Interacting RNA species identified by combinatorial selection

Cho, Bongrae; Taylor, David C.; Nicholas, Hugh B.; Schmidt, Francis J.

doi:10.1016/s0968-0896(97)00046-1

Cited by 15 publications

(13 citation statements)

References 15 publications

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“…We used RNA-RNA SELEX (Cho et al 1997;Soukup and Maher 1998) to select RNA aptamers that bound to a defined RNA. The target RNA for affinity selection was the columnbound P5.1 stem-loop element from Bacillus subtilis RNase P RNA (Table 1).…”

Section: In Vitro Selectionmentioning

confidence: 99%

Frequency of RNA–RNA interaction in a model of the RNA World

Striggles

Martin²,

Schmidt³

2006

RNA

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The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations. The mechanisms by which these random populations could be generated de novo are unclear. Non-enzymatic and RNA-catalyzed nucleic acid polymerizations are poorly processive, which means that the resulting short-chain RNA population could contain only limited diversity. Nonreciprocal recombination of smaller RNAs provides an alternative mechanism for the assembly of larger species with concomitantly greater structural diversity; however, the frequency of any specific recombination event in a random RNA population is limited by the low probability of an encounter between any two given molecules. This low probability could be overcome if the molecules capable of productive recombination were redundant, with many nonhomologous but functionally equivalent RNAs being present in a random population. Here we report fluctuation experiments to estimate the redundancy of the set of RNAs in a population of random sequences that are capable of non-Watson-Crick interaction with another RNA. Parallel SELEX experiments showed that at least one in 10 6 random 20-mers binds to the P5.1 stem-loop of Bacillus subtilis RNase P RNA with affinities equal to that of its naturally occurring partner. This high frequency predicts that a single RNA in an RNA World would encounter multiple interacting RNAs within its lifetime, supporting recombination as a plausible mechanism for prebiotic RNA evolution. The large number of equivalent species implies that the selection of any single interacting species in the RNA World would be a contingent event, i.e., one resulting from historical accident.

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Section: In Vitro Selectionmentioning

confidence: 99%

Frequency of RNA–RNA interaction in a model of the RNA World

Striggles

Martin²,

Schmidt³

2006

RNA

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“…Target molecules include proteins, amino acids, nucleotides, antibiotics and RNA. [14][15][16][17][18][19][20][21][22][23][24][25][26] We used SELEX technique to get the information for the RNA-RNA interaction and got the similar results with affinity chromatography and gel mobility shift assay. According to this result, we knew that similar results could be got irrespective of SELEX techniques employed.…”

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confidence: 99%

“…According to this result, we knew that similar results could be got irrespective of SELEX techniques employed. 21 We have already isolated RNA molecules binding to the guanine-rich RNA in the 5'-UTR RNA of N-ras oncogene from an RNA pool containing 48 randomized nucleotides.…”

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confidence: 99%

Conserved Sequence Motif of RNA Aptamers Binding to the G-rich Sequence RNA

Cho

2013

Bulletin of the Korean Chemical Society

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Guanine-rich tracts are observed in terminal segments of eukaryotic genomes.1,2 These guanine-rich sequences have the potential to form the non-carnonical four-stranded topology called G-quadruplexes. The G-quadruplexes are built from the stacking of successive GGGG tetrads and stabilized by bound monovalent Na + and K + cations.3 They play a biological role in DNA telomere ends, the purine-rich DNA strands of the oncogenic promoter elements such as c-myc and c-kit, and RNA 5'-untranslated region (UTR) close to translational start sites. Telomeres located at the ends of eukaryotic chromosomes are composed of the tandem DNA repeats of guanine-rich sequences and essential for chromosome stability. They appear to play a critical role in cellular aging and cancer.4-8 The end of telomeric DNA decreases in length after each round of cell division in somatic cells.9 But the telomere length can be maintained by the enzyme telomerase, a ribonucleoprotein complex with reverse transcriptase activity expressed in most cancer cells.10 So telomeres and telomerases correlated with cancer progression and have been used for the targets of anti-cancer agents.Attention has been paid to DNA quadruplexes and their potential role in biology. On the other hand, RNA quadruplexes have got less attention, despite of the implication of their involvement at the site of translational control. The guanine-rich sequences, putative G-quadruplex-forming elements in the 5'-UTRs of the human genome have been indentified.11 One of these sequences, an 18-mer containing four guanine-tracts, 5'-GGGAGGGGCGGGUCUGGG-3' is associated with the 5'-UTR of the oncogenic N-ras sequence. This sequence is located in 14-nucleotides downstream of the 5'-cap and 222-nucleotides upstream of the translation start site. The measured T m of this sequence was 63 o C in 1 mM K + cation and the stabilization decreased in the order KAccording to a cell-free translation system coupled to a reporter gene assay, the N-ras G-quadruplex can inhibit gene expression at the translational level.11 This result indicates that molecules stabilizing 5'-UTR RNA Gquadruplex formation can be the candidates for therapeutic agents, thereby inhibiting the translation of the oncogene.The expression of genetic information in RNA can be regulated by designing DNA or RNA oligonucleotide complementary to the target sequence. For example, antisense oligonucleotides were developed to specifically repress the complementary target genes.12,13 But the down regulation of specific mRNA with antisense oligonucleotide needs to be studied further because mRNAs have diverse conformers.To overcome this structural problem, SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was applied to isolate RNA aptamers which specifically bind to the N-ras G-quadruplex RNA in this study.SELEX is a technique for isolating nucleic acid molecules (aptamers) with affinities for a target molecule from a random pool with a large number of sequences by the iterative rounds of affinity selection and amplification...

