Linear Bounds on the Size of Conformations in Greedy Deterministic Oritatami

2021 ◽  
pp. 1-22
Author(s):  
Szilárd Zsolt Fazekas ◽  
Hwee Kim ◽  
Ryuichi Matsuoka ◽  
Reoto Morita ◽  
Shinnosuke Seki
Keyword(s):  
Computational Model ◽  
Upper Bound ◽  
Graph Representation ◽  
Folding Pathways ◽  
Template Dna ◽  
Rna Transcript

Oritatami is a computational model of RNA cotranscriptional folding, in which an RNA transcript is folding upon itself while being synthesized from its template DNA. This model is known to be Turing universal. Under the restriction on its parameters delay and arity both being 1, however, any deterministically foldable conformation is known to be at most ten times as large as its initial conformation (seed), and hence, the model becomes weaker. In this paper, we shall improve the size upper bound from [Formula: see text] down to [Formula: see text] and also provide a system that can fold into a conformation of size [Formula: see text]. These tighter bounds result from a novel graph representation of deterministic oritatami folding pathways. We shall also study the case in which a transcript is trapped in a region closed by a seed and show that under this confinement, the upper bound is further improved to [Formula: see text].

scholarly journals Competition between the RNA Transcript and the Nontemplate DNA Strand during R-Loop Formation In Vitro: a Nick Can Serve as a Strong R-Loop Initiation Site

2009 ◽  
Vol 30 (1) ◽  
pp. 146-159 ◽  
Author(s):  
Deepankar Roy ◽  
Zheng Zhang ◽  
Zhengfei Lu ◽  
Chih-Lin Hsieh ◽  
Michael R. Lieber
Keyword(s):  
Somatic Hypermutation ◽  
Initiation Site ◽  
Loop Formation ◽  
Class Switch ◽  
Dna Strands ◽  
Dna Strand ◽  
Template Dna ◽  
Rna Transcript

ABSTRACT Upon transcription of some sequences by RNA polymerases in vitro or in vivo, the RNA transcript can thread back onto the template DNA strand, resulting in an R loop. Previously, we showed that initiation of R-loop formation at an R-loop initiation zone (RIZ) is favored by G clusters. Here, using a purified in vitro system with T7 RNA polymerase, we show that increased distance between the promoter and the R-loop-supporting G-rich region reduces R-loop formation. When the G-rich portion of the RNA transcript is downstream from the 5′ end of the transcript, the ability of this portion of the transcript to anneal to the template DNA strand is reduced. When we nucleolytically resect the beginning of the transcript, R-loop formation increases because the G-rich portion of the RNA is now closer to the 5′ end of the transcript. Short G-clustered regions can act as RIZs and reduce the distance-induced suppression of R-loop formation. Supercoiled DNA is known to favor transient separation of the two DNA strands, and we find that this favors R-loop formation even in non-G-rich regions. Most strikingly, a nick can serve as a strong RIZ, even in regions with no G richness. This has important implications for class switch recombination and somatic hypermutation and possibly for other biological processes in transcribed regions.

scholarly journals Distributed algorithm for painting by a swarm of randomly deployed robots under limited visibility model

2018 ◽  
Vol 15 (5) ◽  
pp. 172988141880450
Author(s):  
Deepanwita Das ◽  
Srabani Mukhopadhyaya
Keyword(s):  
Mobile Robots ◽  
Computational Model ◽  
Upper Bound ◽  
Distributed Algorithm ◽  
Initial Distribution ◽  
Horizontal Line ◽  
Target Area ◽  
Rectangular Region ◽  
Swarm Robots ◽  
The Given

