THE MOLECULAR ALGORITHM OF CONNECTIVITY BASED ON THREE DIMENSIONAL DNA STRUCTURE

Inspired by the potential computational capability of 3-Dimensional (3D) DNA structure,this paper presents a graph structure constructed by k-armed (k = 3or 4) branched junction DNA molecules to explore the possibility of solving some intractable problems. In the proposed procedure,vertex building blocks consisting of 3,4-armed branched junction molecules are selectively used to form different graph structures. After separating these graph structures by gel electrophoresis,the connec-tivity of this graph can be determined. Furthermore,the amount of potential solutions can be reduced by a theorem of graph theory.

New Mathematical Tools for the Study of the DNA Structure

We propose a number of new mathematical tools for the study of the DNA structure. In particular, we establish a connection between the DNA molecule and the Grassmann-Plücker coordinates, which, in both in mathematics and physics, are of great importance.

Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution

A-form DNA is one of the biologically active double helical structure.The study of A-DNA structure has an extensive application for developing the field of DNA packaging in biotechnology.In aqueous solution,the A-DNA structure will have a free transformation,the A-DNA structure will be translated into B-form structure with the evolution of time,and eventually stabilized in the B-DNA structure.To explore the stability function of the bivalent metal ions on the A-DNA structure,a series of molecular dynamics simulations have been performed on the A-DNA of sequence(CCCGGCCGGG).The results show that bivalent metal ions(Mg^(2+),Zn^(2+),Ca^(2+))generate a great effect on the structural stability of A-DNA in the environment of high concentration.As the interaction between metal ions and electronegative DNA chains,the stability of A-DNA in solution is gradually improved with the increasing solution concentration of ions.In metal salt solution with high concentration,metal ions can be easily distributed in the solvation shells around the phosphate groups and further lead to the formation of shorter and more compact DNA structure.Also,under the condition of the same concentration and valency of the metal ions,the stability of A-DNA structure is different.The calculations indicate that the structure of A-DNA in CaCl_(2)solution is less stable than in MgCl_(2)and ZnCl_(2)solution.

Addressable DNA Information Processing System with a Fluorescent Readout for Rewritable Memory

DNA-based nanostructure allows the construction of molecular devices useful in biological computing and information processing.Herein,an addressable and editable DNA information processing system established on a fluorescence intensity signal detection platform to save and encrypt information is proposed.The system operates by encoding information into distinct and changeable units of the trigger strands decoding by fluorescence intensity signal detection.Through toehold-mediated strand displacement reactions,the trigger strand can be precisely added to and removed from the memorizer and reporter to implement the function of editing,encrypting,and decrypting.Our strategy is simple to implement,requiring only two mixing steps at room temperature for each operation and fluorescence intensity signal detection to read the data.And the system can realize accurate retrieval of specific individual information,eliminating all unnecessary redundant readouts.Because of its point-to-point accurate readout and programmability,the system is expected to become a powerful tool for the future development of information storage and sensing of biological molecules.

Interaction between human telomeric G-quadruplexes characterized by single molecule magnetic tweezers

Human telomeric G-quadruplex plays a crucial role in regulating the genome stability. Despite extensive studies on structures and kinetics of monomeric G-quadruplex, the interaction between G-quadruplexes is still in debate. In this work,we employ magnetic tweezers to investigate the folding and unfolding kinetics of two contiguous G-quadruplexes in 100-mM K~＋buffer. The interaction between G-quadruplexes and the consequent effect on the kinetics of G-quadruplex are revealed. The linker sequence between G-quadruplexes is further found to play an important role in the interaction between two G-quadruplexes. Our results provide a high-resolution insight into kinetics of multimeric G-quadruplexes and genome stability.

A cost-effective detection of low-abundance mutation with DNA three-way junction structure and lambda exonuclease

We presented a low-abundance mutation detection method with lambda exonuclease and DNA threeway junction structure.The assistant strand in the DNA three-way junction structure could regulate the reaction system from the kinetics and thermodyna mics aspects.The optimization of the assista nt strand helps to improve the selectivity of the mutant-type DNA to the wild-type DNA about 35 times.Moreover,the cost of the optimization process could be saved by about 90%.The method was applied to the detection of a human ovarian cancer-related gene mutation BRCA1(rs1799949,c.2082 C>T).The limit of detection to the mutation abundance in the DNA three-way junction structure system(0.2%) was one order lower compared with that in the double-stranded DNA structure system(2%).The mutation abundance in different standard samples was quantitively measured,and the results were consistent with the initial abundance in the standard samples.

