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Kyungsook Han - One of the best experts on this subject based on the ideXlab platform.
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An efficient algorithm for planar drawing of RNA structures with Pseudoknots of any type.
Journal of bioinformatics and computational biology, 2016Co-Authors: Yanga Byun, Kyungsook HanAbstract:An RNA Pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA Pseudoknots is a graph that has an inner cycle within a Pseudoknot and possibly outer cycles formed between the Pseudoknot and other structural elements. Visualizing a large-scale RNA structure with Pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both Pseudoknots and an entire structure enclosing the Pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a Pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and Pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with Pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large Pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure.
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PseudoViewer3: generating planar drawings of large-scale RNA structures with Pseudoknots
Bioinformatics (Oxford England), 2009Co-Authors: Yanga Byun, Kyungsook HanAbstract:Motivation: Pseudoknots in RNA structures make visualization of RNA structures difficult. Even if a Pseudoknot itself is represented without a crossing, visualization of the entire RNA structure with a Pseudoknot often results in a drawing with crossings between the Pseudoknot and other structural elements, and requires additional intervention by the user to ensure that the structure graph is overlap-free. Many programs such as web services prefer to obtain an overlap-free graph in one-shot rather than get a graph with overlaps to be edited. There are few programs for visualizing RNA Pseudoknots, and PseudoViewer has been the almost only program that automatically draws RNA secondary structures with Pseudoknots. The previous version of PseudoViewer visualizes all the known types of RNA Pseudoknots as planar drawings, but visualizes some hypothetical Pseudoknots as non-planar drawings. Results: We developed a new version of PseudoViewer for efficiently visualizing large RNA structures with any types of Pseudoknots, both known and hypothetical, as planar drawings in one-shot. It is about 10 times faster than the previous algorithm, and produces a more compact and aesthetic structure drawing. PseudoViewer3 supports both web services and web applications. Availability: The new version of PseudoViewer, PseudoViewer3, is available at http://pseudoviewer.inha.ac.kr. Contact: khan@inha.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.
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Prediction of RNA structures containing Pseudoknots
Interdisciplinary Bio Central, 2006Co-Authors: Ksbsb Ibc, Dongkyu Lee, Kyungsook HanAbstract: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. Corresponding Author: Kyungsook Han (Email: khan@inha.ac.kr) This work was supported by the Korea Science and Engineering Foundation (KOSEF) under grant R01-2003000-10461-0. Introduction The prediction of an RNA structure with a Pseudoknot using computational methods requires much computation. Predicting the most stable structure with minimal free energy from an RNA sequence is an optimization problem (Lee and Han, 2002; Lee and Han, 2003; Deiman and Pleij, 1997). Computational methods for predicting RNA structure generally make use of two algorithms, one combinatorial the other recursive. The combinatorial algorithm first creates an inventory of all possible stem lists that can be formed by a given RNA sequence, and then determines the combination with the lowest free energy. This algorithm has the advantage that it can include Pseudoknot structures, but the number of possible structures increases immensely with sequence length (Rivas and Eddy, 1999; Akutsu, 2000). The recursive algorithm finds the lowest free energy structure from the sub-fragments of a sequence. It makes a systematic search of all sub-fragments for the lowest free energy structure containing at least one base pair. The first sub-fragments considered are those capable of forming a hairpin loop closed by a single base pair. So in a first pass it will find the lowest free energy structures for all pentanucleotides in the sequence. This method always finds the structure with least free energy, but it does not identify structures such as Pseudoknots because of their computational complexity. A genetic algorithm (GA) is an optimization procedure that implements the mechanism of biological evolution. It begins with a set of solutions called populations. Solutions are then taken and used to form a new population in the hope that the new population will be superior