DNA: Structure and function

Whole-Body Physiologically Based Pharmacokinetic Modeling of GalNAc-Conjugated siRNAs

Background/Objectives: N-acetyl-galactosamine small interfering RNAs (GalNAc-siRNA) are an emerging class of drugs due to their durable knockdown of disease-related proteins. Direct conjugation of GalNAc onto the siRNA enables targeted uptake into hepatocytes via GalNAc recognition of the Asialoglycoprotein Receptor (ASGPR). With a transient plasma exposure combined with a prolonged liver half-life, GalNAc-siRNA exhibits distinct disposition characteristics. We aimed to develop a generic GalNAc-siRNAs whole-body physiologically based pharmacokinetic-pharmacodynamic (WB-PBPK-PD) model for describing the pharmacokinetic-pharmacodynamic (PK-PD) relationship and overall tissue distribution in the open-source platform Open Systems Pharmacology Suite. Methods: Model development was performed using published studies in mice leveraging the PK-Sim® standard implementation for large molecules with added implementations of ASGPR-mediated liver disposition and downstream target effects. Adequate model performance was achieved across study measurements and included studies adopting a combination of global and compound-specific parameters. Results: The analysis identified significant compound dependencies, e.g., endosomal stability, with direct consequences for the pharmacological effect. Additionally, knowledge gaps in mechanistic understanding related to extravasation and overall tissue distribution were identified during model development. The presented study provides a generic WB-PBPK-PD model for the investigation of GalNAc-siRNAs implemented in a standardized open-source platform.

From straight to curved: A historical perspective of DNA shape

DNA is the macromolecule responsible for storing the genetic information of a cell and it has intrinsic properties such as deformability, stability and curvature. DNA Curvature plays an important role in gene transcription and, consequently, in the subsequent production of proteins, a fundamental process of cells. With recent advances in bioinformatics and theoretical biology, it became possible to analyze and understand the involvement of DNA Curvature as a discriminatory characteristic of gene-promoting regions. These regions act as sites where RNAp (ribonucleic acid-polymerase) binds to initiate transcription. This review aims to describe the formation of Curvature, as well as highlight its importance in predicting promoters. Furthermore, this article provides the potential of DNA Curvature as a distinguishing feature for promoter prediction tools, as well as outlining the calculation procedures that have been described by other researchers. This work may support further studies directed towards the enhancement of promoter prediction software.

Comprehensive genomic identification of cotton starch synthase genes reveals that GhSS9 regulates drought tolerance

Introduction

Starch metabolism is involved in the stress response. Starch synthase (SS) is the key enzyme in plant starch synthesis, which plays an indispensable role in the conversion of pyrophosphoric acid to starch. However, the SS gene family in cotton has not been comprehensively identified and systematically analyzed.

Result

In our study, a total of 76 SS genes were identified from four cotton genomes and divided into five subfamilies through phylogenetic analysis. Genetic structure analysis proved that SS genes from the same subfamily had similar genetic structure and conserved sequences. A cis-element analysis of the SS gene promoter showed that it mainly contains light response elements, plant hormone response elements, and abiotic stress elements, which indicated that the SS gene played key roles not only in starch synthesis but also in abiotic stress response. Furthermore, we also conducted a gene interaction network for SS proteins. Silencing GhSS9 expression decreased the resistance of cotton to drought stress. These findings suggested that SS genes could be related to drought stress in cotton, which provided theoretical support for further research on the regulation mechanism of SS genes on abiotic starch synthesis and sugar levels.

A Mathematical Model for Vibration Behavior Analysis of DNA and Using a Resonant Frequency of DNA for Genome Engineering

