• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.228-233
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• 2008

Effects of chaperones on mRNA stability and gene expression were studied in order to develop an efficient Escherichia coli expression system that can maximize gene expression. The stability of mRNA was modulated by introducing various secondary structures at the 5'-end of mRNA. Four vector systems providing different 5'-end structures were constructed, and genes encoding GFPuv and endoxylanase were cloned into the four vector systems. Primer extension assay revealed different mRNA half-lives depending on the 5'-end secondary structures of mRNA. In addition to the stem-loop structure at the 5'-end of mRNA, coexpression of dnaK-dnaJ-grpE or groEL-groES, representative heat-shock genes in E. coli, increased the mRNA stability and the level of gene expression further, even though the degree of stabilization was varied. Our work suggests that some of the heat-shock proteins can function as mRNA stabilizers as well s protein chaperones.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.17-23
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• 2007

Shot interfering RNA (siRNA) can be used to silence specific gene expression and have many potential therapeutic applications. However, how to design an effective siRNA is still not clear. Highly effective siRNA has sequence-specific properties which are low G/C content, low internal stability at the sense strand 3'-terminus, sense strand base bias(position 1 is G/C, position 19 is /AU). Recently, mRNA secondary structure playsan important role in RNAi. Target site of siRNA in high-ordered structure (i.e hairpin loop, multi loop) or base pair of many hydrogen bonds dramatically reduce function of siRNA mediated gene silencing. Possible off-target effects of siRNA is detecting from BLAST search.

• Proceedings of the Zoological Society Korea Conference
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• 1998.04a
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• pp.37.1-37
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• 1998

No Abstract, See Full Text

• Proceedings of the Korean Biophysical Society Conference
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• 1999.06a
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• pp.37-37
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• 1999

The influenza A viruses which are the most severe and common among the influenza viruses have 8 segmented RNA genomes Each RNA segment has highly conserved 3' and 5' terminal sequence except a single U\longrightarrowC variation especially in the 4 position of the 3' terminal of the 3 segments encoding own RNA polymerase.(omitted)

• Journal of Microbiology
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• v.41 no.3
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• pp.239-247
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• 2003

The LRV1-4 capsid protein possesses an endoribonuclease activity that is responsible for the single site-specific cleavage in the 5' untranslated region (UTR) of its own viral RNA genome and the formation of a conserved stem-loop structure (stem-loop IV) in the UTR is essential for the accurate RNA cleavage by the capsid protein. To delineate the nucleotide sequences, which are essential for the correct formation of the stem-loop structure for the accurate RNA cleavage by the viral capsid protein, a wildtype minimal RNA transcript (RNA 5' 249-342) and several synthetic RNA transcripts encoding point-mutations in the stem-loop region were generated in an in vitro transcription system, and used as substrates for the RNA cleavage assay and RNase mapping studies. When the RNA 5' 249-342 transcript was subjected to RNase T1 and A mapping studies, the results showed that the predicted RNA secondary structure in the stem-loop region using FOLD analysis only existed in the presence of Mg$\^$2＋/ ions, suggesting that the metal ion stabilizes the stem-loop structure of the substrate RNA in solution. When point-mutated RNA substrates were used in the RNA cleavage assay and RNase T1 mapping study, the specific nucleotide sequences in the stem-loop region were not required for the accurate RNA cleavage by the viral capsid protein, but the formation of a stem-loop like structure in a region (nucleotides from 267 to 287) stabilized by Mg$\^$2＋/ ions was critical for the accurate RNA cleavage. The RNase T1 mapping and EMSA studies revealed that the Ca$\^$2＋/ and Mn$\^$2＋/ ions, among the reagents tested, could change the mobility of the substrate RNA 5' 249-342 on a gel similarly to that of Mg$\^$2＋/ ions, but only Ca$\^$2＋/ ions identically showed the stabilizing effect of Mg$\^$2＋/ ions on the stem-loop structure, suggesting that binding of the metal ions (Mg$\^$2＋/ or Ca$\^$2＋/) onto the RNA substrate in solution causes change and stabilization of the RNA stem-loop structure, and only the substrate RNA with a rigid stem-loop structure in the essential region can be accurately cleaved by the LRV1-4 viral capsid protein.

• Korean Journal of Microbiology
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• v.30 no.6
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• pp.472-478
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• 1992

Synthesis of the pol gene products of HTLV-I requires rihosomes to shift frame twice in - I direction while translating genome-size mRNA. We havc made a lI1utagcni/cd RNA in which the gag and pro genes are aligned to allow synthe,.is of a largcr amount of the Gag-Pro-Pol polyproteins by a single frameshifting. Using this mutant, wc could examine the questions whether the predicted RNA secondary or tertiary structure downstream of the shift site is operative as a determinant for - I frameshifting. Deletion analysis showed that the stem-loop structure is essential for efficient frameshifting in the pro-pol overlap, but formation of a pseudoknot is less important.

• Journal of the Korean Chemical Society
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• v.46 no.1
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• pp.46-51
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• 2002

The recognition and cleavage of 5S rRNA from P. alcaligenes by metallopeptides to the form $Ni(II){\cdot}Gly$-Gly-His(Arg)COOH and $Cu(II){\cdot}Gly$-Gly-His(Arg)COOH were investigated. The results of RNA cleavage analyses suggest that metallopeptides selectively target the unpaired or unstably paired bases of stem-loop structure of 5S rRNA. The selectivity of metallopeptides was little affected by the species of metal ion, Ni(II) or Cu(II). When the result of cleavage by metallopeptides was compared with that of by metal complexes M(II)CR, the recognition by metallopeptides was more selective and structure specific. The cleavage data by metallopeptides and other metal complexes were used to probe the secondary structure of 5S rRNA from P. alcaligenes.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2005.04a
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• pp.20-21
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• 2005

• Molecules and Cells
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• v.26 no.3
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• pp.308-313
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• 2008

In animals, microRNAs (miRNAs) and small interfering RNAs (siRNAs) repress expression of protein coding genes by assembling distinct RNA-induced silencing complexes (RISCs). It has previously been shown that passenger-strand cleavage is the predominant mechanism when siRNA duplexes are loaded into Argonaute2 (Ago2)-containing RISC, while an unwinding bypass mechanism is favored for miRNA duplexes with mismatches. Here I present experimental data indicating that some mammalian miRNAs are assembled into Ago2-containing RISC by cleaving their corresponding miRNA star strands. This phenomenon may depend on the secondary structure near the scissile phosphate of the miRNA duplex. In addition, I show that ATP is not required for star-strand cleavage in this process. Taken together, the data here provide insight into the miRNA-loading mechanisms in mammals.

• ALGAE
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• v.35 no.1
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• pp.1-15
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• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.