A kinetic hairpin transfer model for parvoviral DNA replication

The DNAs encapsidated by parvoviruses show distinctly different patterns with respect to the ratio of plus-to-minus strands and sequence heterogeneity at the ends. A kinetic model, based on differential rates of hairpin transfer at 3' termini, is described and shown to account for all known parvoviral DNA distributions.     

Analysis of the kinetic hairpin transfer model for parvoviral DNA replication

All linear DNA molecules face special problems in replicating their 5' ends, as DNA polymerases add nucleotides only to pre-existing strands with free 3'-OH groups. Parvoviruses, a group of small animal viruses with a linear single-stranded DNA genome, cope with this problem by having palindromic terminal sequences that can fold back on themselves to form hairpin structures essential in priming DNA replication. The 3' terminal sequence that initiates replication becomes reversed in orientation during the process, and if the palindrome is imperfect, two different, reverse-complementary terminal sequences are generated. The relative abundances of the terminal sequence orientations at each end of the DNA molecules can be measured and give information about the replication process. From such clues, we developed a "kinetic hairpin transfer model" based on differential rates of hairpin formation and inversion processes depending on the conformations of the 3' termini. Numerical studies showed that this simple idea can account for the diverse pattern of DNA distributions observed in the family Parvoviridae. In this paper, we simplify the model to a set of coupled linear first-order ordinary differential equations in order to delineate its essential properties by Perron-Frobenius theory. Secondly, we examine our assumption of linear kinetics by modeling enzyme catalysis of the component steps of the hairpin transfer process. We show that the rate-determining step of the process is the binding of initiation complex to the self-priming hairpin structures. Furthermore, we find that if the replication machinery is saturated by DNA substrate late in an infection, the differential equations become non-linear but the steady-state DNA distribution is still given by the solution of our original linear equations.     

A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences

DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA computing. Although the strategy is only for the two-dimensional data, it provides a new idea to consider the grids to be vertexes in a graph and transform the search problem into a combinatorial problem.     

分子信标DNA计算模型的研究进展与展望

由于分子信标具有结构简单,灵敏度高及反应迅速等优点,因此,利用分子信标进行数学问题的求解将成为可能.通过对分子信标的计算模型进行详细的介绍,并对分子信标的计算模型的研究思路进行了展望,据此思路,可以建立多种组合优化问题及逻辑门的分子信标计算模型.     

Amino acid residues in Rag1 crucial for DNA hairpin formation

The Rag proteins carry out V(D)J recombination through a process mechanistically similar to cut-and-paste transposition. Specifically, Rag complexes form DNA hairpins through direct transesterification, using a catalytic Asp-Asp-Glu (DDE) triad in Rag1. How is sufficient DNA distortion introduced to allow hairpin formation? We hypothesized that, like certain transposases, the Rag proteins might use aromatic amino acid residues to stabilize a flipped-out base. Through in vivo and in vitro experiments and structural predictions, we identified residues in Rag1 crucial for hairpin formation. One of these, a conserved tryptophan (Trp893), probably participates in base-stacking interactions near the cleavage site, as do Trp298, Trp265 and Trp319 in the Tn5, Tn10 and Hermes transposases, respectively. Other residues surrounding the catalytic glutamate (YKEFRK) may share functional similarities with the YREK motif in IS4 family transposases.     

A model for triplet mutation formation based on error-prone translesional DNA synthesis opposite UV photolesions

A triplet mutation is defined as multiple base substitutions or frameshifts within a three-nucleotide sequence which includes a dipyrimidine sequence. Triplet mutations have recently been identified as a new type of UV-specific mutation, although the mechanism of their formation is unknown. A total of 163 triplet mutations were identified through an extensive search of previously published data on UV-induced mutations, including mutations from skin, skin cancer, and cultured mammalian cells. Seven common patterns of sequence changes were found: Type I, NTC-->TTT; Type IIa, NCC-->PyTT or PyCT (Py, pyrimidine); Type IIb, TCC-->PuTT or PuCT (Pu, purine); Type III, NCC-->NAT or NTA; Type IV, NTT-->AAT; Type Va, NCT-->NTX; and Type Vb, PuCT-->XTT (N and X, independent anonymous bases). Furthermore, it is suggested that the type of UV lesion responsible for each of these triplet mutation classes are (a) pyrimidine(6-4)pyrimidone photoproducts for Types I, IIb, III, IV and Vb, (b) cyclobutane pyrimidine dimers for Type Va, and (c) Dewar valence isomers for Types IIa and IIb. These estimations are based primarily on results from previous studies using photolyases specific for each type of UV lesion. A model is proposed to explain the formation of each type of triplet mutation, based on error-prone translesional DNA synthesis opposite UV-specific photolesions. The model is largely consistent with the 'A-rule', and predicts error-prone insertions not only opposite photolesions but also opposite the undamaged template base one-nucleotide downstream from the lesions.     