The DNA molecule is the most evolved and most complex molecule created by nature. The primary role of DNA in medicine is long-term storage of genetic information. Genetic modifying is one of the most critical challenges that scientists face. On the other hand, it is said that under the influence of acoustic, electromagnetic, and scalar waves, the genetic code of DNA can be read or rewritten. In this article, the most accurate and comprehensive dynamic model will be presented for DNA. Each of the two strands is modeled with an out of plane curved beam and then by doubling this two strands with springs, consider the hydrogen bond strength between this two strands. Beams are traditionally descriptions of mechanical engineering structural elements or building. However, any structure such as automotive automobile frames, aircraft components, machine frames, and other mechanical or structural systems contain beam structures that are designed to carry lateral loads are analyzed similarly. Also, in this model, the mass of the nucleobases in the DNA structure, the effects of the fluid surrounding the DNA (nucleoplasm) and the effects of temperature changes are also considered. Finally, by deriving governing equations from Hamilton's principle method and solving these equations with the generalized differential quadrature method (GDQM), the frequency and mode shape of the DNA is obtained for the first time. In the end, validation of the obtained results from solving the governing equations of mathematical model compared to the obtained results from the COMSOL software is confirmed. By the help of these results, a conceptual idea for controlling cancer with using the DNA resonance frequency is presented. This idea will be presented to stop the cancerous cell's protein synthesis and modifying DNA sequence and genetic manipulation of the cell. On the other hand, by the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely.

Nanomaterials-Based siRNA Delivery: Routes of Administration, Hurdles and Role of Nanocarriers

Ribonucleic acid interference (RNAi) is a potential alternative therapeutic approach to knock down the overexpression of genes in several disorders especially cancers with underlying genetic dysfunctions. For silencing of specific genes involved in cell cycle, small/short interfering ribonucleic acids (siRNAs) are being used clinically. The siRNA-based RNAi is more efficient, specific and safe antisense technology than other RNAi approaches. The route of siRNA administration for siRNA therapy depends on the targeted site. However, certain hurdles like poor stability of siRNA, saturation, off-target effect, immunogenicity, anatomical barriers and non-targeted delivery restrict the successful siRNA therapy. Thus, advancement of an effective, secure, and long-term delivery system is prerequisite to the medical utilization of siRNA. Polycationic nanocarriers mediated targeted delivery system is an ideal system to remove these hurdles and to increase the blood retention time and rate of intracellular permeability. In this chapter, we will mainly discuss the different biocompatible, biodegradable, non-toxic (organic, inorganic and hybrid) nanocarriers that encapsulate and shield the siRNA from the different harsh environment and provides the increased systemic siRNA delivery.

Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies

Amino acid and nucleic acid interactions are central in biology and may have played a role in the evolutionary development of protein-based life from an early "RNA Universe." To explore the possible role of single amino acids in promoting nucleic acid folding, single-molecule Förster resonance energy transfer experiments have been implemented with a DNA hairpin construct (7 nucleotide double strand with a 40A loop) as a simple model for secondary structure formation. Exposure to positively charged amino acids (arginine and lysine) is found to clearly stabilize the secondary structure. Kinetically, each amino acid promotes folding by generating a large increase in the folding rate with little change in the unfolding rate. From analysis as a function of temperature, arginine and lysine are found to significantly increase the overall exothermicity of folding while imposing only a small entropic penalty on the folding process. Detailed investigations into the kinetics and thermodynamics of this amino acid-induced folding stability reveal arginine and lysine to interact with nucleic acids in a manner reminiscent of monovalent cations. Specifically, these observations are interpreted in the context of an ion atmosphere surrounding the nucleic acid, in which amino acid salts stabilize folding qualitatively like small monovalent cations but also exhibit differences because of the composition of their side chains.

Discontinuous growth of DNA plectonemes due to atomic scale friction

We develop a model to explain discontinuities in the increase of the length of a DNA plectoneme when the DNA filament is continuously twisted under tension. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuation. We postulate that a corrugated energy landscape that contains energy barriers is the cause of jumps in the length of the plectoneme as the number of turns is increased. Thus, our model is similar to the Prandtl-Tomlinson model of atomic scale friction. The existence of a corrugated energy landscape can be justified due to the close proximity of the neighboring pieces of DNA in a plectoneme. We assume the corrugated energy landscape to be sinusoidal since the plectoneme has a periodic helical structure and rotation of the bead is a form of periodic motion. We perform calculations with different tensile forces and ionic concentrations, and show that rotation-extension curves manifest stair-step shapes under relatively high ionic concentrations and high forces. We show that the jump in the plectonemic growth is caused by the flattening of the energy barrier in the corrugated landscape.

