A universal method to produce in vitro transcripts with homogeneous 3' ends

A method is described that allows a general drawback of in vitro transcription assays to be overcome: RNA polymerases tend to add extra nucleotides to the RNA 3' end that are not encoded in the linearized DNA template. Furthermore, these polymerases show a considerable rate of premature termination close to the RNA's 3' end. These features lead to a decreased yield of full-length transcripts and often make it difficult to determine and isolate the correctly transcribed full-length RNA. The hammerhead ribozyme is frequently used in cis to cleave off these extra nucleotides. However, the upstream sequence requirements of this ribozyme restrict its general usability. In contrast, the hepatitis delta virus ribozyme has no such requirements and can therefore be applied to any RNA sequence in cis. Due to the catalytic activity of the ribozyme, the desired transcript is released as an RNA molecule with a homogeneous 3' end. The resulting 2',3'-cyclo-phosphate group of the released RNA can be easily and efficiently removed by T4 polynucleotide kinase treatment. The presented method can be applied for virtually any sequence to be transcribed and is therefore superior to other ribozyme strategies, suggesting possible applications in every field where transcripts with homogeneous 3' ends are required.

C-F...H-C hydrogen bonds in ribonucleic acids

We report the synthesis of 1'-deoxy-1'-(benzimidazol-1-yl)-beta-D-ribofuranose 7 and 1'-deoxy-1'-phenyl-beta-D-ribofuranose 2. With these two ribonucleoside analogues we have a set of nine different RNA building blocks in hand, which are isostere to the natural bases. Now it is possible to investigate their duplex stabilizing forces. These forces are hydrogen bonds, base stacking, and solvation. The phosphoramidites of all building blocks were incorporated into a 12mer RNA, and the resulting RNA duplexes were investigated by UV- and CD-spectroscopy. We found that some of the RNA analogues are universal bases. The best universal bases with the lowest destabilization and the smallest discrimination between the natural bases are 1 (B) and 9 (E). On the basis of UV measurements we determined the melting points and the thermodynamic data. We were able to show that there are no hydrogen bonds between the natural bases and the RNA analogues. From thermodynamic data we calculated the contributions for base stacking and solvation of all modified building blocks. Comparison of calculated and measured data of double modified base pairs in 12mer RNA duplexes showed a further duplex stabilizing force in base pairs containing fluorine atoms at the Watson-Crick binding site. This stabilizing force can be defined as C-F.H-C hydrogen bond as is observed in crystal structures of 1'-deoxy-1'-(4-fluorophenyl)-beta-D-ribofuranose.

Substituted 1,8-naphthyridin-2(1H)-ones are superior to thymine in the recognition of adenine in duplex as well as triplex structures

The synthesis and evaluation of a series of novel nucleobases based on substituted 1,8-naphthyridin-2(1H)-ones are reported. The nucleobases were designed to meet the requirements for incorporation into peptide nucleic acids (PNAs) and were evaluated as part of PNA duplex and triplex nucleic acid recognition systems. Of the various nucleobases tested, only the 7-chloro-1,8-naphthyridin-2(1H)-one (7-Cl-bT) nucleobase led to consistently increased affinity in all recognition systems, duplex (Watson-Crick) as well as triplex (Hoogsteen). For multiply modified systems, the increase in thermal stability per modification was dependent on the sequence context, ranging from 2.0 degrees C (in separate positions) to 3.5 degrees C (in adjacent positions) in PNA-DNA duplexes and from 1.2 degrees C (in separate positions) to 3.2 degrees C (in adjacent positions) in PNA-RNA duplexes. Singly mismatched oligonucleotide targets were employed to demonstrate uncompromised sequence discrimination. When part of multiply modified triplex (Hoogsteen) recognition systems, the 7-Cl-bT unit gave rise to increases in the thermal stability ranging from 2.7 to 3.5 degrees C when incorporated into separated and adjacent positions, respectively. Our results furthermore indicate that the duplex stabilization is predominantly enthalpic and therefore most likely not a consequence of single-strand preorganization. Finally, and most surprisingly, we find no direct correlation between the end-stacking efficiency of this type of nucleobase and its helix stabilization when involved in Watson-Crick base pairing within a helix.