Delaminated layered double hydroxide delivers DNA molecules as sandwich nanostructure into cells via a non-endocytic pathway

Layered double hydroxides （LDHs） are effective molecular carriers in cytological research, gene therapy, and transgenic applications. Herein, we investigated the internalization behavior of the LDH-DNA biocon- jugates via a microscopic approach and analyzed the internalization pathway by dissipative particle dynamics （DPD） simulations. We experimentally found that LDH can efficiently carry DNA into the nucleus of cell in BY-2 suspension cells. Furthermore, atomic force microscopy and X-ray diffraction anal- ysis demonstrated that the LDH-DNA bioconjugates mainly exist as a DNA-LDH-DNA sandwich complex, while the LDH-DNA-LDH sandwich complex and DNA-LDH complex cannot be excluded. The DPD simu- lations further indicated that only the DNA-LDH-DNA sandwich structure could penetrate the plasma membrane （PM）, while PM is impermeable to the LDH-DNA-LDH sandwich complex and the DNA-LDH complex. This work provides novel perspective for understanding the membrane penetration mechanism of LDH nano-sheets and new insights into the design of novel molecular delivery systems.

Y-Shaped Circular Aptamer–DNAzyme Conjugates for Highly Efficient in Vivo Gene Silencing

Oligonucleotide drugs have been used widely as therapeutic agents for gene therapy,while their instability in biological media and inefficiency for intracellular delivery remain major hurdles for practical in vivo applications.Herein,we report a circular Y-shaped aptamer–DNAzyme conjugate(cYAD)for highly efficient in vivo gene silencing via RNA cleavage,which can been employed in various disease treatments,including cancer,inflammation,as well as viral infections.Systematic studies revealed that cyclization of the DNA structure could improve the stability of oligonucleotide drugs in vivo.Besides,the bivalent aptamer motifs provided a specific and enhanced tumor cell targeting ability for accumulation and retention of the oligonucleotide drugs at the tumor site.As a proof of concept,a widely applicable Na+-dependent fluorescent sensor,NaA43 DNAzyme,was used to inhibit MET gene expression in mice tumor model tissues,which exhibited highly efficient gene silencing performance in vivo,which confirmed our findings with cYAD.This strategy provides a novel approach for the construction of oligonucleotide drugs for practical therapeutic applications.

DNA-Based Architectures for in situ Target Biomolecule Analysis in Confined Nano-space

In situ target biomolecule analysis is of great significance for real-time monitoring and regulation of endogenous biomarkers and elementary biomolecules in vivo.Gratifyingly,the rapid evolution of structural DNA nanotechnology during past decades has established an appealing toolbox for biological analysis and medical detection.The modulated self-assembly and underlying canonical Watson-Crick base-pairing rules provide possibilities for accurate controlling of the topologies and functions of obtained nanomaterials.The probes composed of diverse DNA nanostructures and DNA-nanoparticle complexes can create a confined space,which increases target accessibility and improves probe stability,sensitivity and specificity.In this minireview,we retrospect the research progress of in-situ biomolecular analysis based on DNA nanostructures for intracellular and in vivo biosensors in confined space.The characteristics of distinct DNA nanomaterials are first introduced,and then the fundamentals of biosensing process of designed DNA nanostructures are emphasized.Moreover,we elucidate our perspective over the challenges of this field and discuss the potential directions of this kind of application-oriented fabrication technique.

Versatile Magnetic Nanoparticles for Spatially Organized Assemblies of Enzyme Cascades:A Comprehensive Investigation of Catalytic Performance

Inspired by nature,precise spatial organization of enzyme cascades of interest is crucial to the improvement of catalytic performance.Herein,DNA scaffolds were introduced to construct a toolkit for versatile immobilization of enzyme pairs on dextran-coated magnetic nanoparticles(MNPs).After the glucose oxidase(GOx)and horseradish peroxidase(HRP)pair was immobilized through random cova-lent,DNA-directed and DNA tile-directed strategies,the immobilized GOx/HRP pair on the MNP-based carrier assembled with DNA tile(TD@MNPs)exhibited the highest activity due to rational spatial organization and less conformational change of constituent enzymes.With a decrease in interenzyme distance on TD@MNPs,furthermore,the catalytic efficiency of the HRP/GOx pair increased further for both substrates,2,2'-azinobis(3-ethyl-benzthiazoline-6-sulfonate)(ABTS)and 3,3',5,5'-tetramethyl benzidine(TMB).As the assembled HRP was closer to the carrier surface,the catalytic efficiency of the GOx/HRP pair increased by 6.2-fold for positively charged TMB and only by 62%for negatively charged ABTS compared with the free GOx/HRP pair.Moreover,a reversal of catalytic efficiency was found after the GOx/HRP pair was assembled on a positively charged carrier(TD@pMNPs).This research demonstrated that MNP-based car-riers had the potential to become a versatile toolkit for shedding an insight into catalytic performance and the development of new biocatalysts.