A new model for biological pattern formation

Various non-equilibrium growth models have been used to explore the development of morphology in biological systems. Here we review a class of biological growth models which exhibit fractal structures and discuss the relationship of these models to a variety of other phenomena.     

A DNA computing readout operation based on structure-specific cleavage.

We describe a structure-specific cleavage-based READOUT strategy for surface-based DNA computing. The strategy was demonstrated in the solution of a 4-variable/3-satisfiability (SAT) problem. The READOUT step identifies the DNA molecules present at the end of the computational process. The specificity of the sequence detection used here derives from the sequence specificity of DNA hybridization coupled with the structure specificity of the enzymatic cleavage. The process is linear, yielding a higher uniformity of detection of the DNA computing products compared to that obtained with PCR amplification. The structure-specific cleavage-based readout is simple, accurate, and compatible with multiple-word DNA computing.     

A secure smart-work service model based OpenStack for Cloud computing

Cloud computing technology is a general concept and idea such as existing distributed computing, parallel computing, Pervasive computing and Ubiquitous computing. We have been studying OpenStack which was an Open cloud project under the KOREN (Korea Advanced Research Network) environments. In this paper, we propose a secure smart-work service model-based OpenStack. There are mainly two kinds of security breaches that can occur under the proposed environment. Nova is vulnerable to DoS attack in OpenStack. SQL Injection can be attacked in the process during which the user requests authorization, which results in data being saved in Swift. Looking more deeply into these two types of attack, we can divide DoS attack into Jolt2, Tear-drop, and SYN-Flooding attack. We simulated attacks in an experimental environment and summarized the results. With the objective of being able to provide Smart-Work service in the KOREN environment, we proposed solutions to various kinds of attacks against the security system and carried out modeling work with the data from the experiment conducted in the Cloud service environment we examined above.     

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops.

We determined the melting temperatures (Tm) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCl, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C.G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C.G, or G.C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37 degrees C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with delta G degrees 37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C.G to G.C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures.     

Review fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation

This article reviews the application of fluorescence correlation spectroscopy (FCS) and related techniques to the study of nucleic acid hairpin conformational fluctuations in free aqueous solutions. Complimentary results obtained using laser-induced temperature jump spectroscopy, single-molecule fluorescence spectroscopy, optical trapping, and biophysical theory are also discussed. The studies cited reveal that DNA and RNA hairpin folding occurs by way of a complicated reaction mechanism involving long- and short-lived reaction intermediates. Reactions occurring on the subnanoseconds to seconds time scale have been observed, pointing out the need for experimental techniques capable of probing a broad range of reaction times in the study of such complex, multistate reactions.     

与非门(NAND)的DNA计算模型

近年来,随着DNA计算研究的深入,基于DNA的布尔电路的模拟成为其中一个热门的研究方向.分子信标是一种特殊的探针分子,广泛应用于各种生物技术的检测方面,具有结果稳定,特异性强的优点,本文提出了一种基于诱导"发夹"形式的DNA与非门模型,和已有的模型相比,该模型具有简单,可靠性更高且可以重复使用等优点.     