This article studies the problem of painting an obstacle free rectangular region by a swarm of mobile robots. Initially the robots are deployed randomly within the target area subject to the condition that the distribution is d*-dense, where [Formula: see text], and a robot can view up to a distance d. By d*-dense, it is meant that if all the robots are projected on a horizontal line, then the distance between two consecutive robots must be less than or equal to d*. Non-consideration of the popular CORDA (computational) model in the field of area coverage by swarm robots has been addressed here. The proposed algorithm assumes CORDA model. The robots follow a completely distributed algorithm to paint the region. The robots do not need to be synchronous, but they are assumed to have equal velocities. However, the proposed algorithm supports the robots with different speed. In that case, if r is the given upper bound on the ratios of the speeds of any two robots, then the initial distribution has to be D*-dense, where [Formula: see text].

scholarly journals Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase

2019 ◽  
Author(s):  
Yeonoh Shin ◽  
Mark Hedglin ◽  
Katsuhiko S. Murakami
Keyword(s):  
Rna Polymerase ◽  
Rna Synthesis ◽  
X Ray ◽  
The Core ◽  
Core Enzyme ◽  
Biochemical Assays ◽  
Bacterial Rna ◽  
Reiterative Transcription ◽  
Template Dna ◽  
Rna Transcript

ABSTRACTReiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains 8 poly-G RNA bases synthesized using 3 C bases in the DNA as a template and extends RNA without displacement of the promoter recognition σ factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak trigger freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Structures and biochemical assays revealed how the RNA transcript from the pyrG promoter is guided toward the Rifampin-binding pocket then the main channel of RNA polymerase and provided insight into RNA slippage during reiterative transcription of the pyrG promoter. Lastly, we determined a structure of a reiterative transcription complex at the pyrBI promoter and revealed an alternative mechanism of RNA slippage and extension requiring the σ dissociation from the core enzyme.SIGNIFICANCE STATEMENTRNA polymerase synthesizes multiple bases of RNA using a single base of the template DNA due to slippage between RNA transcript and template DNA. This noncanonical RNA synthesis is called “reiterative transcription,” playing several regulatory roles cellular organisms and viruses. In this study, we determined a series of X-ray crystal structures of a bacterial RNA polymerase engaged in reiterative transcription and characterized a role of template DNA during reiterative transcription by biochemical assays. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. We also provide insights into the regulation of gene expression using two alternative ways of reiterative transcription.

Self-Attraction Removal from Oritatami Systems

2019 ◽  
Vol 30 (06n07) ◽  
pp. 1047-1067 ◽  
Author(s):  
Yo-Sub Han ◽  
Hwee Kim ◽  
Trent A. Rogers ◽  
Shinnosuke Seki
Keyword(s):  
Rna Polymerase ◽  
Computational Model ◽  
Finite Alphabet ◽  
Its Sequence ◽  
Rule Set ◽  
Rna Transcript

RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene by an RNA polymerase. Oritatami is a computational model of this phenomenon, which lets its sequence of beads (abstract molecules) taken from a finite alphabet [Formula: see text] fold cotranscriptionally via interactions between beads according to its rule set. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. Self-attraction is one of the major challenges in the construction of intrinsic oritatami systems, which can simulate even the dynamics of all the oritatami systems.

ON THE SPACE-TIME MAPPING OF WHILE-LOOPS

1994 ◽  
Vol 04 (03) ◽  
pp. 221-232 ◽  
Author(s):  
MARTIN GRIEBL ◽  
CHRISTIAN LENGAUER
Keyword(s):  
Computational Model ◽  
Upper Bound ◽  
Automatic Parallelization ◽  
Space Time

A WHILE-loop can be viewed as a FOR-loop with a dynamic upper bound. The computational model of polytopes is useful for the automatic parallelization of FOR-loops. We investigate its potential for the parallelization of WHILE-loops.

Inference making and memory for text: A computational model

2001 ◽  
Author(s):  
Paul Van Den Broek ◽  
Yuhtsuen Tzeng ◽  
Sandy Virtue ◽  
Tracy Linderholm ◽  
Michael E. Young
Keyword(s):  
Computational Model ◽  
Inference Making ◽  
Memory For Text

Computational Model of Novel Popout

1992 ◽  
Author(s):  
William A. Johnston ◽  
Kevin J. Hawley ◽  
James M. Farnham
Keyword(s):  
Computational Model
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