Therapeutic approaches for the delivery of TNF-α siRNA

Immune-mediated diseases are emerging as a major healthcare concern in the present era. TNF-α, a proinflammatory cytokine, plays a major role in the manifestation of these diseases by mediating different pathways and inducing the expression of other cytokines. In last decades, monoclonal antibodies and extracellular portion of human TNF-α receptors are explored in this area; however, the risk of immunological response and undesired effects urge a need to develop more effective therapies to control TNF-α levels. siRNA therapeutic strategies are emerging for the treatment of myriad of diseases, but the delivery challenges associated with siRNA require the development of suitable delivery vectors. For delivery of TNF-α siRNA, both viral and nonviral vectors are explored. This review attempts to describe different delivery approaches for TNF-α siRNA with special focus on nonviral delivery vectors.

Chitosan-coated red fluorescent protein nanoparticle as a potential dual-functional siRNA carrier

AIMS

Developing safe and efficient nano vectors is critical for the success of siRNA therapy.

MATERIALS & METHODS

By encapsulating red fluorescent protein (RFP) with chitosan (CS), a dual-functional siRNA delivery nano vector, RFP@CS, has been synthesized.

RESULTS

RFP@CS has an optimum size of 7-23 nm for siRNA delivery; and the fluorescence of RFP, protected by CS coating, provides an excellent probe to track the delivery of siRNA. RFP@CS delivers siRNA efficiently into cells and the targeted gene could be completely silenced even after 48 h. No cytotoxicity or acute toxicity in mice was observed.

CONCLUSION

The high transfection efficacy and safety demonstrate RFP@CS is a promising nano vector for the gene therapy.

Discovery of the unique self-assembly behavior of terminal suckers-contained dsDNA onto GNP and novel "light-up" colorimetric assay of nucleic acids

Noble metal nanoparticles are currently of great interest because of their unique optical properties and potential applications in disease diagnostics and cancer treatment. In the present work, a discovery was reported that dsDNA with terminal thiols at its two ends could lie easily flat onto the gold nanoparticle (GNP) surface rather than cross linked different GNPs, indicating an unique self-assembly behavior of newly-designed molecules on GNPs. This could intensively stabilize gold nanoparticles against aggregation even at a high salt concentration. On the basis of this discovery, a novel light-up colorimetric sensing strategy was developed for the detection of p53 gene by combining with the cyclical nucleic acid strand-displacement polymerization (CNDP). For the described colorimetric system, GNPs require no any surface functionalization, and target recognition reaction and CNDP amplification could be conducted under the optimized conditions to achieve a high efficiency. The high detection sensitivity and desirable selectivity are achieved, and the potential practical application was demonstrated. Besides, this sensing system can function in a wide range of salts, making it a suitable platform to cooperate with many biological processes.

Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)(10), (GC)(10), (AT)(5)(GC)(5), and (AT-GC)(5) where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)(5)(GC)(5) and (AT-GC)(5) models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO(4) + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

DNA assembled gold nanoparticles polymeric network blocks modular highly sensitive electrochemical biosensors for protein kinase activity analysis and inhibition

A highly sensitive electrochemical biosensor was built for the detection of kinase activity based on the DNA induced gold nanoparticles (AuNPs) polymeric network block signal amplification. In this strategy, the DNA1 conjugated AuNPs were integrated with the phosphorylated peptide by Zr(4+) and assembled into DNA-AuNPs polymeric network block by the hybridization of cDNA with each side sequences of DNA1 and joint DNA2. The kinase activity was determined by the amperometric responses of [Ru(NH3)6](3+) absorbed on the network block by electrostatic interaction. Due to its excellent electroactivity and high accommodation of the DNA-AuNPs polymeric network block for [Ru(NH3)6](3+), the current signal was significantly amplified, affording a highly sensitive electrochemical analysis of kinase activity. The as-proposed biosensor presents a low detection limit of 0.03 U mL(-1) for protein kinase A (PKA) activity, wide linear range (from 0.03 to 40 U mL(-1)), and excellent stability even in cell lysates and serum samples. This biosensor can also be applied for quantitative kinase inhibitor screening. Finally, the PKA activities from BE4S-2B, A549, and MCF-7 cell lysates were further analyzed, which provided a valuable strategy in developing a high-throughput assay of in vitro kinase activity and inhibitor screening for clinic diagnostics and therapeutics.

How adsorption influences DNA denaturation

The thermally induced denaturation of DNA in the presence of an attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the surface, the denaturation phase transition disappears. Instead, there is a smooth crossover to a weakly naturated state. Our second conclusion is that even when the interstrand attraction alone is too weak for creating a naturated state at the given temperature and also when the surface-strand attraction alone is too weak for creating an adsorbed state, the combined effect of the two attractions can lead to a naturated and adsorbed state.