to the old one. They are selected to generate new solutions according to their fitness; the fitter they are, the more opportunities they have to reproduce. This procedure is repeated until some specified condition is satisfied. Genetic algorithms have been theoretically and empirically proven to provide robust searches in highly complex and uncertain spaces, and they are finding widespread application in commerce, science and engineering. They are computationally simple and powerful search methods, and many workers have used them to predict RNA structures and sequence alignments; they have been used to seek optimal and sub-optimal secondary RNA structures (Benedetti and Morosetti, 1995; Shapiro and Navetta, 1994) and to simulate RNA folding pathways (Gultyaev et al., 1995; Shapiro et al., 2001). Massively parallel genetic algorithms have been employed to predict RNA structures that include Pseudoknots (Shapiro and Wu, 1996; Shapiro and Wu, 1997). However the structures predicted contained only H (Hairpin)-type Pseudoknots and the computations were extremely complex as they used randomly generated initial populations. Dynamic programming algorithms also used to predict RNA structures including Pseudoknots (Rivas and Eddy, 1999) again could only predict structures with H type Pseudoknots, and only from short RNA sequences. We have developed a GA that is able to predict efficiently
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PseudoViewer2: visualization of RNA Pseudoknots of any type
Nucleic acids research, 2003Co-Authors: Kyungsook Han, Yanga ByunAbstract:Visualizing RNA Pseudoknot structures is computationally more difficult than depicting RNA secondary structures, because a drawing of a Pseudoknot structure is a graph (and possibly a nonplanar graph) with inner cycles within the Pseudoknot, and possibly outer cycles formed between the Pseudoknot and other structural elements. We previously developed PSEUDOVIEWER for visualizing H-type Pseudoknots. PSEUDOVIEWER2 improves on the first version in many ways: (i) PSEUDOVIEWER2 is more general because it can visualize a Pseudoknot of any type, including H-type Pseudoknots, as a planar graph; (ii) PSEUDOVIEWER2 computes a drawing of RNA structures much more efficiently and is an order of magnitude faster in actual running time; and (iii) PSEUDOVIEWER2 is a web-based application program. Experimental results demonstrate that PSEUDOVIEWER2 generates an aesthetically pleasing drawing of Pseudoknots of any type and that the new representation offered by PSEUDOVIEWER2 ensures uniform and clear drawings, with no edge crossing, for all types of Pseudoknots. The PSEUDOVIEWER2 algorithm is the first developed for the automatic drawing of RNA secondary structures, including Pseudoknots of any type. PSEUDOVIEWER2 is accessible at http://wilab.inha.ac.kr/pseudoviewer2/.
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VECPAR - Visualization of RNA Pseudoknot structures
Lecture Notes in Computer Science, 2003Co-Authors: Wootaek Kim, Yujin Lee, Kyungsook HanAbstract:RNA Pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frame-shifting, 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. This paper describes the first algorithm for automatically generating a drawing of H-type Pseudoknots with RNA secondary 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 containing Pseudoknots as well as the Pseudoknots themselves should be recognized quickly and clearly. Experimental results show that this algorithm generates uniform and clear drawings with no edge crossing for all H-type RNA Pseudoknots. The algorithm is currently being extended to handle other types of Pseudoknots.
Ian Brierley - One of the best experts on this subject based on the ideXlab platform.
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Viral RNA Pseudoknots: versatile motifs in gene expression and replication.
Nature reviews. Microbiology, 2007Co-Authors: Ian Brierley, Simon Pennell, Robert J. C. GilbertAbstract:RNA Pseudoknots are structural elements found in almost all classes of RNA. First recognized in the genomes of plant viruses, they are now established as a widespread motif with diverse functions in various biological processes. This Review focuses on viral Pseudoknots and their role in virus gene expression and genome replication. Although emphasis is placed on those well defined Pseudoknots that are involved in unusual mechanisms of viral translational initiation and elongation, the broader roles of Pseudoknots are also discussed, including comparisons with relevant cellular counterparts. The relationship between RNA Pseudoknot structure and function is also addressed.
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Ribosomal pausing at a frameshifter RNA Pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency.