Alpha-L-RNA (alpha-L-ribo configured RNA): synthesis and RNA-selective hybridization of alpha-L-RNA/alpha-L-LNA chimera

Synthesis of the novel alpha-L-ribofuranosyl phosphoramidite derivative was accomplished via the alpha-L-ribofuranosyl thymine nucleoside. Amidite was used in automated syntheses of chimeric oligonucleotides composed of mixtures of the novel alpha-L-RNA nucleotide monomer ((alphaL)T, alpha-L-ribo configured RNA), and DNA, LNA (T(L), locked nucleic acid) or alpha-L-LNA ((alphaL)T(L), alpha-L-ribo configured locked nucleic acid) nucleotide monomers. For alpha-L-RNA/DNA and alpha-L-RNA/alpha-L-LNA chimeras, RNA-selective hybridization was obtained, for alpha-L-RNA/alpha-L-LNA chimera we found increased binding affinity compared to the corresponding DNA:RNA reference duplex. In addition, alpha-L-RNA/alpha-L-LNA chimera displayed significant stabilization towards 3'-exonucleolytic degradation. These results indicate that alpha-L-RNA/alpha-L-LNA chimeras deserve further evaluation as antisense molecules.

Selection of RNA aptamers to the Alzheimer's disease amyloid peptide

Alzheimer's disease is correlated with the deposition of amyloid peptides in the brain of the patients. The amyloid is thus a major target in the search for novel diagnostic and therapeutic approaches. The present work employs in vitro selection to develop new tools for the study of the Alzheimer's disease. The selection strategy enables the design of specific nucleic acids (aptamers) against virtually any target molecule. High-affinity RNA aptamers against the betaA4(1-40) were isolated from a combinatorial library of approximately 10(15) different molecules. The apparent dissociation constants K(d) of these aptamers are 29-48 nM. The binding of the RNA to the amyloid fibrils was confirmed by electron microscopy. The chemical synthesis of these nucleic acids enables tailor-made modifications. By introduction of specific reporter groups these RNAs can become suitable tools for analytical and diagnostic purposes. Thus, this study may introduce a new approach for diagnosis of the Alzheimer's disease.

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

Algorithms for predicting RNA secondary structure require approximations for the free energies of multibranch loops, also called junctions. The stabilities of 62 RNA duplexes with three- and four-way multibranch loops were determined by optical melting. To account for the observed sequence dependence, a revised loop free-energy approximation is proposed that accounts for the strain in three-way junctions with fewer than two unpaired nucleotides, penalizes asymmetry in the distribution of unpaired nucleotides, and gives a bonus for four-way loops relative to three-way loops. Parameters for this equation were determined by linear regression.

Maxizymes, novel allosterically controllable ribozymes, can be designed to cleave various substrates

We demonstrated previously that an allosterically controllable novel ribozyme, designated the maxizyme, is a powerful tool for disruption of an abnormal chimeric RNA target [BCR-ABL (b2a2) mRNA], and we proposed that it might provide the basis for future gene therapy for the treatment of chronic myelogenous leukemia (Kuwabara et al. Mol. Cell 1998, 2, 617-627). The maxizyme has sensor arms that can recognize a specific sequence and, in the presence exclusively of such a specific sequence, it can form a cavity for capture of catalytically indispensable Mg2+ ions. Cleavage of the target RNA then occurs at a site distant from the specific sequence. Clearly, the specific sequences recognized by sensor arms should not be limited to those of the above mentioned abnormal chimeric target. Thus, to demonstrate the general applicability of maxizyme technology, we constructed maxizymes targeted to other mRNAs, such as PML-RAR alpha mRNA, sDLST mRNA, and BCR-ABL (b1a2) mRNA, that are not cleaved with high specificity by the wild-type hammerhead ribozyme. Specific and efficient cleavage in vitro of these mRNAs by the custom-designed maxizymes demonstrated clearly that maxizyme technology is not limited to a specific case but may have broad general applicability in molecular biology and, also, in a clinical setting.

