Identification of a structural motif of 23S rRNA interacting with 5S rRNA

Ko, Jin Hong; Lee, Younghoon; Park, Inwon; Cho, Bongrae

doi:10.1016/s0014-5793(01)03068-x

Cited by 25 publications

(14 citation statements)

References 17 publications

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“…This region is located in domain IV or loop D of 5S rRNA. From the structure of the large subunit ( Figure 8C and 8D), it is clear that these nucleotides make a bridging interaction with domain II and V of 23S rRNA and are critical for ribosomal function [63][64][65]. Mutation of a conserved nucleotide (U89) in loop D of 5S rRNA disturbs ribosomal function [66,67].…”

Section: The Footprint Of the Bacterial Rf On The Ribosomementioning

confidence: 99%

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

et al. 2007

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The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to span the decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site crafted for a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide, the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein that results in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial termination complex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stop codon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix a5. The anticodon loop also makes contact with the base following the stop codon that is known to strongly influence termination efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. The mRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflect structural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiased SELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in its different binding conformations within the active centre of the ribosome.

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Section: The Footprint Of the Bacterial Rf On The Ribosomementioning

confidence: 99%

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

et al. 2007

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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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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. [14][15][16][17][18][19][20][21][22][23][24][25][26] In this study, RNA molecules binding to the guanine-rich RNA in the RNA 5'-UTR of N-ras oncogene, were selected from an RNA pool containing 48 randomized nucleotides. An RNA pool for SELEX was prepared by in vitro transcription using T7 RNA polymerase from the corresponding double-stranded DNA library of about 10 14 independent sequences.…”

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confidence: 99%

Identification of Structural Motif of RNAs Interacting with the G-rich Sequence RNA

Cho

2012

Bulletin of the Korean Chemical Society

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Guanine-rich tracts are observed in the 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 The Gquadruplexes 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) in 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 Telomeric DNA ends decrease 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 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 recently identified.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 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 oncogenes.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 ampl...

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Identification of a structural motif of 23S rRNA interacting with 5S rRNA

Cited by 25 publications

References 17 publications

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

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

Identification of Structural Motif of RNAs Interacting with the G-rich Sequence RNA

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