2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR

The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how ¹ H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.

Heterogeneous Pyrophosphate-Linked DNA-Oligonucleotides: Aversion to DNA but Affinity for RNA

Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by pyrophosphate as backbones of primordial oligomers, DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) were synthesized and investigated for their base-pairing properties. As expected, pyrophosphate inserts into the backbone compromised the thermal stability of ppDNA-DNA duplexes. In contrast, the ppDNA-RNA duplex exhibited, remarkably, duplex stability, even with accumulation of pyrophosphate linkages. This seems to be a consequence of an increase in the diameter of the double-helix with eight-bond-repeat units, and higher inclination of the base-pair axis with respect to the backbone in RNA (A-form), compared with that in DNA (B-form). These results suggest that pyrophosphate-linked oligonucleotides could harbor functional capabilities with implications for their roles in the origins of life and chemical biology.

Nonenzymatic ligation of short-chained 2'-5'- or 3'-5'-linked oligoribonucleotides on 2'-5'- or 3'-5'-linked complementary templates

5'-pACUG tetraribonucleotides containing 2'-5' or 3'-5' linkages self-condensed on 2'-5'- or 3'-5'-linked complementary decaribonucleotide (5'-CAGUCAGUCA) templates. CD and UV melting studies showed that helix formation took place in all four possible combinations of linkage isomers of the substrate tetramer and the template decamer under the ligation conditions. The hybridization ability followed the order: [3'-5' tetramer with 3'-5' decamer] > [2'-5' tetramer with 3'-5' decamer] > [2'-5' tetramer with 2'-5' decamer] > or = [3'-5' tetramer with 2'-5' decamer]. Each tetramer condensed on the complementary decaribonucletide template to form the corresponding octamer, but the ligation efficiency varied considerably, depending on the types of linkage in the tetramer substrate and the template decamer. The yields of the octamers obtained by the template-directed ligation followed the order: [2'-5' substrate: 2'-5' template] > [3'-5':3'-5'] > [2'-5':3'-5'] > [3'-5':2'-5']. The results demonstrate that a homo-linkage system is preferable for the template-directed synthesis of RNA. The resulting linkage of the octamer formed from the 2'-5'-linked substrate and the 2'-5'-linked template is mainly 2'-5'.

2',5'-linked DNA is a template for polymerase-directed DNA synthesis

Genomes are composed of nucleic acids bearing 3',5'-phosphodiester-linked sugars. The 2',5'-phosphodiester linkage is a fundamental alternative to the natural linkage and is the predominant product of most nontemplate, nonenzymatic oligomerizations of nucleotide monomers. This fact suggests a chemical bias for the formation of 2',5'-phosphodiester bonds, an important consideration in the context of molecular evolution on Earth or elsewhere. Although 2',5'-linked RNA occurs naturally, it is evidently not used to encode genetic information. Nevertheless, the capacity of the 2',5'-phosphodiester linkage to serve as a genetic material has been probed in laboratory experiments. Initial studies examined both self-pairing and pairing with natural nucleic acids. These studies showed that, while 2',5'-linked DNA and RNA form double and triple helices with themselves, their interactions with natural nucleic acids are asymmetric-pairing is seen with 3',5'-linked RNA but not DNA. Although the ability to form a stable structure (such as a helix) is likely a necessary condition for nonenzymatic information transfer, in the case of enzymatic reactions this precondition may be expected to be lifted in cases where the enzyme can serve as a "template for the template" and make up for structural deficiencies that would be fatal to its abiotic counterpart. In support of this suggestion, we demonstrate that 2',5'-linked DNA is a template for enzymatic synthesis of natural DNA with a variety of DNA polymerases and reverse transcriptases directing the incorporation of all four natural nucleotides with fidelity.

Remarkable stability of hairpins containing 2',5'-linked RNA loops

We report here the results of a comparative study of hairpin loops that differ in the connectivity of phosphodiester linkages (3',5'- versus 2',5'-linkages). In addition, we have studied the effect of changing the stem composition on the thermodynamic stability of hairpin loops. Specifically, we constructed hairpins containing one of six stem duplex combinations, i.e., DNA:DNA ("DD"), RNA:RNA ("RR"), DNA:RNA ("DR"), 2',5'-RNA:RNA ("RR"), 2',5'-RNA:DNA ("RD"), and 2',5'-RNA:2',5'-RNA ("RR"), and one of three tetraloop compositions, i.e., 2',5'-RNA ("R"), RNA ("R"), and DNA ("D"). All hairpins contained the conserved and well-studied loop sequence 5'-...C(UUCG)G...-3' [Cheong et al. Nature 1990, 346, 680-682]. We show that the 2',5'-linked loop C(UUCG)G, i.e.,...C(3'p5')U(2'p5')U(2'p5')C(2'p5')G(2'p5')G(3'p5')..., like its "normal" RNA counterpart, forms an unusually stable tetraloop structure. We also show that the stability imparted by 2',5'-RNA loops is dependent on base sequence, a property that is shared with the regioisomeric 3',5'-RNA loops. Remarkably, we find that the stability of the UUCG tetraloop is virtually independent of the hairpin stem composition (DD, RR, RR, etc.), whereas the native RNA tetraloop exerts extra stability only when the stem is duplex RNA (R:R). As a result, the relative stabilities of hairpins with a 2',5'-linked tetraloop, e.g. ggac(UUCG)gtcc (T(m) = 61.4 degrees C), are often superior to those with RNA tetraloops, e.g. ggac(UUCG)gtcc (T(m) = 54.6 degrees C). In fact, it has been possible to observe the formation of a 2',5'-RNA:DNA hybrid duplex by linking the hybrid's strands to a (UUCG) loop. These duplexes (RD), which are not stable enough to form in an intermolecular complex [Wasner et al. Biochemistry 1998, 37, 7478-7486], were stable at room temperature (T(m) approximately 50 degrees C). Thus, 2',5'-loops have potentially important implications in the study of nucleic acid complexes where structural data are not yet available. Furthermore, they may be particularly useful as structural motifs for synthetic ribozymes and nucleic acid "aptamers".