Generation of species cross-reactive aptamers using "toggle" SELEX

Species cross-reactivity facilitates the preclinical evaluation of potentially therapeutic molecules in animal models. Here we describe an in vitro selection strategy in which RNA ligands (aptamers) that bind both human and porcine thrombin were selected by "toggling" the protein target between human and porcine thrombin during alternating rounds of selection. The "toggle" selection process yielded a family of aptamers, all of which bound both human and porcine thrombin with high affinity. Toggle-25, a characteristic member, inhibited two of thrombin's most important functions: plasma clot formation and platelet activation. If appropriate targets are available, the toggle strategy is a simple measure that promotes cross-reactivity and may be generalizable to related proteins of the same species as well as to other combinatorial library screening strategies. This strategy should facilitate the isolation of ligands with needed properties for gene therapy and other therapeutic and diagnostic applications.

Drug-RNA footprinting

RNase I and RNase T1 can be used to obtain high-quality footprinting information for paromomycin binding to a 176-mer RNA from the packaging region of HIV-1 (LAI). Controls and scanning procedures are necessary for quantitation of autoradiographic data, so that footprinting plots showing cutting behavior as a function of drug concentration can be used to identify binding sites and regions of altered structure on the 176-mer. From the RNase I footprinting results the primary paromomycin binding sites on the 176-mer are on the main stem and on the stem of SL1, but noncontiguous sequences may be involved in the same binding event. Strong enhancements in cleavage with added drug are also observed, indicating drug-induced structural changes. Drug binding may cause linker regions between stem-loops of the 176-mer to change structure, possibly providing a site or sites for additional drug binding. Because drug binding changes the structure of the packaging region, which may alter its function, paromomycin analogs with enhanced specificity for HIV psi RNA have potential as a new class of agent for treating AIDS.

Synthesis and analysis of RNA containing 6-trifluoromethylpurine ribonucleoside

We report the synthesis of a 5'-DMT-2'-TBDMS-protected phosphoramidite of 6-trifluoromethylpurine ribonucleoside ((TFM)P) and its use in the site-specific incorporation of 6-trifluoromethylpurine into RNA. Properties of (TFM)P-substituted RNA suggest it will be valuable in the study of RNA structure and the binding of RNA-modifying enzymes, particularly the RNA-editing adenosine deaminases. Reaction: see text.

N-cyanoimidazole and diimidazole imine: water-soluble condensing agents for the formation of the phosphodiester bond

The reaction of BrCN with imidazole results in the formation of N-cyanoimidazole and diimidazole imine. These compounds were shown to be useful condensing agents for the formation of the phosphodiester bound in aqueous solution.

Montmorillonite catalysis of RNA oligomer formation in aqueous solution. A model for the prebiotic formation of RNA

Oligomers of adenylic acid of up to the 11-mer in length are formed by the reaction of the phosphorimidazolide of adenosine (ImpA) in pH 8 aqueous solution at room temperature in the presence of Na(+)-montmorillonite. These oligomers are joined by phosphodiester bonds in which the 3',5'-linkage predominates over the 2',5'-linkage by a 2:1 ratio. Reaction of a 9:1 mixture of ImpA, A5'ppA results in the formation of oligomers with a 3:1 ratio of 3',5'- to 2',5'-linked phosphodiester bonds. A high proportion of these oligomers contain the A5'ppA grouping. A5'ppA reacts much more rapidly with ImpA than does 5'-ADP (ppA) or 5'-ATP (pppA). The exchangeable cation associated with the montmorillonite effects the observed catalysis with Li+, Na+, NH4+, and Ca2+ being the more effective while Mg2+ and Al3+ are almost ineffective catalysts. 2',5'-Linked oligomers, up to the tetramer in length, are formed using UO2(2+)-montmorillonite. The structure analysis of individual oligomer fractions was performed by selective enzymatic and KOH hydrolytic studies followed by HPLC analysis of the reaction products. It is concluded from the composition of the oligomers that the rate of addition ImpA to a 3'-terminus containing a 2',5'-linkage is slower than the addition to a nucleoside joined by a 3',5'-linked phosphodiester bond. The potential importance of mineral catalysis of the formation of RNA and other oligomers on primitive Earth is discussed.

