The tyranny of adenosine recognition among RNA aptamers to coenzyme A

Saran, Dayal; Frank, Joseph J.; Burke, Donald H.

doi:10.1186/1471-2148-3-26

Cited by 25 publications

(26 citation statements)

References 17 publications

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“…327,503 Indeed, targeting the phosphate group seems to be very challenging and hard to obtain by in Vitro selection. 503 Nevertheless, a recent example demonstrates that in Vitro selection experiments can actually be driven in a way that favors triphosphate over nucleotide binding of RNA aptamers.…”

Section: Natural Versus In Vitro Selected Aptamersmentioning

confidence: 99%

Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy

2007

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Introduction 3715 2. Aptamers 3717 2.1. Aptamers as Protein Detecting Reagents 3717 2.1.1. Aptamers in Standard Diagnostic Assays 3718 2.1.2. Aptamers as Capture Ligands 3719 2.2. Aptamers as Therapeutics 3720 3. Intramers 3724 3.1. Applications of Aptamers in Vivo 3724 3.1.1. Intracellular Expression 3724 3.1.2. Optimization Studies for in Vivo Applications 3726 3.2. Aptamers as Antiviral Agents 3726 3.3. Aptamers in Animal Models 3728 3.4. Aptamers as Delivery Molecules 3729 4. Allosteric Ribozymes and Riboswitches 3729 4.1. Aptamers and Aptazymes as Molecular Switches 3729 4.1.1. Aptazymes Based on the Hammerhead Ribozyme (HHR) 3730 4.1.2. Aptazymes Based on the Hairpin Ribozyme 3732 4.1.3. Aptazymes Based on Ligase Ribozymes 3733 4.1.4. Aptazymes Based on the Diels−Alderase Ribozyme 3734 4.2. Riboswitches: Natural Regulatory Aptamers 3734 4.3. Artificial Riboswitches 3735 4.4. Natural versus in Vitro Selected Aptamers 3735 5. Conclusion 3736 6. Acknowledgments 3737 7. References 3737

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Section: Natural Versus In Vitro Selected Aptamersmentioning

confidence: 99%

Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy

2007

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“…It could have been a handle through which ribozymes got hold of the coenzyme before the protein world 28,29 . Aptamers evolved to bind CoA are always binding the coenzyme through the adenine part, and never through the sulfonated pantothenic acid part 30 . These coenzymes are the ones found to be autocatalytic in metabolism 31 , which also suggests their ancient origin.…”

Section: Hypercyclesmentioning

confidence: 99%

“…, which is around 10 30 . The important enzymes need to emerge from this sequence space, from which at any particular time only an infinitesimally small fraction can be realized.…”

Section: I/1 the Combinatorial Approachmentioning

confidence: 99%

The dynamics of the RNA world: insights and challenges

Kun

Szilágyi

Könnyű

et al. 2015

Annals of the New York Academy of Sciences

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The problem of the origin of life is not only one of structure but also that of dynamics. Ever since the seminal result of Manfred Eigen in 1971 showing that early template replication suffers from an error threshold, research has tackled the issue of how early genomes could have been dynamically stable without highly evolved mechanisms such as accurate replication and chromosomes. We review the theory of the origin, maintenance and enhancement of the RNA world as an evolving population of dynamical systems. Investigation of sequence space has revealed how structures are allocated in sequence space and how this affects the nature of the error threshold that sets the selectively maintainable genome length. New applications of old dynamical theory are still possible: the application of Gause's principle of competitive exclusion, based on resource utilisation, to RNA replication predicts that at most four pairs (plus and minus strands) can stably be maintained on four nucleotides. Other mechanisms of early template coexistence should be regarded as additional means to raise the number of coexisting species above the number set by the competitive exclusion principle. One such example is the hypercycle in which templates were postulated to help replication of the next member in a cycle superimposed on individual replication cycles. Although the hypercycle is ecologically unstable it is evolutionarily unstable because it cannot efficiently compete against emerging parasites. Population structure can modify this conclusion but not without further qualification. The simplest form of population structure is limited diffusion on a surface. This simple mechanism can ensure the coexistence of competing ribozymes contributing to surface metabolism as well as the spread of efficient replicases despite the parasite problem. Hypercyclescan only be saved by active compartmentalization when replicators are enclosed in reproducing protocells. Once there are protocells there is no need for internal hypercyclic organization, however. Finally we review two crucial adaptations that enhanced the RNA world: chromosomes and enzymatic metabolism. Interestingly, it was shown that these two have been presumably coevolutionarily linked because protocells harbouring unlinked, competing ribozymes are better off if the ribozymes remain inefficient but generalists. The appearance of chromosomes alleviates intragenomic conflict and is enabling constraint for the emergence of specific and efficient enzymes.The possibility of an RNA world, a period in the origin of life on Earth, when RNA molecules acted both as enzymes and as genetic material, was suggested well before the name was coined by Gilbert in 1986 1 . The history of the research on the origin of life 2 tells us that the potential prebiotic importance of RNA was suggested as early as in the late 50's. When it became established that living cells harbour much more RNA than DNA some biologist have proposed that RNA preceded DNA during evolution 3,4 . The discovery of the details of protein ...

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“…From a modern perspective, on the other hand, specific recognition of purine nucleobases and nucleotides through a diverse set of base-base interactions observed in biological RNAs (Leontis & Westhof, 1998; Leontis & Westhof, 2001) can be achieved by informationally simple motifs (Carothers et al, 2004). For example, the “classic” ATP aptamer (Sassanfar & Szostak, 1993) has emerged multiple times across independent experiments (Saran et al, 2003). Currently, there are a number of structurally distinct ATP and GTP aptamers that exhibit a diverse range of both affinity and specificity, indicating many solutions exist to the problem of recognizing purines and their derivatives (Huang & Szostak, 2003; Sazani et al, 2004; Weill et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Structure and mechanism of purine-binding riboswitches

Batey

2012

Quart. Rev. Biophys.

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A riboswitch is a non-protein coding sequence capable of directly binding a small molecule effector without the assistance of accessory proteins to regulate expression of the mRNA in which it is embedded. Currently, over 20 different classes of riboswitches have been validated in bacteria with the promise of many more to come, making them an important means of regulation of the genome in the bacterial kingdom. Strikingly, half of the known riboswitches recognize effector compounds that contain a purine or related moiety. In the last decade significant progress has been made to determine how riboswitches specifically recognize these compounds against the background of many other similar cellular metabolites and transduce this signal into a regulatory response. Of the known riboswitches, the purine family containing guanine, adenine, and 2’-deoxyguanosine binding classes are the most extensively studied, serving as a simple and useful paradigm for understanding how these regulatory RNAs function. This review provides a comprehensive summary of the current state of knowledge regarding the structure and mechanism of these riboswitches, as well as insights into how they might be exploited as therapeutic targets and novel biosensors.

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The tyranny of adenosine recognition among RNA aptamers to coenzyme A

Cited by 25 publications

References 17 publications

Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy

Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy

The dynamics of the RNA world: insights and challenges

Structure and mechanism of purine-binding riboswitches

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