Relevant bibliographies by topics / Loop unwinding

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Academic literature on the topic 'Loop unwinding'

Author: Grafiati
Published: 11 March 2023

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Journal articles on the topic "Loop unwinding"

1

Nicolau, Alexandru. "Loop quantization: A generalized loop unwinding technique." Journal of Parallel and Distributed Computing 5, no. 5 (October 1988): 568–86. http://dx.doi.org/10.1016/0743-7315(88)90013-5.

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2

Blagosklonny, MV. "Unwinding the loop of Bcl-2 phosphorylation." Leukemia 15, no. 6 (June 2001): 869–74. http://dx.doi.org/10.1038/sj.leu.2402134.

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3

Yang, Tao, Lin Yin Liu, and Wei Rong Dai. "Dynamic Characteristics and Double Closed Loop Control Method of Warping Machine." Advanced Materials Research 627 (December 2012): 428–34. http://dx.doi.org/10.4028/www.scientific.net/amr.627.428.

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The warp tension is caused by the speed difference between rewinding shaft and unwinding shaft. The mathematical dynamic models of the system are established based on rewinding shaft and unwinding shaft．Double closed loop are included in the control system. One is winding speed closed loop which could control warping speed according to the requirements; the other is tension closed loop which ensure the yarn tension to be kept constant. The experimental results show the curve of tension enters a stable state after two or three times’ oscillation. The accuracy of the yarn tension has reached ±3%.
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Howard, Jamieson A. L., Stephane Delmas, Ivana Ivančić-Baće, and Edward L. Bolt. "Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein." Biochemical Journal 439, no. 1 (September 14, 2011): 85–95. http://dx.doi.org/10.1042/bj20110901.

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CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) is a nucleic acid processing system in bacteria and archaea that interacts with mobile genetic elements. CRISPR DNA and RNA sequences are processed by Cas proteins: in Escherichia coli K-12, one CRISPR locus links to eight cas genes (cas1, 2, 3 and casABCDE), whose protein products promote protection against phage. In the present paper, we report that purified E. coli Cas3 catalyses ATP-independent annealing of RNA with DNA forming R-loops, hybrids of RNA base-paired into duplex DNA. ATP abolishes Cas3 R-loop formation and instead powers Cas3 helicase unwinding of the invading RNA strand of a model R-loop substrate. R-loop formation by Cas3 requires magnesium as a co-factor and is inactivated by mutagenesis of a conserved amino acid motif. Cells expressing the mutant Cas3 protein are more sensitive to plaque formation by the phage λvir. A complex of CasABCDE (‘Cascade’) also promotes R-loop formation and we discuss possible overlapping roles of Cas3 and Cascade in E. coli, and the apparently antagonistic roles of Cas3 catalysing RNA–DNA annealing and ATP-dependent helicase unwinding.
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Ivanov, Ivan E., Addison V. Wright, Joshua C. Cofsky, Kevin D. Palacio Aris, Jennifer A. Doudna, and Zev Bryant. "Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling." Proceedings of the National Academy of Sciences 117, no. 11 (March 2, 2020): 5853–60. http://dx.doi.org/10.1073/pnas.1913445117.

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The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.
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Dudas, Kathleen C., and Kenneth N. Kreuzer. "UvsW Protein Regulates Bacteriophage T4 Origin-Dependent Replication by Unwinding R-Loops." Molecular and Cellular Biology 21, no. 8 (April 15, 2001): 2706–15. http://dx.doi.org/10.1128/mcb.21.8.2706-2715.2001.

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ABSTRACT The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) andori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional gel analyses show that the replicative intermediates formed atori(uvsY) persist longer in a uvsWmutant infection than in a wild-type infection. In addition, the inappropriate early expression of UvsW protein results in the loss of these replicative intermediates. Using a synthetic origin R-loop, we also demonstrate that purified UvsW functions as a helicase that efficiently dissociates RNA from R-loops. These and previous results from a number of studies provide strong evidence that UvsW is a molecular switch that allows T4 replication to progress from a mode that initiates from R-loops at origins to a mode that initiates from D-loops formed by recombination proteins.
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7

Wei, Ze Ding, Han Chao Xu, and Hui Su. "A Constant Tension Control Device of Mechanical Feedback." Applied Mechanics and Materials 397-400 (September 2013): 409–12. http://dx.doi.org/10.4028/www.scientific.net/amm.397-400.409.

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A constant tension control device of mechanical feedback is designed for the tension adjustment between the unwinding and rewinding of the flexible material, and the structure and size of the device are given. According to torque balance principle and based on purely mechanical structure, this device can control tension by adjusting the frictional force between the brake block and the unwinding wheel. The tension of controlling the unwinding and rewinding of the flexible material is analyzed, and then the control method of the tension is illustrated. Compared with the common closed loop control devices with tension feedback, the structure of the proposed device is simpler, and it has a stronger capacity of resisting disturbance in complicated electromagnetic environment.
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8

Guo, Yong, Shen-Min Song, and Xue-Hui Li. "Backstepping sliding mode control for formation flying spacecraft." Aircraft Engineering and Aerospace Technology 90, no. 1 (January 2, 2018): 56–64. http://dx.doi.org/10.1108/aeat-08-2014-0129.

