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Modified Nucleotides May Have Enhanced Early RNA Catalysis

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Modified Nucleotides May Have Enhanced Early RNA Catalysis PERSPECTIVE Modified nucleotides may have enhanced early RNA catalysis PERSPECTIVE Steven K. Wolka, Wesley S. Mayfielda, Amy D. Gelinasa, David Astlinga, Jessica Guillota, Edward N. Brodya, Nebojsa Janjica, and Larry Golda,1 Edited by Jack W. Szostak, Massachusetts General Hospital, Boston, MA, and approved February 28, 2020 (received for review June 8, 2018) The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication. RNA world | modified nucleotides | catalytic RNA There remains a robust debate about the transition partitioning to allow molecules the chance to not lose from a primordial soup of molecules to organisms with each other in the vastness of the early Earth. For later Darwinian descent, a moment that Carl Woese (1, 2) steps, such as energy utilization and genetics, forma- called the Darwinian Threshold. Many scientists carry tion of membranes and eventually, cells could have the idea that the RNA World Hypothesis, an expres- created the needed molecular localization. For early sion first coined by Gilbert (3), provides the framework chemical condensations, the partitions could have for the earliest piece of what was likely a gradual tran- been small primordial pools, where proximity was fa- sition from chemical soup to catalysts and genetics. cilitated by evaporation or the presence of rocks com- The critical first pieces of the RNA World Hypothesis posed of useful minerals (4). It has also been proposed are simple: the early Earth was complex chemically, that an ice–water interface during colder periods may and at some moment, RNA molecules, made ini- have served as a protocellular medium that, among tially through nontemplated condensations of acti- other features, concentrated the reactant molecules vated monomers (4, 5), assumed the diverse roles of to levels not easily achievable by other means (6). templates for replication, catalysts/ribozymes to do In this paper, we have tried to focus only on one that replication, facilitators of other critical steps (such issue within this long chain of events: how is it possible as energy utilization), and eventually, the storage of to evolve catalytic RNAs that function as short mole- genetic information. cules with enough catalytic power to bootstrap the Each of the stages of evolution—going from sim- development of those short, chemically derived RNAs ple molecules, like cyanide, to more complex mole- into replicators/genetics? In other words, what were cules, like nucleic acids, to polymers capable of the earliest ribozymes in an RNA World, and how complex functions and ultimately, to systems capable did they get their start? These huge questions are of catalysis and templated replication—represents addressed, along with many others, in wonderful distinct and poorly understood problems. Although (but slightly dated) reviews of the RNA World Hypoth- these steps involve vastly different processes and un- esis (7, 8). Bernhardt (8) noted that “[c]atalysis is a doubtedly involve progressively increasing molecu- relatively rare property of long RNA sequences only,” lar complexity, each also required some form of and he did note that some catalytic RNAs are short aSomaLogic, Inc., Boulder, CO 80301 Author contributions: S.K.W., E.N.B., N.J., and L.G. designed research; W.S.M., A.D.G., and J.G. performed research; A.D.G. contributed new reagents/analytic tools; S.K.W., D.A., E.N.B., N.J., and L.G. analyzed data; and S.K.W., N.J., and L.G. wrote the paper. The authors declare no competing interest. This article is a PNAS Direct Submission. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY). 1To whom correspondence may be addressed. Email: [email protected]. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1809041117/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1809041117 PNAS Latest Articles | 1of7 Downloaded by guest on September 28, 2021 and that one might imagine that the environment of the early modifications in the loop independently contribute to significant Earth could have facilitated RNA-mediated catalysis. Essentially, stabilization. It is possible that some of this stabilization results from Bernhardt (8) said, “please do not worry about this problem.” the reduced conformational flexibility of the ribose ring associated Here, we have ignored his plea. with the presence of the 2′-O-methyl, which could be tested with Scientists have imagined that RNAs randomly assembled at NMR studies. In any event, the benzyl rings still provide a significant sufficient lengths are all one might need to