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay: the effect of mononucleotide structure on phosphodiester bond formation

Adenine deoxynucleotides bind more strongly to Na(+)-montmorillonite than do the corresponding ribonucleotides. Thymidine nucleotides binds less strongly to Na(+)-montmorillonite than do the corresponding adenine deoxynucleotides. Oligomers of 2'-dpA up to the tetramer were detected in the reaction 2'-d-5'-AMP with EDAC (a water-soluble carbodiimide) in the presence of Na(+)-montmorillonite. Reaction of 3'-d-5'-AMP with EDAC on Na(+)-montmorillonite yields 3'-d-2',5'-pApA while the reaction of 2'-d-3'-AMP yields almost exclusively 3',5'-cdAMP. The reaction of 5'-TMP under the same reaction conditions give 3',5'-cpTpT and 3',5'-pTpT while 3'-TMP gives mainly 3',5'-cpT. The yield of dinucleotide products (dpNpN) containing the phosphodiester bond is 1% or less when Na(+)-montmorillonite is omitted from the reaction mixture.

Template-directed oligomerization of 5'-deoxy-5'-nucleosideacetic acid derivatives

5'-Deoxy-5'-nucleosideacetic acids II-V are isostructural analogues of nucleotides with a carboxylate group in the place of the 5'-phosphate group. We have studied their oligomerization in aqueous solution using a water-soluble carbodiimide as the condensing agent in the presence or absence of an appropriate polynucleotide template. Condensation of adenylic acid analogues IIa, IIIa, and Va in the presence of polyuridylic acid were found to be the most efficient reactions. Cyclization of the activated monomers to lactones and the insolubility of the oligomers in aqueous solution were found to be obstacles to the efficient formation of long oligomers.

Acid/azole complexes as highly effective promoters in the synthesis of DNA and RNA oligomers via the phosphoramidite method

The utility of various kinds of acid salts of azole derivatives as promoters for the condensation of a nucleoside phosphoramidite and a nucleoside is investigated. Among the salts, N-(phenyl)imidazolium triflate, N-(p-acetylphenyl)imidazolium triflate, N-(methyl)benzimidazolium triflate, benzimidazolium triflate, and N-(phenyl)imidazolium perchlorate have shown extremely high reactivity in a liquid phase. These reagents serve as powerful activators of deoxyribonucleoside 3'-(allyl N,N-diisopropylphosphoramidite)s or 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite)s employed in the preparation of deoxyribonucleotides, and 3'-O-(tert-butyldimethylsilyl)ribonucleoside 2'-(N,N-diisopropylphosphoramidite)s or 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-(N,N-diisopropylphosphoramidite)s used for the formation of 2'-5' and 3'-5' internucleotide linkages between ribonucleosides, respectively. The azolium salt has allowed smooth and high-yield condensation of the nucleoside phosphoramidite and a 5'-O-free nucleoside, in which equimolar amounts of the reactants and the promoter are employed in the presence of powdery molecular sieves 3A in acetonitrile. It has been shown that some azolium salts serve as excellent promoters in the solid-phase synthesis of oligodeoxyribonucleotides and oligoribonucleotides. For example, benzimidazolium triflate and N-(phenyl)imidazolium triflate can be used as effective promoters in the synthesis of an oligodeoxyribonucleotide, (5')CGACACCCAATTCTGAAAAT(3') (20mer), via a method using O-allyl/N-allyloxycarbonyl-protected deoxyribonucleoside 3'-phosphoramidites or O-(2-cyanoethyl)/N-phenoxyacetyl-protected deoxyribonucleotide 3'-phosphoramidite as building blocks, respectively, on high-cross-linked polystyrene resins. Further, N-(phenyl)imidazolium triflate is useful for the solid-phase synthesis of oligoribonucleotides, such as (5')AGCUACGUGACUACUACUUU(3') (20mer), according to an allyl/allyloxycarbonyl-protected strategy. The utility of the azolium promoter has been also demonstrated in the liquid-phase synthesis of some biologically important substances, such as cytidine-5'-monophosphono-N-acetylneuraminic acid (CMP-Neu5Ac) and adenylyl(2'-5')adenylyl(2'-5')adenosine (2-5A core).