An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telomeres

The termini of linear chromosomes are protected by specialized DNA structures known as telomeres that also facilitate the complete replication of DNA ends. The simplest type of telomere is a covalently closed DNA hairpin structure found in linear chromosomes of prokaryotes and viruses. Bidirectional replication of a chromosome with hairpin telomeres produces a catenated circular dimer that is subsequently resolved into unit-length chromosomes by a dedicated DNA cleavage-rejoining enzyme known as a hairpin telomere resolvase (protelomerase). Here we report a crystal structure of the protelomerase TelK from Klebsiella oxytoca phage varphiKO2, in complex with the palindromic target DNA. The structure shows the TelK dimer destabilizes base pairing interactions to promote the refolding of cleaved DNA ends into two hairpin ends. We propose that the hairpinning reaction is made effectively irreversible by a unique protein-induced distortion of the DNA substrate that prevents religation of the cleaved DNA substrate.     

A resource-sharing model based on a repeated game in fog computing

With the rapid development of cloud computing techniques, the number of users is undergoing exponential growth. It is difficult for traditional data centers to perform many tasks in real time because of the limited bandwidth of resources. The concept of fog computing is proposed to support traditional cloud computing and to provide cloud services. In fog computing, the resource pool is composed of sporadic distributed resources that are more flexible and movable than a traditional data center. In this paper, we propose a fog computing structure and present a crowd-funding algorithm to integrate spare resources in the network. Furthermore, to encourage more resource owners to share their resources with the resource pool and to supervise the resource supporters as they actively perform their tasks, we propose an incentive mechanism in our algorithm. Simulation results show that our proposed incentive mechanism can effectively reduce the SLA violation rate and accelerate the completion of tasks.     

Simple colorimetric DNA detection based on hairpin assembly reaction and target-catalytic circuits for signal amplification

A simple strategy of colorimetric DNA detection is presented based on a hairpin assembly reaction and target-catalytic DNA circuits to achieve enzyme-free signal amplification. The method employed two hairpin species (H1 and H2), which were stable and unable to hybridize in the absence of target. In the presence of target, the target hybridized with hairpin H1 and the opened hairpin H1 hybridized with hairpin H2, allowing the target to be displaced. H1 and H2 were respectively attached to gold nanoparticles, allowing the duplex formed from H1 and H2 to be visualized with the naked eye. The displaced target again triggered the next round of strand exchange reaction to achieve signal amplification. The method may have a wide range of sensor applications because it is enzyme-free and simple to perform.     

A new method for computing the macromolecular electric potential

A general methodology is developed for the rigorous computation of the electrostatic potential for a protein of arbitrary shape, assuming the presence of linear dielectric media. The theory proceeds by considering the distribution of induced polarization charge at the dielectric interface, rather than by attempting a direct solution of Poisson's equation (as in the finite-difference approach of Warwicker & Watson). The method is applied to a study of two-dimensional model proteins, where it is shown that the presence of a cleft is associated with a region of relatively high potential in the solvent medium. The results of a preliminary calculation in three dimensions for the protein lysozyme are also discussed; again, a region of enhanced potential is observed near the cleft at the active site. Our computational evidence supports the suggestion of Warwicker & Watson that clefts are associated with important electrostatic effects.     

Au-NPs enhanced SPR biosensor based on hairpin DNA without the effect of nonspecific adsorption

Gold nanoparticles (Au-NPs) are usually used to amplify surface plasmon resonance (SPR) signals, however, the serious nonspecific adsorption has largely limited their practical applications. Here, we developed a novel Au-NPs enhanced biosensor without the effect of nonspecific adsorption: cutting Au-NPs off from the biosensor surface by RsaI endonuclease. In order to further improve the sensitivity, the probe DNA was designed specially. After the cleavage reaction, the residual probe DNA formed hairpin structure, which also resulted in a great change in SPR dip shift. Then, with the coaction of Au-NPs and conformation change of probe DNA, the SPR signal was amplified greatly. Using this method, we monitored the process of DNA cleavage in real-time and achieved a detection level of 5×10(-8) M. Moreover, the result of X-ray photoelectron spectroscopy (XPS) experiment further confirmed that large nonspecific adsorption existed. However, because SPR recorded a process in which the Au-NPs were cut off, the serious nonspecific adsorption did not affect the experimental result.     

A model of pattern formation based on signaling pathways

A model of pattern formation in the early embryo is presented. It is motivated by the necessary interaction of kinases and phosphatases, and in particular by the family of Wnt kinase and RPTP phosphatase signaling pathways. It is seen as complementary to the more short-range patterning of the Delta/Notch (or juxtacrine) signaling pathway.