Selection of RNA amide synthases

Wiegand, Torsten W.; Janssen, Rachel C.; Eaton, Bruce E.

doi:10.1016/s1074-5521(97)90223-4

Cited by 156 publications

(101 citation statements)

References 32 publications

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“…Selection amplification, or SELEX (Ellington and Szostak 1990;Robertson and Joyce 1990;Tuerk and Gold 1990;Ellington et al 2000), has revealed many novel reactions-carbon-carbon bond formation (Tarasow 1997;Sengle et al 2001), amide bond synthesis (Lohse and Szostak 1996;Wiegand et al 1997;Zhang and Cech 1997), acetyl-CoA synthesis (Jadhav and Yarus 2002), anhydride activation of carbonyl groups (Kumar and Yarus 2001), and aminoacyl-RNA synthesis both in cis (Illangasekare et al 1995;Yarus 1999a, 1999b) and in trans (Lee et al 2000). This list could easily be lengthened.…”

Section: Introductionmentioning

confidence: 99%

Finding specific RNA motifs: Function in a zeptomole world?

Knight

Yarus²

2003

RNA

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We have developed a new method for estimating the abundance of any modular (piecewise) RNA motif within a longer random region. We have used this method to estimate the size of the active motifs available to modern SELEX experiments (picomoles of unique sequences) and to a plausible RNA World (zeptomoles of unique sequences: 1 zmole = 602 sequences). Unexpectedly, activities such as specific isoleucine binding are almost certainly present in zeptomoles of molecules, and even ribozymes such as self-cleavage motifs may appear (depending on assumptions about the minimal structures). The number of specified nucleotides is not the only important determinant of a motif's rarity: The number of modules into which it is divided, and the details of this division, are also crucial. We propose three maxims for easily isolated motifs: the Maxim of Minimization, the Maxim of Multiplicity, and the Maxim of the Median. These maxims together state that selected motifs should be small and composed of as many separate, equally sized modules as possible. For evenly divided motifs with four modules, the largest accessible activity in picomole scale (1-1000 pmole) pools of length 100 is about 34 nucleotides; while for zeptomole scale (1-1000 zmole) pools it is about 20 specific nucleotides (50% probability of occurrence). This latter figure includes some ribozymes and aptamers. Consequently, an RNA metabolism apparently could have begun with only zeptomoles of RNA molecules.

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Section: Introductionmentioning

confidence: 99%

Finding specific RNA motifs: Function in a zeptomole world?

Knight

Yarus²

2003

RNA

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“…Some effort has been devoted to developing in vitro selection processes that use modified monomer triphosphates as substrates for polymerases (27)(28)(29)(30)(31)(32)(33)(34)(35)(36), and several in vitro selection experiments have been undertaken to select for catalysts or aptamers whose functions depend on the presence of modified nucleotides (37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48), with notable success (39,40,(43)(44)(45)(46)(47). On the other hand, modified building blocks have not proven to always be critical in obtaining superior receptors or catalysts (40,42,48,49). For example, comparable or better Diels-Alderase ribozymes were obtained from pools assembled with natural nucleotides (49) vs corresponding modified pools (41).…”

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confidence: 99%

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality

et al. 2003

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An analogue of uridine triphosphate containing a cationic functional group was incorporated into a degenerate RNA library by enzymatic polymerization. In vitro selection experiments using this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner completely dependent on the presence of the cationic functionality. The consensus sequence and a secondary structure model for the ATP binding site were obtained by the analysis of functional sequences selected from a partially randomized pool based on the minimal parental sequence. Mutational studies of this receptor indicated that several of the modified uridines are critical for ATP binding. Analysis of the binding of ATP analogues revealed that the modified RNA receptor makes numerous contacts with ATP, including interactions with the triphosphate group. In contrast, the aptamer repeatedly isolated from natural RNA libraries does not interact with the triphosphate group of ATP. The incorporation of a cationic amine into nucleic acids clearly allows novel interactions to occur during the molecular recognition of ligands, which carries interesting implications for the RNA world hypothesis. In addition, new materials generated from such functionalized nucleic acids could be useful tools in research and diagnostics.

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“…Beyond representing a convenient vector for the functionalization of nucleic acids, modified dNTPs can be engaged in SELEX and other related combinatorial methods of in vitro selection for the generation of modified catalytic nucleic acids [21][22][23][24][25][26][27][28][29][30] and aptamers for various practical applications 10,[31][32][33][34][35][36] . The additional side-chains that are introduced by the polymerization of the modified dNTPs are thought to increase the chemical space that can be explored during a selection experiment and supplement the rather poor functional arsenal of nucleic acids 37 .…”

Section: Introductionmentioning

confidence: 99%

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

Hollenstein

Smith

Räz

2014

JoVE

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The traditional strategy for the introduction of chemical functionalities is the use of solid-phase synthesis by appending suitably modified phosphoramidite precursors to the nascent chain. However, the conditions used during the synthesis and the restriction to rather short sequences hamper the applicability of this methodology. On the other hand, modified nucleoside triphosphates are activated building blocks that have been employed for the mild introduction of numerous functional groups into nucleic acids, a strategy that paves the way for the use of modified nucleic acids in a wide-ranging palette of practical applications such as functional tagging and generation of ribozymes and DNAzymes. One of the major challenges resides in the intricacy of the methodology leading to the isolation and characterization of these nucleoside analogues.In this video article, we present a detailed protocol for the synthesis of these modified analogues using phosphorous(III)-based reagents. In addition, the procedure for their biochemical characterization is divulged, with a special emphasis on primer extension reactions and TdT tailing polymerization. This detailed protocol will be of use for the crafting of modified dNTPs and their further use in chemical biology. Video LinkThe video component of this article can be found at

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Selection of RNA amide synthases

Cited by 156 publications

References 32 publications

Finding specific RNA motifs: Function in a zeptomole world?

Finding specific RNA motifs: Function in a zeptomole world?

A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality

Nucleoside Triphosphates - From Synthesis to Biochemical Characterization

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