Molecular and Cellular Biology, 2001Co-Authors: Harry Kontos, Sawsan Napthine, Ian BrierleyAbstract:Here we investigated ribosomal pausing at sites of programmed −1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA Pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter Pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV Pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental Pseudoknot. Secondly, an identical pausing pattern was induced by two Pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the Pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding.
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evidence for an rna Pseudoknot loop helix interaction essential for efficient 1 ribosomal frameshifting
Journal of Molecular Biology, 1999Co-Authors: Jan Liphardt, Sawsan Napthine, Harry Kontos, Ian BrierleyAbstract:Abstract RNA Pseudoknots are structural elements that participate in a variety of biological processes. At −1 ribosomal frameshifting sites, several types of Pseudoknot have been identified which differ in their organisation and functionality. The Pseudoknot found in infectious bronchitis virus (IBV) is typical of those that possess a long stem 1 of 11-12 bp and a long loop 2 (30-164 nt). A second group of Pseudoknots are distinguishable that contain stems of only 5 to 7 bp and shorter loops. The NMR structure of one such Pseudoknot, that of mouse mammary tumor virus (MMTV), has revealed that it is kinked at the stem 1-stem 2 junction, and that this kinked conformation is essential for efficient frameshifting. We recently investigated the effect on frameshifting of modulating stem 1 length and stability in IBV-based Pseudoknots, and found that a stem 1 with at least 11 bp was needed for efficient frameshifting. Here, we describe the sequence manipulations that are necessary to bypass the requirement for an 11 bp stem 1 and to convert a short non-functional IBV-derived Pseudoknot into a highly efficient, kinked frameshifter Pseudoknot. Simple insertion of an adenine residue at the stem 1-stem 2 junction (an essential feature of a kinked Pseudoknot) was not sufficient to create a functional Pseudoknot. An additional change was needed: efficient frameshifting was recovered only when the last nucleotide of loop 2 was changed from a G to an A. The requirement for an A at the end of loop 2 is consistent with a loop-helix contact similar to those described in other RNA tertiary structures. A mutational analysis of both partners of the proposed interaction, the loop 2 terminal adenine residue and two G·C pairs near the top of stem 1, revealed that the interaction was essential for efficient frameshifting. The specific requirement for a 3′-terminal A residue was lost when loop 2 was increased from 8 to 14 nt, suggesting that the loop-helix contact may be required only in those Pseudoknots with a short loop 2.
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the role of rna Pseudoknot stem 1 length in the promotion of efficient 1 ribosomal frameshifting
Journal of Molecular Biology, 1999Co-Authors: Sawsan Napthine, Jan Liphardt, Alison J Bloys, Samantha Routledge, Ian BrierleyAbstract:The ribosomal frameshifting signal present in the genomic RNA of the coronavirus infectious bronchitis virus (IBV) contains a classic hairpin-type RNA Pseudoknot that is believed to possess coaxially stacked stems of 11 bp (stem 1) and 6 bp (stem 2). We investigated the influence of stem 1 length on the frameshift process by measuring the frameshift efficiency in vitro of a series of IBV-based Pseudoknots whose stem 1 length was varied from 4 to 13 bp in single base-pair increments. Efficient frameshifting depended upon the presence of a minimum of 11 bp; Pseudoknots with a shorter stem 1 were either non-functional or had reduced frameshift efficiency, despite the fact that a number of them had a stem 1 with a predicted stability equal to or greater than that of the wild-type IBV Pseudoknot. An upper limit for stem 1 length was not determined, but Pseudoknots containing a 12 or 13 bp stem 1 were fully functional. Structure probing analysis was carried out on RNAs containing either a ten or 11 bp stem 1; these experiments confirmed that both RNAs formed Pseudoknots and appeared to be indistinguishable in conformation. Thus the difference in frameshifting efficiency seen with the two structures was not simply due to an inability of the 10 bp stem 1 construct to fold into a Pseudoknot. In an attempt to identify other parameters which could account for the poor functionality of the shorter stem 1-containing Pseudoknots, we investigated, in the context of the 10 bp stem 1 construct, the influence on frameshifting of altering the slippery sequence-Pseudoknot spacing distance, loop 2 length, and the number of G residues at the bottom of the 5'-arm of stem 1. For each parameter, it was possible to find a condition where a modest stimulation of frameshifting was observable (about twofold, from seven to a maximal 17 %), but we were unable to find a situation where frameshifting approached the levels seen with 11 bp stem 1 constructs (48-57 %). Furthermore, in the next smaller construct (9 bp stem 1), changing the bottom four base-pairs to G.C (the optimal base composition) only stimulated frameshifting from 3 to 6 %, an efficiency about tenfold lower than seen with the 11 bp construct. Thus stem 1 length is a major factor in determining the functionality of this class of Pseudoknot and this has implications for models of the frameshift process.