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Purpose This paper aims to investigate the problem of finite-time consensus tracking control without unwinding for formation flying spacecraft in the presence of external disturbances. Design/methodology/approach Two distributed finite-time controllers are developed using the backstepping sliding mode. The first robust controller can compensate for external disturbances with known bounds, and the second one can compensate for external disturbances with unknown bounds. Findings Because the controllers are designed on the basis of rotation matrix, which represents the set of attitudes both globally and uniquely, the system can overcome the drawback of unwinding, which results in extra fuel consumption. Through introducing a novel virtual angular velocity, exchange of control signals between neighboring spacecraft becomes unnecessary, and it is able to reduce the communication burden. Practical implications The two robust controllers can deal with unwinding that may result in fuel consumption by traveling a long distance before returning to a desired attitude when the closed-loop system is close to the desired attitude equilibrium. Originality/value Two finite-time controllers without unwinding are proposed for formation flying spacecraft by using backstepping sliding mode. Furthermore, exchange of control signals between neighboring spacecraft is unnecessary.
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9

Baggs, Eric, and Lisa Warner. "Larp6 Regulates Collagen mRNA by Targeted Unwinding of a Conserved Stem‐Loop." FASEB Journal 34, S1 (April 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.09740.

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10

Manthei, Kelly A., Morgan C. Hill, Jordan E. Burke, Samuel E. Butcher, and James L. Keck. "Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases." Proceedings of the National Academy of Sciences 112, no. 14 (March 23, 2015): 4292–97. http://dx.doi.org/10.1073/pnas.1416746112.

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RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3′ single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.
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Books on the topic "Loop unwinding"

1

Thomas, Alease Allen. Slowly Unwinding #3: Another Look at Slavery. RoseDog Books, 2006.

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Book chapters on the topic "Loop unwinding"

1

Nicolau, Alexandru. "Loop quantization or unwinding done right." In Lecture Notes in Computer Science, 294–308. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/3-540-18991-2_17.

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2

Dutta, Arijit, Youngho Kwon, and Patrick Sung. "Biochemical Analysis of RNA–DNA Hybrid and R-Loop Unwinding Via Motor Proteins." In R-Loops, 305–16. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2477-7_20.

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Ponce-de-León, Hernán, Florian Furbach, Keijo Heljanko, and Roland Meyer. "Dartagnan: Bounded Model Checking for Weak Memory Models (Competition Contribution)." In Tools and Algorithms for the Construction and Analysis of Systems, 378–82. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-45237-7_24.

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Abstract Dartagnanis a bounded model checker for concurrent programs under weak memory models. What makes it different from other tools is that the memory model is not hard-coded inside Dartagnanbut taken as part of the input. For SV-COMP’20, we take as input sequential consistency (i.e. the standard interleaving memory model) extended by support for atomic blocks. Our point is to demonstrate that a universal tool can be competitive and perform well in SV-COMP. Being a bounded model checker, Dartagnan’s focus is on disproving safety properties by finding counterexample executions. For programs with bounded loops, Dartagnanperforms an iterative unwinding that results in a complete analysis. The SV-COMP’20 version of Dartagnanworks on Boogiecode. The C programs of the competition are translated internally to Boogieusing SMACK.
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Conference papers on the topic "Loop unwinding"

1

Liao, Jung-Chi, and George Oster. "The Engines of Biomolecular Motors." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46094.

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The majority of biomolecular motors are powered by nucleoside triphosphate (NTP), especially adenosine triphosphate (ATP). These motors consist of a β-sheet with highly conserved motifs and the nucleotide binding domain around it. The highly conserved protein folds are the engines of these motors, which convert the energy of NTP hydrolysis cycle to mechanical work. Although functions of molecular motors are widely diverse, (including cargo movement, DNA unwinding, protein degradation, ion pumping, etc), the nucleotide binding domains are very similar. In the binding site, NTP undergoes a hydrolysis cycle E+NTP⇄E·NTP⇄E•NTP⇄E•NDP•Pi⇄E•NDP+Pi⇄E+NDP+Pi where E is the enzyme (motor protein), the small dot represents the docking of NTP, and the large dot represents the tightly-bound states. The hydrogen bond network formed in the NTP binding step, as shown in Figure 1 [1], deforms the β-sheet and adjacent structures. The local deformation propagates to conformational changes of functional residues to do mechanical work or to change the affinity to the substrate [2]. For multimeric motor proteins, we must also consider the stress paths among subunits which control the sequence and the activity of the protein. Stress trajectories emanating from a binding site either passes through a circumferential stress loop or a stress loop through the substrate.
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Journal articles
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