On the nature of DNA hyperchromic effect

Unravelling the Link between Oligonucleotide Structure and Diastereomer Separation in Hydrophilic Interaction Chromatography

Therapeutic oligonucleotides (ONs) commonly incorporate phosphorothioate (PS) modifications. These introduce chiral centers and generate ON diastereomers. The increasing number of ONs undergoing clinical trials and reaching the market has led to a growing interest to better characterize the ON diastereomer composition, especially for small interfering ribonucleic acids (siRNAs). In this study, and for the first time, we identify higher-order structures as the major cause of ON diastereomer separation in hydrophilic interaction chromatography (HILIC). We have used conformational predictions and melting profiles of several representative full-length ONs to first analyze ON folding and then run mass spectrometry and HILIC to underpin the link between their folding and diastereomer separation. On top, we show how one can either enhance or suppress diastereomer separation depending on chromatographic settings, such as column temperature, pore size, stationary phase, mobile-phase ionic strength, and organic modifier. This work will significantly facilitate future HILIC-based characterization of PS-containing ONs; e.g., enabling monitoring of batch-to-batch diastereomer distributions in full-length siRNAs, a complex task that is now for the first time shown as possible on this delicate class of therapeutic double-stranded ONs.

Imiquimod Solubility in Different Solvents: An Interpretative Approach

Imiquimod (IMQ) has been successfully formulated to date mainly as semi-solid lipophilic formulations for topical application. In this study, we investigated the solubility of IMQ in solvents suitable for developing innovative formulations in the form of powder obtained, for instance, by spray drying; thus, water, ethanol, methanol, acetone, acetonitrile, and dimethyl sulfoxide were tested at different temperatures. Temperature variations, stirring intensity, and the contact time between IMQ and the solvent greatly affected the evaluation of IMQ equilibrium solubility. The attainment of the solid-liquid equilibrium requires 13 days starting from solid IMQ and 2 days from a cooled-down supersaturated IMQ solution. A correlation between IMQ solubility and the solubility parameters of solvents was not found. IMQ solutions in water, ethanol, methanol, acetonitrile, and dimethyl sulfoxide were neither ideal nor regular. The Scatchard-Hildebrand equation does not apply to IMQ solutions because of association phenomena due to intermolecular hydrogen bonds and/or π-stacking, as supported by the hyperchromic effect that was very pronounced in highly polar solvents, such as water, with the increase in temperature. Finally, IMQ solubility values measured in acetone cannot be considered reliable due to the reaction with the solvent, leading to the formation of new molecules.

Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine-Propargyl Group

The structure of the pyridine-based Schiff base compound containing the propargyl group was characterized by NMR spectroscopy. Binding of compound 2 with double-stranded fish sperm DNA (Fsds-DNA) was investigated using viscosity measurement studies and UV/VIS and fluorescence spectral techniques. Binding of compound 2 with Fsds-DNA results in minor hypochromism with no change in absorption maxima and fluorescence quenching with almost no shift in emission maxima, which can be attributed to the groove-binding mode of the interaction. The binding constant was found to be 4.7×104  M-1 . The Fsds-DNA viscosity measurement, KI quenching and NaCl quenching studies and the competitive interaction between compound 2 and ethidium bromide with DNA confirm the proposed binding mode. In addition, interactions between compound 2 and the DNA double helix were analysed by molecular docking study in order to determine the binding mode and binding affinity. As a result of molecular docking, the binding affinity of the 2-DNA complex, which has the most stable conformation -8.10 kcal/mol and it is located in its minor groove. In addition, molecular docking and ADME studies for compound 2 were also performed.

Conformation-dependent UV inactivation efficiency of a conjugative, multi-drug resistant plasmid

A conjugative, multi-drug-resistant plasmid was irradiated in-vivo and in-vitro with a 265-nm UV-light emitting diode (UV-LED) to investigate the gene inactivation efficiency of a plasmid deoxyribonucleic acid (pDNA) carrying DNA transfer and replication genes. The clinical-isolate 60 kb RP4 plasmid of the IncPα group containing the traG gene, was irradiated intracellularly in E. coli DH5α and extracellularly in a water medium at pH 8.5. Real-time quantitative polymerase chain reaction (RT-qPCR) measurements of the UV-fluence response gene inactivation rate constants revealed a decreasing pattern via a pseudo-1st-order inactivation kinetics in all forms examined. Our findings showed that the intracellular-supercoiled conformation, with k = 6.1 × 10-3 cm2/mJ, has the lowest UV susceptibility (lowest inactivation rate). UV absorbance measurements and a computational approach showed that the host's RNA provides the photo-shielding, demonstrating this high UV resistance. When UV exposure was measured in-vitro, the condensed DNA exhibited a self-shielding effect over supercoiled and denatured DNA due to the hypochromic-hyperchromic effects. This study has shown that large-sized conjugative plasmids with conformation-dependent UV/UV-LED-based gene inactivation play a significant role in preventing the spread of antibiotic resistance.