Hans A. Heus - One of the best experts on this subject based on the ideXlab platform.
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Functional analysis of the SRV-1 RNA frameshifting Pseudoknot
Nucleic Acids Research, 2010Co-Authors: René C. L. Olsthoorn, Richard Reumerman, Cornelis W. A. Pleij, Cornelis W. Hilbers, Hans A. HeusAbstract:Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair Pseudoknot. The solution structure of this Pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the Pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109–1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base–base and base–sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for � 1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter Pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in � 1 frameshifting.
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solution structure of the Pseudoknot of srv 1 rna involved in ribosomal frameshifting
Journal of Molecular Biology, 2001Co-Authors: Paul J. A. Michiels, Cornelis W. A. Pleij, Cornelis W. Hilbers, Alexandra A M Versleijen, Paul W G Verlaan, Hans A. HeusAbstract:RNA Pseudoknots play important roles in many biological processes. In the simian retrovirus type-1 (SRV-1) a Pseudoknot together with a heptanucleotide slippery sequence are responsible for programmed ribosomal frameshifting, a translational recoding mechanism used to control expression of the Gag-Pol polyprotein from overlapping gag and pol open reading frames. Here we present the three-dimensional structure of the SRV-1 Pseudoknot determined by NMR. The structure has a classical H-type fold and forms a triple helix by interactions between loop 2 and the minor groove of stem 1 involving base-base and base-sugar interactions and a ribose zipper motif, not identified in Pseudoknots so far. Further stabilization is provided by a stack of five adenine bases and a uracil in loop 2, enforcing a cytidine to bulge. The two stems of the Pseudoknot stack upon each other, demonstrating that a Pseudoknot without an intercalated base at the junction can induce efficient frameshifting. Results of mutagenesis data are explained in context with the present three-dimensional structure. The two base-pairs at the junction of stem 1 and 2 have a helical twist of approximately 49 degrees, allowing proper alignment and close approach of the three different strands at the junction. In addition to the overwound junction the structure is somewhat kinked between stem 1 and 2, assisting the single adenosine in spanning the major groove of stem 2. Geometrical models are presented that reveal the importance of the magnitude of the helical twist at the junction in determining the overall architecture of classical Pseudoknots, in particular related to the opening of the minor groove of stem 1 and the orientation of stem 2, which determines the number of loop 1 nucleotides that span its major groove.
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nmr structure of a classical Pseudoknot interplay of single and double stranded rna
Science, 1998Co-Authors: M H Kolk, Cornelis W. A. Pleij, Hans A. Heus, M Van Der Graaf, Sybren S Wijmenga, Cornelis W. HilbersAbstract:Pseudoknot formation folds the 3' ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the Pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5' end of the RNA, and by the intricate interactions related to the loops of the Pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA Pseudoknots that regulates their interaction with proteins or other RNA molecules.
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New developments in structure determination of Pseudoknots.
Biopolymers, 1998Co-Authors: Cornelis W. Hilbers, Paul J. A. Michiels, Hans A. HeusAbstract:Recently, several high-resolution structures of-RNA Pseudoknots have become available. Here we review the progress in this area. The majority of the structures obtained belong to the classical or H-type Pseudoknot family. The most complicated Pseudoknot structure elucidated so far is the Hepatitis Delta Virus ribozyme, which forms a nested double Pseudoknot. In particular, the structure-function relationships of the H-type Pseudoknots involved in translational frameshifting have received much attention. All molecules considered show interesting new structural motifs.
