Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA.

The transition from inanimate materials to the earliest forms of life must have involved multiplication of a catalytically active polymer that is able to replicate. The semiconservative replication that is characteristic of genetic information transfer requires strands that contain more than one type of nucleobase. Short strands of RNA can act as catalysts, but attempts to induce efficient self-copying of mixed sequences (containing four different nucleobases) have been unsuccessful with ribonucleotides. Here we show that inhibition by spent monomers, formed by the hydrolysis of the activated nucleotides, is the cause for incomplete extension of growing daughter strands on RNA templates. Immobilization of strands and periodic displacement of the solution containing the activated monomers overcome this inhibition. Any of the four nucleobases (A/C/G/U) is successfully copied in the absence of enzymes. We conclude therefore that in a prebiotic world, oligoribonucleotides may have formed and undergone self-copying on surfaces.

Counterion effects on the columnar mesophases of triphenylene-substituted [18]crown-6 ethers: is flatter better?

The twisted lateral tetraalkyloxy ortho-terphenyl units in dibenzo[18]crown-6 ethers 1a-f were readily converted into the flat tetraalkyloxytriphenylene systems 2a-f by oxidative cyclization with FeCl(3) in nitromethane. Reactions of the latter with potassium salts gave complexes KX.2, which displayed mesomorphic properties. The aromatization increased both the clearing and melting points; the mesophase stabilities, however, were mainly influenced by the respective anions upon complexation with various potassium salts. In contrast, the alkyl chain lengths played only a secondary role. Among the potassium complexes of triphenylene-substituted crown ethers KX.2, only those with the soft anions I(-) and SCN(-) displayed mesophases with expanded phase temperature ranges of 93 degrees C and 132 degrees C (for KX.2e), respectively, as compared to the corresponding o-terphenyl-substituted crown ether complexes KI.1e (DeltaT=51 degrees C) and KSCN.1e (plastic crystal phase). Anions such as Br(-), Cl(-), and F(-) decreased the mesophase stability, and PF(6)(-) led to complete loss of the mesomorphic properties of KPF(6).2 although not for KPF(6).1. For crown ether complexes KX.2 (X=F, Cl, Br, I, BF(4), and SCN), columnar rectangular mesophases of different symmetries (c2mm, p2mg, and p2gg) were detected. In contrast to findings for the twisted o-terphenyl crown ether complexes KX.1, the complexation of the flat triphenylene crown ethers 2 with KX resulted in the formation of organogels. Characterization of the organogel of KI.2e in CH(2)Cl(2) revealed a network of fibers.

Columnar mesophases controlled by counterions in potassium complexes of dibenzo[18]crown-6 derivatives.

Dibenzo[18]crown-6 derivatives 1 with two lateral tetraalkyloxy o-terphenyl units were prepared and converted to the corresponding complexes KX1 (X = halide, BF(4), PF(6), SCN) and NH(4)PF(6)1. Complexation was probed by MALDI-TOF spectrometry and NMR spectroscopy. Downfield shifts of (1)H NMR signals for complexes with soft anions Br, I, SCN, and PF(6) indicated the presence of tight ion pairs, whereas complexes with hard anions F, Cl, or BF(4) showed no or little shifts. In (13)C NMR spectra, upfield shifts were detected for soft anions. The character of the anion also influenced the mesomorphic properties of complexes MX1 (M = K, NH(4)), which were investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and XRD in comparison to neat 1. Hard anions slightly stabilize or even destabilize the mesophase. Soft anions, however, improve the mesomorphic properties yielding mesophases with up to 70 degrees C phase widths in the case of KI1, KPF(6)1, and NH(4)PF(6)1. For complexes KSCN1 with a soft and bridging anion, the balance between mesophase stabilization and high order is shifted in favor of the plastic crystal phase.

Modifications in small interfering RNA that separate immunostimulation from RNA interference.

Synthetic small interfering RNA (siRNA) can suppress the expression of endogenous mRNA through RNA interference. It has been reported that siRNA can induce type I IFN production from plasmacytoid dendritic cells, leading to off-target effects. To separate immunostimulation from the desired gene-specific inhibitory activity, we designed RNA strands with chemical modifications at strategic positions of the ribose or nucleobase residues. Substitution of uridine residues by 2'-deoxyuridine or thymidine residues was found to decrease type I IFN production upon in vitro stimulation of human PBMC. Thymidine residues in both strands of a siRNA duplex further decreased immunostimulation. Fortunately, the thymidine residues did not affect gene-silencing activity. In contrast, 2'-O-methyl groups at adenosine and uridine residues reduced both IFN-alpha secretion and gene-silencing activity. Oligoribonucleotides with 2'-O-methyladenosine residues actively inhibited IFN-alpha secretion induced by other immunostimulatory RNAs, an effect not observed for strands with 2'-deoxynucleosides. Furthermore, neither 5-methylcytidine nor 7-deazaguanosine residues in the stimulatory strands affected IFN-alpha secretion, suggesting that recognition does not involve sites in the major groove of duplex regions. The activity data, together with structure prediction and exploratory UV-melting analyses, suggest that immunostimulatory sequences adopt folded structures. The results show that immunostimulation can be suppressed by suitable chemical modifications without losing siRNA potency by introducing seemingly minor structural changes.

Enzyme-free interrogation of RNA sites via primers and oligonucleotides 3'-linked to gold surfaces.

The synthesis of a phosphoramidite is described that was used for the preparation of oligonucleotides with a 3'-terminal thiol, linked to the DNA via a SAM-forming undecyl chain and a nonadsorptive tetraethylene glycol unit. A gold surface featuring oligonucleotide probes allowed for label-free in situ mass spectrometric determination of a nucleotide in subpicomole quantities of an RNA transcript.

Chemical primer extension: individual steps of spontaneous replication.

The replication of genetic information, as we know it from today's biology, relies on template-directed, polymerase-catalyzed extension of primers. It is known that short stretches of complementary RNA can form on templates in the absence of enzymes. This account summarizes recent work on efficient enzyme-free primer extension, both with 3'-amino-terminal deoxyribonucleotide primers and with primers made of unmodified RNA. Near-quantitative primer extension with half-life times on the order of hours has been demonstrated by using azaoxybenzotriazolides of nucleotides and downstream-binding oligomers. Further, small non-nucleosidic substituents placed on the terminus of the template or the downstream-binding oligomer have been shown to increase the rate and fidelity of primer-extension reactions. Since all four templating bases (A, C, G, T/U) direct sequence-selective primer-extension steps, we feel that there is renewed hope that full, nonenzymatic replication from monomers may eventually be achieved.

Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements.

Template-directed single nucleotide extension of an RNA primer with oxyazabenzotriazolides of ribonucleotides is shown to be fast and sequence-selective; downstream-binding RNA strands contribute to the acceleration of the reaction.