• The Plant Pathology Journal
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• 제24권3호
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• pp.289-295
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• 2008

RNA-RNA interactions and the dynamic RNA conformations are important regulators in virus replication in several RNA virus systems and may also involved in the regulation of many important virus life cycle phases, including translation, replication, assembly, and switches in these important stages. The 5' non-translated region of Potato virus X(PVX) contains multiple cis-acting elements that facilitate various viral processes. It has previously been proposed that RNA-RNA interactions between various RNA elements present in PVX RNA genome are required for PVX RNA accumulation(Hu et al., 2007; Kim and Hemenway, 1999). This model was based on the potential base-pairing between conserved sequence elements at the upstream of subgenomic RNAs(sgRNAs) and at the 5' and 3' end of RNA genome. We now provide more evidence that RNA-RNA base-pairing between elements present at the 5' end and upstream of each sgRNA is required for efficient replication of genomic and subgenomic plus-strand RNA accumulation. Site-directed mutations introduced at the 5' end of plus-strand RNA replication defective mutant(${\Delta}12$) increasing base-pairing possibility with conserved sequence elements located upstream of each sgRNAs restored genomic and subgenomic plus-strand RNA accumulation and caused symptom development in inoculated Nicotiana benthamiana plants. Serial passage of a deletion mutant(${\Delta}8$) caused more severe symptoms and restored wild type sequences and thus retained possible RNA-RNA base-pairing. Altogether, these results indicate that the RNA element located at the 5' end of PVX genome involved in RNA-RNA interactions and play a key role in high-level accumulation of plus-strand RNA in vivo.

• 한국자기공명학회논문지
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• 제8권2호
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• pp.96-107
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• 2004

We prepared two oligonucleotides containing same base pairing, but different base sequence in the middle region, d(CGAATTCG) and d(CGTATACG). NMR and UV absorbance data represented that such variation in base sequence could cause a significant difference in melting temperature and dynamics between d(CGAATTCG)$_2$ and d(CGTATACG)$_2$ duplexes, which are regarded to be associated with the stacked structure and the width of the minor groove of them. The latter showed poor stability compared to the former, because of poor stacking of bases. And berenil could bind to the minor groove of d(CGAATTCG)$_2$ which is relatively narrow, more strongly than d(CGTATACG)$_2$ and this gave rise to large improvement in thermal stability of the d(CGAATTCG)$_2$ duplex, compared to d(CGTATACG)$_2$.

• BMB Reports
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• 제42권6호
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• pp.373-379
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• 2009

5-Hydroxyuridine (5-OHU) is a major lesion of uridine and cytosine produced in RNA by various chemical oxidants. To elucidate its biochemical and biophysical effects on RNA replication, the site-specifically modified oligoribonucleotides containing 5-OHU were synthesized with C5-hydroxy-5'-ODMTr-2'-TBDMS-uridine phosphoramidite using automated solid phase synthesis. The base-pairing properties of nucleotides opposite 5-OHU in 24 mer oligoribonulcleotides with dNTP were studied using three reverse transcriptases (Super-$Script^{TM}II$-, AMV-, MMLV-RT) in cDNA synthesis. Adenine as well as guanine was incorporated preferentially by all reverse transcriptases. In the UV-melting temperature experiment, the results from the relative stabilities of the base pairs were A : 5-OHU > G : 5-OHU > T : 5-OHU $\approx$ C : 5-OHU. Circular Dichroism (CD) studies showed that DNA-RNA containing 5- OHU heteroduplexes exhibit a similar conformation between the A-type RNA and B-type DNA. These results suggest that 5- OHU from oxidative damage was mainly influenced by adenine mismatch.

• BMB Reports
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• 제37권6호
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• pp.657-662
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• 2004

