Flavin Recognition by an RNA Aptamer Targeted toward FAD

Roychowdhury-Saha, Manami; Lato, Susan M.; Shank, Eric D.; Burke, Donald H.

doi:10.1021/bi015719d

Cited by 38 publications

(31 citation statements)

References 35 publications

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“…It has been shown that artificial RNA sequences (aptamers) can bind FMN with very high affinity. 44,45 It has also been shown that the regulation of the riboflavin biosynthesis operon in Bacillaceae is based on the interaction of FMN with the mRNA specified by the rib operon resulting in premature transcription termination. 46 A hypothetical RNA world would most probably have required catalytic redox processes, and flavin derivatives would have been excellent candidates due to the fact that the isoalloxazine chromophore can arise by a highly unusual reaction in the absence of any catalyst.…”

Section: Discussionmentioning

confidence: 99%

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea

Fischer

Schott

Römisch

et al. 2004

Journal of Molecular Biology

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Section: Discussionmentioning

confidence: 99%

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea

Fischer

Schott

Römisch

et al. 2004

Journal of Molecular Biology

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“…Anti-FMN and anti-FAD aptamers were first isolated by Burgstaller and Famulok [63], while Lauhon and Szostak later isolated additional flavin-binding aptamers [70]. An additional class of anti-FAD aptamers was isolated by Burke and co-workers [71]. These aptamers all recognize riboflavin with K d values ranging from 0.5 to 50 mm but have different sequences, and adopt different secondary and tertiary structures: the anti-FMN and anti-FAD binding aptamers found by Burgstaller and Famulok have simple loop structures, the anti-riboflavin aptamers isolated by Lauhon and Szostak fold into intramolecular G-quartets, and the anti-FAD aptamer isolated by Burke and coworkers contains three helices interrupted by several internal bulges.…”

mentioning

confidence: 99%

Ribozyme Catalysis of Metabolism in the RNA World

Chen¹,

Li²,

Ellington³

2007

Chemistry & Biodiversity

172

105

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In vitro selection has proven to be a useful means of explore the molecules and catalysts that may have existed in a primordial 'RNA world'. By selecting binding species (aptamers) and catalysts (ribozymes) from random sequence pools, the relationship between biopolymer complexity and function can be better understood, and potential evolutionary transitions between functional molecules can be charted. In this review, we have focused on several critical events or transitions in the putative RNA world: RNA self-replication; the synthesis and utilization of nucleotide-based cofactors; acyl-transfer reactions leading to peptide and protein synthesis; and the basic metabolic pathways that are found in modern living systems.

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“…Furthermore the aptamers from the NaCl selection also weakly bound adenosylcobalamin. Roychowdhury-Saha et al (2002) isolated flavin-binding RNA aptamers in a selection targeting FAD. The approximate K d for FAD was 50 mmol/L.…”

Section: Aptamers To Cofactorsmentioning

confidence: 99%

Aptamers to Small Molecules

Fickert

Fransson

Hahn

2006

The Aptamer Handbook

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fluence on binding. Furthermore, the sizes of the RNA and DNA aptamers to ATP were similar (40 versus 42, respectively), so one could draw the conclusion that aptamers (of similar complexity) for one target molecule can be isolated from both RNA and DNA pools. However, the selected RNA and DNA aptamers had significantly different sequences and fold into different structures because the DNA lacks the 2l-hydroxyl group of the RNA. This was demonstrated when the DNA version of the RNA aptamer for ATP and the RNA version of the DNA aptamer for ATP were tested for binding, respectively, and neither recognized ATP. A difference between the RNA and DNA aptamers was detected by nuclear magnetic resonance (NMR) studies of the aptamers, revealing that the DNA aptamer binds two ATP molecules, while the RNA aptamer binds just one (Lin and Patel, 1997). Kiga et al. (1998) isolated an RNA aptamer binding xanthine and guanine ( Fig. 4.1). The aptamers were selected via affinity chromatography with xanthine agarose; bound RNA was eluted with free xanthine. A representative RNA aptamer was truncated to 32 nucleotides and turned out to bind xanthine with a K d of 3.3 mmol/L. Guanine was bound by the aptamer as well, while adenenine, cytosine, and uracil were not bound.RNA aptamers that exhibited a new mode of purine recognition were published by Meli et al. (2002). The aptamer contained two relatively independent secondary structure elements, which formed a bipartite RNA structure that bound adenine with a K d of 10 mmol/L. In this aptamer the imidazole moiety of adenine is not trapped in the binding side, as it is in other adenine/ATP-binding aptamers. Hence this aptamer could be supposed to be a cofactor-binding site in a complex ribozyme.In 2004 RNA aptamers that recognized the triphosphate of ATP were selected in the laboratory of Jack W. Szostak (Sazani et al., 2004). By employing a restrictive selection protocol containing AMP-agarose for counterselection and washing the selection column (ATP-agarose) with free AMP prior to elution of ATP-bound RNA, they could isolate aptamers that strongly interacted with the b and g phosphate. The K d -value of a 57-nucleotide minimized aptamer was 11 mmol/L for ATP and 1700 mmol/L for AMP. In contrast to other ATP aptamers, this aptamer showed binding to GTP, UTP, and CTP, also. The aptamer was not isolated in an earlier selection for ATP aptamers, although it had an affinity comparable to other ATP aptamers. That might be due to its more complex structure. Therefore, this triphosphate-binding aptamer could first be isolated after counterselection for the simpler ATP-binding molecules. 96 4 Aptamers to Small MoleculesFig. 4.1 Xanthine and guanine. The RNA aptamer selected for xanthine also binds guanine, while adenine, cytosine, and uracil are not bound.97 Aptamers to Cofactors

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Flavin Recognition by an RNA Aptamer Targeted toward FAD

Cited by 38 publications

References 35 publications

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea

Evolution of Vitamin B2 Biosynthesis. A Novel Class of Riboflavin Synthase in Archaea

Ribozyme Catalysis of Metabolism in the RNA World

Aptamers to Small Molecules

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