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“…Target molecules include proteins, amino acids, nucleotides, antibiotics and RNA. [12][13][14][15][16][17][18][19][20][21][22][23][24] We isolated RNA molecules binding to the guanine-rich RNA (Fig. 1) in the 5'-UTR RNA of N-ras oncogene from an RNA pool.…”

mentioning

confidence: 99%

Identification of a Conserved Sequence Motif of an RNA Aptamer Binding to a G-rich Sequence RNA with Structural Probes

Choi

Cho²

2013

Bulletin of the Korean Chemical Society

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Guanine-rich sequences observed in terminal segments of eukaryotic genomes 1,2 have the potential to form the noncanonical four-stranded topology called G-quadruplexes, which are built from the stacking of successive GGGG tetrads and stabilized by bound monovalent Na + and K + cations.3 They appear to play a critical role in cellular aging and cancer.4-8 The end of telomeric DNA decreases in length after each round of cell division in somatic cells.9 But the telomere length can be maintained by the enzyme telomerase, a ribonucleoprotein complex with reverse transcriptase activity in most cancer cells.10 The guanine-rich sequences, putative G-quadruplex-forming elements in the 5'-UTRs of the human genome have been indentified.11 One of these sequences, an 18-mer containing four guanine-tracts, 5'-GGGAGGGGCGGGUCUGGG-3' is associated with the 5'-UTR of the oncogenic N-ras sequence. According to a cellfree translation system coupled to a reporter gene assay, the N-ras G-quadruplex can inhibit gene expression at the translational level.11 This result indicates that molecules stabilizing 5'-UTR RNA G-quadruplex formation can be the candidates for therapeutic agents, thereby inhibiting the translation of the oncogene.SELEX is a technique for isolating nucleic acid molecules (aptamers) with affinities for a target molecule from a random pool with a large number of sequences by the iterative rounds of affinity selection and amplification. Target molecules include proteins, amino acids, nucleotides, antibiotics and RNA.12-24 We isolated RNA molecules binding to the guanine-rich RNA (Fig. 1) in the 5'-UTR RNA of N-ras oncogene from an RNA pool.25 After the 11th round of in vitro selection, the sequences of the selected RNA aptamers were closely related and had the consensus sequence GGGAUCCGCAUGCAAGCUUA.26 This sequence is thought to be important to the interaction between the selected RNA aptamer and the ligand G-rich sequence RNA. The selected RNA aptamers can recognize the specific domain of RNA structure like a monoclonal antibody and be candidates of the anticancer agent at the genetic level. So it is important to determine the structure of the selected RNA aptamers and to get the information for the interaction between an RNA aptamer and a ligand RNA used for selection. In this study, the secondary structure of a selected RNA aptamer was determined with RNA structural probes such as RNase T1 and RNase V1 and the conserved sequence motif for the interaction between an RNA aptamer and a ligand G-rich sequence RNA was identified.The secondary structure of 11-30-24 (Fig. 1), one of RNA aptamers selected from an RNA pool including the constant primer sequences, is predicted and shown in Figure 2. This structure was found by the CLC RNA workbench ver. 4.2 program accessed on the internet (www.clcbio.com). The biochemical experiments to investigate the predicted secondary structure of the RNA aptamer were performed by using RNase T1 that has the specificity for a guanine in singlestranded region and RNase V1 that is double-...

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Interacting RNA species identified by combinatorial selection

Cited by 15 publications

References 15 publications

Frequency of RNA–RNA interaction in a model of the RNA World

Frequency of RNA–RNA interaction in a model of the RNA World

Conserved Sequence Motif of RNA Aptamers Binding to the G-rich Sequence RNA

Identification of a Conserved Sequence Motif of an RNA Aptamer Binding to a G-rich Sequence RNA with Structural Probes

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