Effect of inhibitors on the montmorillonite clay-catalyzed formation of RNA: studies on the reaction pathway

The Langmuir adsorption isotherms of the phosphoroimidazolides of adenosine (ImpA) and uridine (ImpU), dA5' ppdA and N6,N6-dimethyladenine binding on montmorillonite are consistent with their forming a monolayer on the clay surface. This suggests the condensation of ImpA and ImpU to oligomers proceeds on the surface of the clay and not in groups of monomers stacked on the clay surfaces. The binding and reactions of ImpU and ImpA on montmorillonite are blocked by N6,N6-dimethyladenine and dA5' ppdA. dA5' ppdA is a better inhibitor of oligomer formation than N6,N6-dimethyladenine because both adenine rings of dA5' ppdA bind to the clay surface and block adjacent catalytic sites. An upper limit of 5-10 x 10(15) catalytic sites on 50 mg of clay was estimated from the binding of ImpU and the inhibition of oligomer formation by dA5' ppdA.

Thermodynamics of three-way multibranch loops in RNA

RNA multibranch loops (junctions) are loops from which three or more helices exit. They are nearly ubiquitous in RNA secondary structures determined by comparative sequence analysis. In this study, systems in which two strands combine to form three-way junctions were used to measure the stabilities of RNA multibranch loops by UV optical melting and isothermal titration calorimetry (ITC). These data were used to calculate the free energy increment for initiation of a three-way junction on the basis of a nearest neighbor model for secondary structure stability. Imino proton NMR spectra were also measured for two systems and are consistent with the hypothesized helical structures. Incorporation of the experimental data into the mfold and RNA structure computer programs has contributed to an improvement in prediction of RNA secondary structure from sequence.

Efficient synthesis of D-[1'-13C]-ribonucleosides for incorporation into oligo-RNA

Syntheses of the monomer building blocks used for the solid-phase synthesis of specifically 1'-13C-labeled oligoribonucleotides from the D-[1-13C]ribose is presented. Procedure has been used for the selective formation of 2'-O-silylated ribonucleosides. After 5'-O-dimethoxytritylation, the synthesis of D-[1'-13C] ribonucleoside phosphoramidites has been achieved.

A new facile method for spin-labeling of oligonucleotides

A new facile method for spin-labeling suitable for DNA and RNA oligonucleotides is presented. The nitroxide 3-ethenyl-2,2,5,5-tetramethyl-pyrrolin-1-yloxy was directly introduced during automated solid-phase synthesis by a Pd(0) cross coupling reaction. The main advantages of this procedure are the small amount of spin-label needed for the derivatisation of the oligonucleotide and the high coupling efficiency on the solid phase.

Chimeric RNA with modified backbones: alternating methylene(methylimino) linked phosphodiester backbone oligonucleotides with 2'-OH and 2'-OMe groups

Synthesis of a novel ribo-MMI dimer with 2'-OH and 2'-OMe in 5'- and 3'-nucleosides, respectively is presented. The synthesis was accomplished by reductive coupling of 3'-deoxy-3'-C-formyluridine and 2'-O-methyl-5'-O-methylaminouridine via a thioacetal as the key intermediate for the top part of the dimer. Incorporation of ribo-MMI dimers into oligonucleotides increased binding affinity for target RNA.