A Structural Bisulfite Assay to Identify DN Cruciforms

In the half century since the discovery of the double-helix structure of DNA, it has become increasingly clear that DNA functionality is based on much more than its sequence in a double-helical structure. Further advances have highlighted the importance of additional aspects of DNA structure： its packaging in the higher order chromatin structure, positioning of nucleosomes along the DNA, and the occurrence of non-helical DNA structures. Of these, the latter has been problematic to prove empirically. Here, we describe a method that uses non-denaturing bisulfite sequencing on isolated Arabidopsis thaliana nuclei to determine the location of cytosines positioned outside the double helix as a result of non-B-form DNA structures. We couple this with computational methods and S1 nuclease digest to reliably identify stable, non-B-form, cruciform structures. This enables us to identify a palindrome in the promoter of FLOWERING LOCUS T that forms a stable non-B-form structure. The stronger conservation of the ability to form a nonhelical secondary structure than of the sequence suggests that this structure is biologically relevant.

Novel mitochondrial 16S rRNA mutation, 3200T→C, associated with adult-onset type 2 diabetes

Objective To investigate the role of a potential diabetes related mitochondrial region, which includes two previously reported mutations, 3243AG and 3316GA, in Chinese patients with adult onset type 2 diabetes Methods A total of 277 patients and 241 normal subjects were recruited for the study Mitochondrial nt 3116-3353, which spans the 16S rRNA, tRNA leu(UUR) and the NADH dehydrogenase 1 gene, were detected using polymerase chain reaction (PCR), direct DNA sequencing, PCR restriction fragment length polymorphism and allele specific PCR Variants were analyzed by two tailed Fisher exact test The function of the variants in 16S rRNA were predicted for minimal free energy secondary structures by RNA folding software mfold version 3 Results Four homoplasmic nucleotide substitutions were observed, 3200TC, 3206CT, 3290TC and 3316GA Only the 3200TC mutation is present in the diabetic population and absent in the control population No statistically significant associations were found between the other three variants and type 2 diabetes The 3200TC and 3206CT nucleotide substitutions located in 16S rRNA are novel variants The 3200TC caused a great alteration in the minimal free energy secondary structure model while the 3206CT altered normal 16S rRNA structure little Conclusions The results suggest that the 3200TC mutation is linked to the development of type 2 diabetes, but that the other observed mutations are neutral In contrast to the Japanese studies, the 3316GA does not appear to be related to type 2 diabetes

A transposon-introduced G-quadruplex motif is selectively retained and constrained to downregulate CYP321A1

Insects utilize xenobiotic compounds to up-and downregulate cytochrome P450 monooxygenases(P450s)involved in detoxification of toxic xenobiotics including phytochemicals and pesticides.G-quadruplexes(G4)-forming DNA motifs are enriched in the promoter regions of transcription factors and function as cis-acting elements to regulate these genes.Whether and how P450s gain and keep G4 DNA motifs to regulate their expression still remain unexplored.Here,we show that CYP321A1,a xenobiotic-metabolizing P450 from Helicoverpa zea,a polyphagous insect of economic importance,has acquired and preserved a G4 DNA motif by selectively retaining a transposon known as HzIS1-3 that carries this G4 DNA motif in its promoter region.The HzIS1-3 G4 DNA motif acts as a silencer to suppress the constitutive and induced expression of CYP321A1 by plant allelochemicals flavone and xanthotoxin through folding into an intramolecular parallel or hybrid-1 conformation in the absence or presence of K^(+).The G4 ligand N-methylmesoporphyrin IX(NMM)strengthens the silencing effect of HzIS1-3 G4 DNA motif by switching its structure from hybrid-1 to hybrid-2.The enrichment of transposons in P450s and other environment-adaptation genes implies that selective retention of G4 DNA motif-carrying transposons may be the main evolutionary route for these genes to obtain G4 DNA motifs.