Wootaek Kim - One of the best experts on this subject based on the ideXlab platform.
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VECPAR - Visualization of RNA Pseudoknot structures
Lecture Notes in Computer Science, 2003Co-Authors: Wootaek Kim, Yujin Lee, Kyungsook HanAbstract:RNA Pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frame-shifting, 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. This paper describes the first algorithm for automatically generating a drawing of H-type Pseudoknots with RNA secondary 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 containing Pseudoknots as well as the Pseudoknots themselves should be recognized quickly and clearly. Experimental results show that this algorithm generates uniform and clear drawings with no edge crossing for all H-type RNA Pseudoknots. The algorithm is currently being extended to handle other types of Pseudoknots.
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Visualization of RNA Pseudoknot structures
Lecture Notes in Computer Science, 2003Co-Authors: Wootaek Kim, Yujin Lee, Kyungsook HanAbstract:RNA Pseudoknots are not only important structural elements for forming the tertiary structure, but also responsible for several functions of RNA molecules such as frame-shifting, 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. This paper describes the first algorithm for automatically generating a drawing of H-type Pseudoknots with RNA secondary 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 containing Pseudoknots as well as the Pseudoknots themselves should be recognized quickly and clearly. Experimental results show that this algorithm generates uniform and clear drawings with no edge crossing for all H-type RNA Pseudoknots. The algorithm is currently being extended to handle other types of Pseudoknots.
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DaWaK - New Representation and Algorithm for Drawing RNA Structure with Pseudoknots
Data Warehousing and Knowledge Discovery, 2002Co-Authors: Yujin Lee, Wootaek Kim, Kyungsook HanAbstract:Visualization of a complex molecular structure is a valuable tool in understanding the structure. A drawing of RNA Pseudoknot structures is a graph (and a possibly nonplanar graph) with inner cycles within a Pseudoknot as well as possible outer cycles formed between a Pseudoknot and other structural elements. Thus, drawing RNA Pseudoknot structures is computationally more difficult than depicting RNA secondary structures. Although several algorithms have been developed for drawing RNA secondary structures, none of these can be used to draw RNA Pseudoknots and thus visualizing RNA Pseudoknots relies on significant amount of manual work. Visualizing RNA Pseudoknots by manual work becomes more difficult and yields worse results as the size and complexity of the RNA structures increase. We have developed a new representation method and an algorithm for visualizing RNA Pseudoknots as a two-dimensional drawing and implemented the algorithm in a program. The new representation produces uniform and clear drawings with no edge crossing for all kinds of Pseudoknots, including H-type and other complex types. Given RNA structure data, we represent the whole structure as a tree rather than as a graph by hiding the inner cycles as well as the outer cycles in the nodes of the abstract tree. Once the top-level RNA structure is represented as a tree, nodes of the tree are placed and drawn in increasing order of their depth values. Experimental results demonstrate that the algorithm generates a clear and aesthetically pleasing drawing of large-scale RNA structures, containing any number of Pseudoknots. This is the first algorithm for automatically drawing RNA structure with Pseudoknots.
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ISMB - PseudoViewer: automatic visualization of RNA Pseudoknots.