achieve a transition to additional increase in Tm. a stable RNA World. We argue that length is less important than The impact of the 2′-O-methyl groups alone is worthy of note catalytically competent shape, which we refer to as “globularity.” because these modifications are present in modern RNA. These Globularity in RNAs (like the pockets within proteins that consti- ribose modifications are known to increase the Tm values of RNA tute the active sites, which we associate with protein globularity) duplexes (22, 23) but to our knowledge, have not been shown to as well as the availability of nucleobases with catalytic function stabilize loop regions. Tm increases have been reported for 2′-O- could facilitate the emergence of a first set of ribozymes from methyl–modified RNA hairpins in the context of molecular bea- shorter RNAs than one might have predicted, making the start cons (24, 25), but in these examples, both the loop and stem re- of life more likely. gions were modified. That is, in the chemisphere that might have existed, the two This modest thermodynamic dataset suggests that hairpin rate-limiting problems could have been solved simultaneously. A structure stabilization by the addition of hydrophobic modifica- single early chemistry that provides globularity and catalytic tions in the loop is significant for both DNA and RNA. The effect power to short RNAs would have led to the “enzymatic” replica- is surprisingly large. With regard to the RNA World, our experi- tion of template RNAs (e.g., genetics) that had been made initially ment is a metaphor. There is little evidence regarding which without replication either by spontaneous condensation of mono- mers or in reactions catalyzed by other RNAs. We have used our own data about oligonucleotide globularity coupled with Harold B. White’s ideas about catalytic RNA (9–11) and a few simple A O O oligonucleotide hairpin melting temperature (T ) experiments m HN N to address the problem inherent in short RNA molecules, and in H doing so, perhaps, we have increased the plausibility of the RNA O N O World Hypothesis. O Discussion O R 3 Aptamers are single-stranded nucleic acid-based affinity reagents evolved from random libraries using SELEX (systematic evolution Z: R = H (2’-deoxy) of ligands by exponential enrichment) (12, 13). Enhancement in mZ: R = OCH3 (2’-OCH3) the chemical diversity of these random nucleic acid libraries, even with one and the same modification at only one of the four bases (e.g., at a 5-position of a pyrimidine throughout the library), can B dramatically improve both the success rate of DNA-based SELEX 1.00 experiments and the binding affinities of the resulting aptamers 062 (14–16). Crystal structures of these SOMAmer reagents (slow off- AdezilamroN rate modified aptamers) bound to their cognate proteins make it 0.95 clear that the pyrimidine adducts of SOMAmers form direct con- tacts with the protein and participate in shaping the binding in- terface, much like amino acid residues in proteins (17–21). As 0.90 importantly, these crystal structures also show that the hydro- phobic “side chains” of the modified bases participate in internal motifs that stabilize the folded structures (19). 0.85 As a simple model of these interactions, we studied the effect of 0 20 40 60 80 100 hydrophobic modifications on the thermodynamic stability of a Temperature (°C) short-hairpin structure in DNA and RNA (SI Appendix,Fig.S1). For – DNA hairpins containing a stem region of four Watson Crick base C 75 pairs and a loop of seven thymidine nucleotides (the T7 variant), the 70 RNA Tm increases steadily as up to five of these thymidines are replaced )C°(mT with 5-(N-benzylcarboxamide)-deoxyuridines (Bn-dU), with a total 65 change of 14 °C (Fig. 1C). A very similar degree of stabilization is 60 DNA observed for the analogous RNA hairpin series in which the substituted modified nucleotides contain both 5-(N-benzylcarboxamide) 55 base substitutions and 2′-O-methyl ribose substitutions (Fig. 1 B 50 1 2 3 4 5 6 7 and C). As a control, we also included a sequence with a fully 012345670 2′-O-methyl–substituted loop to determine whether any ob- # of Bn-dU mods served stability gain is due to the base modifications, the ri- Fig. 1. (A) Structure of the Bn-dU substitutions and the hairpin motif bose 2′-O-methyl modifications, or both. For this RNA series, (RNA version) utilized in this study. (B) DNA and RNA series hairpin the 2′-O-methyl groups contribute significantly to the T in- m sequences and corresponding Tm values. (C)Tm values for each series as crease, showing that two vastly different types of hydrophobic a function of the number of substitutions in the loop from zero to seven.
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