Oligoribonucleotides containing 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2'-O-methylguanosine (8-oxoG-Me) were synthesized. The base pairing properties of 8-oxoG and 8-oxoG-Me in oligoribonucleotide in cDNA synthesis by reverse transcriptases were studied. dCMP was preferentially incorporated into the site opposite 8-oxoG or 8-oxoG-Me than into other dNMPs. TMP and dCMP were inserted preferentially into sites opposite 8-oxoG or 8-oxoG by reverse transcriptases. HIV-RT did not incorporate TMP, but RAV2-RT incorporated 50% more TMP than dCMP into the site opposite 8-oxoG. In the site opposite 8-oxoG-Me TMP was substantially incorporated by HIV-RT or RAV2-RT. Thermodynamic analysis of the DNA. RNA heteroduplex containing 8-oxoG revealed that 8-oxoG and 8-oxoG-Me formed base pairs with cytidine and thymidine with similar stability. The thermodynamic parameter (${\Delta}G^{\circ}$) demonstrated that the formation of duplexes between 8-oxoG or 8-oxoG-Me and cytidine or thymidine is more thermodynamically favorable than with adenosine and guanosine. However, differences in the melting temperature and ${\Delta}G^{\circ}$'s of 8-oxoG/dC and 8-oxoG/T were much smaller than between G/dC and G/T. CD spectra showed that DNA . RNA containing 8-oxoG or 8-oxoG-Me duplexes showed similarities between the A-type RNA and B-type DNA conformations.

• Bulletin of the Korean Chemical Society
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• 제29권1호
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• pp.205-207
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• 2008

• Bulletin of the Korean Chemical Society
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• 제13권4호
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• pp.345-346
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• 1992

• BMB Reports
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• 제47권11호
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• pp.619-624
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• 2014

Antisense RNA is a type of noncoding RNA (ncRNA) that binds to complementary mRNA sequences and induces gene repression by inhibiting translation or degrading mRNA. Recently, several small ncRNAs (sRNAs) have been identified in Escherichia coli that act as antisense RNA mainly via base pairing with mRNA. The base pairing predominantly leads to gene repression, and in some cases, gene activation. In the current study, we examined how the location of target sites affects sRNA-mediated gene regulation. An efficient antisense RNA expression system was developed, and the effects of antisense RNAs on various target sites in a model mRNA were examined. The target sites of antisense RNAs suppressing gene expression were identified, not only in the translation initiation region (TIR) of mRNA, but also at the junction between the coding region and 3' untranslated region. Surprisingly, an antisense RNA recognizing the upstream region of TIR enhanced gene expression through increasing mRNA stability.

• 산업경영시스템학회지
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• 제24권65호
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• pp.89-102
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• 2001

In this paper, the aircraft route scheduling consists of two steps; the pairing generation and the aircraft assignment. The pairing generation is heuristic approach how flights construct pairings from and to the main base. The aircraft resource assignment which is to establish a aircraft route schedule is constructed by constraint satisfaction problem technique. ILOG solver and schedule is used to solve this problem. In addition, a aircraft route reschedule process against departure-arrival delay or aircraft maintenance schedule change is added by partial constraints satisfaction problem technique. Also, Gantt chart made by ILOG views is used to show aircraft route schedule results more easily.

• ETRI Journal
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• 제40권2호
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• pp.207-217
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• 2018

As implementation of the in-band full duplex (IFD) transceiver becomes feasible, research interest is growing with respect to using IFD communication with cellular networks. However, the cellular network in which the IFD communication is applied inevitably suffers from an increase of the co-channel interference (CCI) due to IFD simultaneous transmission and reception. In this paper, we analyze the performance of a cellular network based on uni-directional IFD (UD-IFD) communication, wherein an IFD base station simultaneously supports downlink and uplink transmissions of half-duplex (HD) users. In addition, a multi-pair CCI cancellation (MP-CCIC) method combining CCIC and user pairing is proposed to improve the performance of the UD-IFD network. Simulation results showed that, compared to a conventional HD cellular network without using CCIC, capacity gain was not obtained in the UD-IFD cellular network. On the other hand, when applying the proposed MP-CCIC, the capacity of the UD-IFD cellular network greatly improved compared to that of an HD cellular network.

• 한국콘텐츠학회논문지
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• 제6권12호
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• pp.12-20
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• 2006

본 논문에서는 유/무선 통합 환경에서 전자상거래를 활성화시키기 위한 지불 수단으로 GDHP 은닉서명 기법을 이용한 전자지불 프로토콜을 제안한다. GDHP 기반의 타원곡선 알고리즘을 적용하여 통신횟수, 계산량 측면에서 기존의 은닉서명 방식의 효율성을 개선하였다. 또한, 기존의 PayWord 프로토콜에서 사용한 인증서 대신 유한체 $F_q$ 에서 타원곡선(Elliptic Curve Cryptosystem) 을 이용한 Weil pairing에 의해 생성된 세션키를 사용하여 개체간의 인증이 이루어지기 때문에 속도의 향상 및 위장공격(Man-in-the-middle attacks)과 Forward secrecy 에 대한 안전성을 제공한다.