Synthesis of isotopically labeled D-[1'-13C]ribonucleoside phosphoramidites

The preparation of fully protected labeled diisopropylamino-beta-cyanoethyl-[1'-13C]ribonucleoside phosphoramidites with regioisomeric purity is described. We demonstrated in this paper that a regioselective 2'-O-silylation, through a 3',5'-O-di-tert-butylsilanediyl protection, has been applied for the synthesis of [1'-13C]ribonucleoside phosphoramidite units. This method allowed us to obtain only the desired 2'-O-silyl-3'-O-phosphoramidites avoiding the undesired 3'-O-silyl-2'-O-phosphoramidite nucleosides isolated by standard procedures. This is a suitable procedure to RNA precursors with respect to the isotope-containing precursors.

Quantification of bacterial transcripts during infection using competitive reverse transcription-PCR (RT-PCR) and LightCycler RT-PCR

Bacteria have evolved sophisticated regulatory circuits to modulate their gene expression in response to disparate environments. In order to monitor bacterial gene expression and regulation in the host, methods for direct transcript analysis from clinical specimens are needed. For most bacterial infections, amplification of the mRNAs of interest is necessary due to the low numbers of cells present and the low levels of specific transcripts. Here we compare two methods of quantitative reverse transcription-PCR (RT-PCR)-competitive RT-PCR using a one-tube system followed by standard gel analysis and the real-time detection of PCR product formation by fluorescence resonance energy transfer technology using the LightCycler unit. We isolated Staphylococcus aureus RNA directly from clinical specimens obtained from cystic fibrosis patients with chronic S. aureus lung infection and from an animal model of foreign-body infection with no further cultivation of the bacteria. Competitive RT-PCR and LightCycler RT-PCR were tested for their ability to quantify the transcription of a constitutively expressed gyrase gene (gyr) and a highly regulated alpha-toxin gene (hla) of S. aureus. Reproducible results were obtained with both methods. A sensitivity of 10(4) (gyr) and 10(3) (hla) copies, respectively, was reached, which was sufficient for the quantification of transcripts during bacterial infection. Overall, the competitive RT-PCR is a robust technique which does not need special RNA purification. On the negative side, it is labor intensive and time consuming, thus limiting the numbers of samples which can be analyzed at a given time. LightCycler RT-PCR is very susceptible to even traces of inhibitors, but it allows high-throughput processing of samples.

RNA oligonucleotide synthesis via 5'-silyl-2'-orthoester chemistry

The chemical synthesis of RNA oligonucleotides is a valuable resource for biological research. A new approach for RNA synthesis that is now as reliable and efficient as DNA synthesis methods is described in this report. A 5'-O-silyl ether is used in conjunction with acid-labile orthoester protecting groups on the 2'-hydroxyls. RNA synthesis proceeds efficiently on commercial synthesizers in high yields. Analysis by anion-exchange HPLC shows that the quality and yields of RNA synthesized with this chemistry are unprecedented. Furthermore, this chemistry enables analysis and purification of stable 2'-O-protected RNA. This property serves to minimize possibilities for degradation of the RNA. In addition, it now possible to analyze troublesome sequences, which, when fully 2'-O-deprotected, do not easily resolve into one major conformation due to strong secondary structure. When ready for use, the RNA is easily 2'-O-deprotected in mild-acidic aqueous buffers in 30 min. This new RNA chemistry has enabled the routine high-quality synthesis of RNA oligonucleotides up to 50 bases in length regardless of sequence or secondary structure.

Crystallization of RNA

Even as the number of RNA structures determined and under study multiplies, the critical step in X-ray diffraction analysis, growth of single well-ordered crystals, remains at the boundary between art and science. Recent advances in methods of RNA synthesis, purification, and characterization, as well as empirical and technical improvements in crystallization techniques, the development of cryo-crystallography, and the wider availability of bright, tunable, X-rays from synchrotron sources are improving the chances of obtaining RNA crystals suitable for X-ray structural analysis. In this review, we summarize the current status of the design, preparation, purification, and analysis of RNA for crystallization and describe the latest approaches to obtaining diffraction-quality crystals.