2002Co-Authors: Kyungsook Han, Yujin Lee, Wootaek KimAbstract:MOTIVATION Several algorithms have been developed for drawing RNA secondary structures, however none of these can be used to draw RNA Pseudoknot structures. In the sense of graph theory, a drawing of RNA secondary structures is a tree, whereas a drawing of RNA Pseudoknots is a graph with inner cycles within a Pseudoknot as well as possible outer cycles formed between a Pseudoknot and other structural elements. Thus, RNA Pseudoknots are more difficult to visualize than RNA secondary structures. Since no automatic method for drawing RNA Pseudoknots exists, visualizing RNA Pseudoknots relies on significant amount of manual work and does not yield satisfactory results. The task of visualizing RNA Pseudoknots by hand becomes more challenging as the size and complexity of the RNA Pseudoknots increase. RESULTS We have developed a new representation and an algorithm for drawing H-type Pseudoknots with RNA secondary structures. Compared to existing representations of H-type Pseudoknots, the new representation ensures uniform and clear drawings with no edge crossing for any H-type Pseudoknots. To the best of our knowledge, this is the first algorithm for automatically drawing RNA Pseudoknots with RNA secondary structures. The algorithm has been implemented in a Java program, which can be executed on any computing system. Experimental results demonstrate that the algorithm generates an aesthetically pleasing drawing of all H-type Pseudoknots. The results have also shown that the drawing has high readability, enabling the user to quickly and easily recognize the whole RNA structure as well as the Pseudoknots themselves.
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New representation and algorithm for drawing RNA structure with Pseudoknots
Lecture Notes in Computer Science, 2002Co-Authors: Yujin Lee, Wootaek Kim, Kyungsook HanAbstract:Visualization of a complex molecular structure is a valuable tool in understanding the structure. A drawing of RNA Pseudoknot structures is a graph (and a possibly nonplanar graph) with inner cycles within a Pseudoknot as well as possible outer cycles formed between a Pseudoknot and other structural elements. Thus, drawing RNA Pseudoknot structures is computationally more difficult than depicting RNA secondary structures. Although several algorithms have been developed for drawing RNA secondary structures, none of these can be used to draw RNA Pseudoknots and thus visualizing RNA Pseudoknots relies on significant amount of manual work. Visualizing RNA Pseudoknots by manual work becomes more difficult and yields worse results as the size and complexity of the RNA structures increase. We have developed a new representation method and an algorithm for visualizing RNA Pseudoknots as a two-dimensional drawing and implemented the algorithm in a program. The new representation produces uniform and clear drawings with no edge crossing for all kinds of Pseudoknots, including H-type and other complex types. Given RNA structure data, we represent the whole structure as a tree rather than as a graph by hiding the inner cycles as well as the outer cycles in the nodes of the tree. Once the top-level RNA structure is represented as a tree, nodes of the tree are placed and drawn in increasing order of their depth values. Experimental results demonstrate that the algorithm generates a clear and aesthetically pleasing drawing of large-scale RNA structures, containing any number of Pseudoknots. This is the first algorithm for automatically drawing RNA structure with Pseudoknots.
David P Giedroc - One of the best experts on this subject based on the ideXlab platform.
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a loop 2 cytidine stem 1 minor groove interaction as a positive determinant for Pseudoknot stimulated 1 ribosomal frameshifting
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Peter V Cornish, Mirko Hennig, David P GiedrocAbstract:The molecular determinants of stimulation of –1 programmed ribosomal frameshifting (–1 PRF) by RNA Pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA Pseudoknot that promotes –1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV Pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3′ nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2′-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1–2′-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2–S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric Pseudoknots reveal that the ScYLV RNA stimulates a higher level of –1 PRF (15 ± 2%) relative to the BWYV Pseudoknot (6 ± 1%), a difference traced largely to the identity of the 3′ nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by ≈1.5 kcal·mol–1 (pH 7.0, 37°C) with respect to the wild-type Pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar Pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.
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Structure, stability and function of RNA Pseudoknots involved in stimulating ribosomal frameshifting.
