately 2 kcal mol-1. The A207 2'-OH only makes its contribution when the U(-1) 2'-OH immediately adjacent to the scissile phosphate is present, suggesting that the 2'-OHs of A207 and U(-1) interact during the chemical step. CONCLUSIONS: These data support a model in which the 3'-oxyanion leaving group of the transesterification reaction is stabilized by a hydrogen-bonding triad consisting of the 2'-OH groups of U(-1) and A207 and the exocyclic amine of G22. Because all three nucleotides occur within highly conserved non-canonical base pairings, this stabilization mechanism is likely to occur throughout group I introns. Although this mechanism utilizes functional groups distinctive of RNA enzymes, it is analogous to the transition states of some protein enzymes that perform similar phosphoryl-transfer reactions.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.