Inverted and mirror repeats in model nucleotide sequences

We analytically and numerically study the probabilistic properties of inverted and mirror repeats in model sequences of nucleic acids. We consider both perfect and nonperfect repeats, i.e., repeats with mismatches and gaps. The considered sequence models are independent identically distributed (i.i.d.) sequences, Markov processes and long-range sequences. We show that the number of repeats in correlated sequences is significantly larger than in i.i.d. sequences and that this discrepancy increases exponentially with the repeat length for long-range sequences.

DNA transitions induced by binding of PARP-1 to cruciform structures in supercoiled plasmids

BACKGROUND

Poly(ADP-ribose)polymerase-1 (PARP-1) binds to single and double-stranded breaks in DNA, but less well known is its affinity for undamaged DNA. Previously, we have shown that PARP-1 also binds to the hairpin structures in DNA models. The mechanism underlying these interactions remains to be defined.

METHODS

We analyzed atomic force microscopy (AFM) images of complex of PARP-1 proteins with supercoiled plasmids containing cruciform structures. Using volume measurement analysis of molecules of PARP-1, we determined the numbers of PARP-1 molecules interacting with supercoiled DNA plasmids containing one cruciform structure. We also determined the extent of supercoiling of plasmids.

RESULTS

Our observations show that PARP-1 binds to sequences that transition from B-DNA to cruciform structures. PARP-1 is present at the ends of hairpin arms, sites containing a 4-base single-stranded DNA. Furthermore, interaction of PARP-1 with supercoiled plasmids leads to a more relaxed plasmid-DNA conformation.

CONCLUSIONS

Binding of PARP-1 to cruciform DNA offers insight into possible mechanisms underlying with changes in DNA conformation. These observations may offer insight into mechanisms involving DNA conformation related to process such as DNA repair and transcription.

Electrical conduction in macroscopically oriented deoxyribonucleic and hyaluronic acid samples

Measurements of the quasistatic and frequency dependent electrical conductivity below 1 MHz were carried out on wet-spun, macroscopically oriented, calf thymus deoxyribonucleic (DNA) and umbilical cord hyaluronic acid (HA) bulk samples. The frequency dependence of the electrical conductivity in the frequency range of approximately 10(-3) - 10(6) Hz of both materials is surprisingly rather similar. Temperature dependence of the quasistatic electrical conductivity above the low temperature saturation plateau can be well described by the activated Arrhenius law with the activation energy of approximately 0.8 eV for both DNA and HA. We discuss the meaning of these findings for the possible conduction mechanism in these particular charged polyelectrolytes.

DNA-DNA interaction beyond the ground state

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic "snap-shot" recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a "torsional alignment transition," which is first order for nonhomologous DNA and weaker order for homologous sequences.

Two sides of the coin: affinity and specificity of nucleic acid interactions

During the past decade, synthetic nucleobase oligomers have found wide use in biochemical sciences, biotechnology and molecular medicine, both as research and/or diagnostic tools and as therapeutics. Numerous applications of common and modified oligonucleotides and oligonucleotide mimics rely on their ability to sequence-specifically recognize nucleic acid targets (DNA or RNA) by forming duplexes or triplexes. In general, these applications would benefit significantly from enhanced binding affinities of nucleobase oligomers in the formation of various secondary structures. However, for high-affinity probes, the selectivity of sequence recognition must also be improved to avoid undesirable associations with mismatched DNA and RNA sites. Here, we review recent progress in understanding the molecular mechanisms of nucleic acid interactions and the development of new high-affinity plus high-specificity oligonucleotides and their mimics, with particular emphasis on peptide nucleic acids.