Journal of Molecular Biology, 2000Co-Authors: David P Giedroc, Carla A. Theimer, Paul L. NixonAbstract:Programmed −1 ribosomal frameshifting has become the subject of increasing interest over the last several years, due in part to the ubiquitous nature of this translational recoding mechanism in pathogenic animal and plant viruses. All cis-acting frameshift signals encoded in mRNAs are minimally composed of two functional elements: a heptanucleotide “slippery sequence” conforming to the general form X XXY YYZ, followed by an RNA structural element, usually an H-type RNA Pseudoknot, positioned an optimal number of nucleotides (5 to 9) downstream. The slippery sequence itself promotes a low level (≈1 %) of frameshifting; however, downstream Pseudoknots stimulate this process significantly, in some cases up to 30 to 50 %. Although the precise molecular mechanism of stimulation of frameshifting remains poorly understood, significant advances have been made in our knowledge of the three-dimensional structures, thermodynamics of folding, and functional determinants of stimulatory RNA Pseudoknots derived from the study of several well-characterized frameshift signals. These studies are summarized here and provide new insights into the structural requirements and mechanism of programmed −1 ribosomal frameshifting.
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Pseudoknot Structures in Retroviral and Bacteriophage Messenger RNA: a Family of Structurally Related RNA Pseudoknots
Microscopy and Microanalysis, 1997Co-Authors: David W. Hoffman, Jason A. Holland, Mark R. Hansen, Y. Wang, David P GiedrocAbstract:Nuclear magnetic resonance (NMR) spectroscopy was used to determine the three-dimensional structure of an RNA Pseudoknot with a sequence corresponding to the 5' end region of the gene 32 messenger RNA of bacteriophage T2. NMR results show that the Pseudoknot contains two coaxial A-form helical stems connected by two loops. One of the loops consists of a single nucleotide, which spans the major groove of the seven base pair helical stem 2. The second loop consists of 7 nucleotides, and spans the minor groove of stem 1. A three-dimensional model of the Pseudoknot that is consistent with the NMR data will be presented, and features that are likely to be important for stabilizing the Pseudoknot structure will be described.A combination of NMR and phylogenetic methods were used to characterize the structural features of RNA Pseudoknots that are associated with frameshift and readthrough sites within the retroviral gag-pro messenger RNA. The majority of the retroviral frameshift and readthrough sites were found to be followed by nucleotide sequences that have the potential to form Pseudoknots with structures that are remarkably similar to that of the bacteriophage T2 gene 32 mRNA.
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Structure of the Autoregulatory Pseudoknot within the Gene 32 Messenger RNA of Bacteriophages T2 and T6: A Model for a Possible Family of Structurally Related RNA Pseudoknots†
Biochemistry, 1996Co-Authors: David P Giedroc, David W. HoffmanAbstract:A 36-nucleotide RNA with a sequence corresponding to the 5' end region of the gene 32 mRNA of bacteriophages T2 and T6 was analyzed by one- and two-dimensional NMR methods. NMR results provide clear evidence that the RNA is folded into a Pseudoknot structure with two coaxial stems connected by two loops, in a classic Pseudoknot topology. The Pseudoknot is unusual in that one of the loops consists of only one nucleotide, which spans the major groove of a seven base pair helical stem. Imino proton resonances indicate the hydrogen bonding pattern within the Pseudoknot, and two-dimensional NOE spectra provide information that describes many of the structural features. The temperature dependence of the UV absorption and imino proton exchange rates provides insight into the stability of the Pseudoknot. A three-dimensional model of the Pseudoknot that is consistent with our NMR data is presented, and features that may be important for stabilizing the Pseudoknot structure are discussed. A substantial number of other putative RNA Pseudoknots described in the literature have sequences and topologies that appear to be related to the T2 and T6 Pseudoknots. We propose that these RNAs may be members of a family of Pseudoknots related by a similar structural motif, which we refer to as "common Pseudoknot motif 1" or CPK1. The bacteriophage T2/T6 Pseudoknot can be considered a structural model for the CPK1 family. The common features of the CPK1 Pseudoknots are a stem 2 with six or seven base pairs, a loop 1 consisting of a single adenosine, and a variable length stem 1 and loop 2. The first "dangling" nucleotide at the 3' end of the molecule probably stabilizes stem 2. The CPK1 family includes several of the retroviral Pseudoknots associated with mRNA frameshifting and readthrough. The work presented here describes the first detailed NMR analysis of an RNA Pseudoknot with an entirely natural nucleotide sequence.
