• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2002년도 봄 학술발표논문집 Vol.29 No.1 (A)
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• pp.685-687
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• 2002

RNA pseudoknot은 RNA 삼차 구조를 형성하는 중요한 구조요소일 뿐만 아니라, RNA 분자에서 중요한 역할을 한다. 지금까지 RNA pseudoknot 구조를 시각화하는 도구는 개발되어 있지 않기 때문에 대부분의 pseudoknot 구조의 시각화 작업은 수작업으로 이루어지고 있다. 본 논문은 RNA pseudoknot을 시각화를 위한 새로운 pseudoknot 표현 기법과 시각화 알고리즘에 대해서 소개한다. 새로운 표현기법은 모든 H-type pseudoknot을 uniform planar graph로 나타내고 RNA sequence의 진행방향을 따라가기가 쉽게 되어있다. 알고리즘을 이용하여 PseudoViewer라는 프로그램을 개발하였으며 PseudoViewer는 어떠한 시스템에서도 작동할 수 있는 Java로 구현되었다. 그 결과는 pseudoknot을 명확히 구분되고 보기 쉽도록 시각화됨을 보여준다.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2002년도 봄 학술발표논문집 Vol.29 No.1 (A)
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• pp.682-684
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• 2002

RNA 분자의 pseudoknot 구조는 이차 구조의 loop에 있는 염기와 이 loop 외부에 있는 염기와의 결합으로 생성되는 삼차 구조 요소이다. pseudoknot은 삼차 구조 형성에 필수적인 구조 요소일 뿐만 아니라, RNA 분자의 기능에 중요한 영향을 미친다. pseudoknot을 포함한 RNA 구조를 예측하는 문제는 매우 어려우며 많은 계산을 필요로 한다. 현재까지, 병렬 구조를 갖는 수퍼 컴퓨터에서 유전자 알고리즘을 이용한 프로그램의 예측 결과가 가장 우수하다고 알려져 있다. 그러나 이 프로그램은 수퍼 컴퓨터에서만 운용되기 때문에 일반 연구자가 쉽게 사용하기 어려운 단점이 있다. 본 논문은 유전자 알고리즘을 이용한 PC 기반의 pseudoknot 예측 프로그램에 대하여 기술한다. 실헙 결과는 PC 기반에서도 유전자 알고리즘을 이용하여 pseudoknot을 포함한 RNA 구조를 효과적으로 예측하고 있음을 보인다.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
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• pp.254.2-254.2
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• 2003

For many viruses, -1 ribosomal frameshifting regulate protein synthesis using an RNA pseudoknot. The integrity of pseudoknot stability and structure is the important feature for efficient frameshifting. Thus, small molecules interacting with viral RNA pseudoknots would be potential antiviral agents targeting\ulcorner frameshifting system in viruses. X-ray structure of RNA pseudoknot complexed with biotin has been reported, in which biotin is bound at the interface between the pseudoknot's stacked helices. (omitted)

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.63-63
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• 2002

RNA pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frameshifting, read-through, and the initiation of translation. There exists no automatic method for drawing RNA pseudoknot structures, and thus representing RNA pseudoknots currently relies on significant amount of manual work. In this talk, I will introduce the first algorithm for automatically generating a drawing of RNA pseudoknot structures. Two basic criteria were adopted when designing the algorithm: (1) Overlapping of structural elements should be minimized to increase the readability of the drawing, and (2) The whole RNA structure as well as the pseudoknots themselves should be recognized quickly and clearly. The algorithm has been implemented in a JAVA program, which can be executed on any computing systems. Experimental results show that this program generates a clear and compact drawing of RNA pseudoknots and allows a biologist to gain insights into RNA pseudoknot structures. The program can also be used as useful aids in designing biochemical experiments to elucidate more precise mechanism of RNA functions associated with pseudoknots.

• Bulletin of the Korean Chemical Society
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• 제30권2호
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• pp.509-512
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• 2009

• Journal of Microbiology and Biotechnology
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• 제16권4호
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• pp.569-575
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• 2006

The 530 stem-loop is a 46 nucleotide stem-loop structure found in all small-subunit ribosomal RNAs. Phylogenetic and mutational studies by others suggest the requirement for Watson-Crick interactions between the nucleotides 505-507 and 524-526 (530 pseudoknot), which are highly conserved. To examine the nature and functional significance of these interactions, a random mutagenesis experiment was conducted in which the nucleotides in the proposed pseudoknot were simultaneously mutated and functional mutants were selected and analyzed. Genetic analysis revealed that the particular nucleotide present at each position except 524 was not exclusively critical to the selection of functional mutants. It also indicated that basepairing interactions between the positions 505-507 and 524-526 were required for ribosomal function, and much weaker base-pairing interactions than those of the wild-type also allowed high ribosomal function. Our results support the hypothesis that the 530 pseudoknot structure may undergo a 'conformational switch' between folded and unfolded states during certain stages of the protein synthesis process by interacting with other ligands present in its environment.

• 미생물학회지
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• 제30권6호
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• pp.472-478
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• 1992

HTLV-1 이 pol 유전자산물을 합성하기 위해서는 genome-size mRNA 를 번역해 나아가는 ribosome 이 -1 방향으로 두차례 frame 을 바꾸어야 한다. 우리는 단 한차계의 frameshifting 만으로도 많은 양의 Gag-Pro-Pol polyprotein 의 합성어 가능하도록 gag 와 pro 유전자의 frame 을 연결시킨 mutant RNA 를 제작하였다. 이 돌연변이를 이용하여 ribosome 의 shift site 하류영역내에 형성이 예상되는 RNA 의 이차구조 또는 삼차 구조가 -1 frameshifting 을 결정하는 인자로서 작용하는지의 여부를 조사하였다. 결손변이주의를 해석한 결과 pro-pol 중첩영역에서 효율적으로 frameshifting 이 일어나기 위해서는 stem-loop 가 필수적으로 형성되어야 하지만 pseudoknot 의 형성은 그다지 중요하지 않다는 사실을 알았다.

• Bulletin of the Korean Chemical Society
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• 제31권4호
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• pp.1021-1024
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• 2010

• Bioinformatics and Biosystems
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• 제1권1호
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• pp.73-81
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• 2006

This paper describes a genetic algorithm for predicting RNA structures that contain various types of pseudoknots. Pseudoknotted RNA structures are much more difficult to predict by computational methods than RNA secondary structures, as they are more complex and the analysis is time-consuming. We developed an efficient genetic algorithm to predict RNA folding structures containing any type of pseudoknot, as well as a novel initial population method to decrease computational complexity and increase the accuracy of the results. We also used an interaction filter to decrease the size of the possible stem lists for long RNA sequences. We predicted RNA structures using a number of different termination conditions and compared the validity of the results and the times required for the analyses. The algorithm proved able to predict efficiently RNA structures containing various types of pseudoknots.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.121-132
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• 2003

This paper describes a genetic algorithm for predicting RNA structures that contain various types of pseudoknots. Pseudolulotted RNA structures are much more difficult to predict by computational methods than RNA secondary structures, as they are more complex and the analysis is time-consuming. We developed an efficient genetic algorithm to predict RNA folding structures containing any type of pseudoknot, as well as a novel initial population method to decrease computational complexity and increase the accuracy of the results. We also used an interaction filter to decrease the size of the possible stem lists for long RNA sequences. We predicted RNA structures using a number of different termination conditions and compared the validity of the results and the times required for the analyses. The algorithm proved able to predict efficiently RNA structures containing various types of pseudoknots in long nucleotide sequences.