Molecular mechanisms of TRS instability

To date several neurodegenerative disorders including myotonic dystrophy, Huntington's disease, Kennedy's disease, fragile X syndrome, spinocerebellar ataxias or Friedreich's ataxia have been linked to the expanding trinucleotide sequences. Although phenotypic features vary among these debilitating diseases, the structural abnormalities of the triplet repeat containing DNA sequences is the primary cause for all of these disorders. Expansions of the CAG repeat within coding regions of miscellaneous genes result in the synthesis of aberrant proteins containing enormously long polyglutamine stretches. Such proteins acquire toxic functions and/or may direct cells into the apoptotic cycle. On the other hand, massive expansions of various triplet repeats (i.e., CTG/CAG, CGG/CCG/, GAA/TTC) inside the noncoding regions lead to the silencing of transcription and therefore affect expression of the adjacent genes. The repetitive character of TRS allows stretches of such tracts to form slipped-stranded structures, self-complementary hairpins, triplexes or more complex configurations called "sticky DNA", which are not equally processed by some cellular mechanisms, as compared to random DNA. It is likely that the instability of the short TRS (below the threshold level) occurs due to the SILC pathway, which is driven by the DNA slippage. Accumulation of the short expansions leads to the disease premutation state where the MLC pathway becomes predominant. Independent of which mechanism is involved in the MLC pathway (replication, transcription, repair or recombination) the process of complementary strand synthesis is crucial for the TRS instability. Generally, dependent on the location of the tract which has higher potential to form secondary DNA structure, further processing of such tract may result in expansions (secondary structure formed at the newly synthesized strand) or deletions (structure present on the template strand). Analyses of molecular mechanisms of the TRS genetic instability using bacteria, yeast, cell lines and transgenic animals as models allowed the scientists to better understand the role of some major cellular processes in the development of neurodegenerative disorders in humans. However, it is necessary to remember that most of these investigations were focused on the involvement of each particular process separately. Much less of this work though was dedicated to the search for the interactions between such cellular systems that in effect could result in different rate of TRS expansions. Thus, more intensive studies are necessary in order to fully understand the phenomenon ofthe dynamic mutations leading to the human hereditary neurodegenerative diseases.

Phase behavior of columnar DNA assemblies

The interaction between two stiff parallel DNA molecules depends not only on the distance between their axes but also on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is investigated, on the basis of the electrostatic pair potential that takes into account DNA helical symmetry and the amount and distribution of adsorbed counterions. A phase diagram obtained by lattice sums predicts a variety of positionally and azimuthally ordered phases and bundling transitions strongly depending on the counterion adsorption patterns.

A DNA structural atlas for Escherichia coli

We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability. The structural values that are computed for the Escherichia coli chromosome are significantly different from (and generally more extreme than) that expected from the nucleotide composition. To aid this analysis, we have constructed tools that plot structural measures for all positions in a long DNA sequence (e.g. an entire chromosome) in the form of color-coded wheels (http://www.cbs.dtu. dk/services/GenomeAtlas/). We find that these "structural atlases" are useful for the discovery of interesting features that may then be investigated in more depth using statistical methods. From investigation of the E. coli structural atlas, we discovered a genome-wide trend, where an extended region encompassing the terminus displays a high of level curvature, a low level of flexibility, and a low degree of helix stability. The same situation is found in the distantly related Gram-positive bacterium Bacillus subtilis, suggesting that the phenomenon is biologically relevant. Based on a search for long DNA segments where all the independent structural measures agree, we have found a set of 20 regions with identical and very extreme structural properties. Due to their strong inherent curvature, we suggest that these may function as topological domain boundaries by efficiently organizing plectonemically supercoiled DNA. Interestingly, we find that in practically all the investigated eubacterial and archaeal genomes, there is a trend for promoter DNA being more curved, less flexible, and less stable than DNA in coding regions and in intergenic DNA without promoters. This trend is present regardless of the absolute levels of the structural parameters, and we suggest that this may be related to the requirement for helix unwinding during initiation of transcription, or perhaps to the previously observed location of promoters at the apex of plectonemically supercoiled DNA. We have also analyzed the structural similarities between groups of genes by clustering all RNA and protein-encoding genes in E. coli, based on the average structural parameters. We find that most ribosomal genes (protein-encoding as well as rRNA genes) cluster together, and we suggest that DNA structure may play a role in the transcription of these highly expressed genes.

Conformations of closed DNA

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.

Three views of microbial genomes

We describe here GenomeAtlases as a method for visualising three different aspects of complete microbial chromosomes: repeats, DNA structural characteristics, and base composition. We have applied this method to all publicly available genomes, and find a general strand preference of global repeats. The atlas for the Mycoplasma genitalium genome is presented as an example, and results from all three views are consistent with known characteristics of the genome.