PyMM: An Open-Source Python Program for QM/MM Simulations Based on the Perturbed Matrix Method

Quantum mechanical/molecular mechanics (QM/MM) methods are important tools in molecular modeling as they are able to couple an extended phase space sampling with an accurate description of the electronic properties of the system. Here, we describe a Python software package, called PyMM, which has been developed to apply a QM/MM approach, the perturbed matrix method, in a simple and efficient way. PyMM requires a classical atomic trajectory of the whole system and a set of unperturbed electronic properties of the ground and electronic excited states. The software output includes a set of the most common perturbed properties, such as the electronic excitation energies and the transitions dipole moments, as well as the eigenvectors describing the perturbed electronic states, which can be then used to estimate whatever electronic property. The software is composed of a simple and complete command-line interface, a set of internal input validation, and three main analyses focusing on (i) the perturbed eigenvector behavior, (ii) the calculation of the electronic absorption spectrum, and (iii) the estimation of the free energy differences along a reaction coordinate.

Pr3+ doped NaYF4 and LiYF4 nanocrystals combining visible-to-UVC upconversion and NIR-to-NIR-II downconversion luminescence emissions for biomedical applications

Lanthanide-doped fluoride nanocrystals (NCs) are known to exhibit unique optical properties, such as upconversion and downconversion luminescence (UCL and DCL), which can be employed for various applications. In this work, we demonstrate that by doping praseodymium(III) and ytterbium(III) ions (Pr³⁺ and Yb³⁺) into a nanosized fluoride matrix (i.e. NaYF₄ and LiYF₄), it is possible to combine their UCL and DCL properties that can be concurrently used for biomedical applications. In particular, the emissive modes combined in a single nanoparticle co-doped with Pr³⁺ and Yb³⁺ include DCL emission (excited at 980 nm and peaked at 1320 nm), which can be used for near infrared (NIR) DCL bioimaging in the NIR-II window of biological tissue transparency (∼1000-1350 nm) and UCL emission (excited at 447 nm and peaked at 275 nm) that can be employed for germicide action (via irradiation by light in the UVC range). A possibility of the latter was demonstrated by the denaturation of double-stranded DNA (dsDNA) into single-stranded ones that was caused by the UVC UCL emission from the NCs under 447 nm irradiation; it was evidenced by the hyperchromicity observed in the irradiated dsDNA solution and also by a fluorometric analysis of DNA unwinding (FADU) assay. Concurrently, the possibility of NIR-II luminescence bioimaging through biological tissues (bovine tooth and chicken flesh) was demonstrated. The proposed concept paves a way for NIR-II imaging guided antimicrobial phototherapy using lanthanide-doped fluoride nanocrystals.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Dynamic and quantitative characterization of antagonism within disinfectant mixtures by a modified area-concentration ratio method

The coexistence of various typical disinfectant pollutants has the potential to produce toxicity interaction towards organisms in the environment. A suitable model is necessary to evaluate the interaction quantitatively. Hence, the area-concentration ratio (ACR) method was modified (MACR) by combing confidence intervals to dynamically and quantitatively evaluate the toxicity interactions within disinfectant mixture pollutants. Disinfectant mixtures were designed by the direct equipartition design ray method using three guanidine disinfectants, chlorhexidine diacetate (CD), chlorhexidine (CHL), and polyhexamethylene biguanidine (POL) and one chlorine-containing disinfectant calcium hypochlorite (CAL). The toxicities of the four disinfectants and their mixtures towards Vibrio qinghaiensis sp.-Q67 (Q67) were determined by the time-dependent toxicity microplate analysis method. And the toxicity mechanism was analyzed by determining the effects of four disinfectants and their binary mixtures on the structure of cell, DNA and proteins (Pro) for Q67. The results show that the toxicities of CD and CHL to Q67vary little with time, but POL and CAL show the obvious time-dependent toxicity. The toxicities of CD, CHL and POL to Q67 are significantly stronger than that of CAL at the same exposure time. The toxicities of three binary mixture systems don't have significant difference in different exposure time. MACR can dynamically, quantitatively and accurately characterize toxicity interactions compared with ACR. According to MACR, the antagonism intensity dynamically changes with the prolongation of exposure time for binary mixture rays of three guanidine disinfectants and CAL, and linearly correlates with the components' concentration ratios. Four disinfectants all can destroy cell membrane and cause desaturation DNA of test organism, and CAL even can destroy the structure of DNA and protein. The probably reason for the antagonism within binary mixtures is the reaction between guanidine group and ClO^-, which is called chemical antaogism.

Selected In Situ Hybridization Methods: Principles and Application

We are experiencing rapid progress in all types of imaging techniques used in the detection of various numbers and types of mutation. In situ hybridization (ISH) is the primary technique for the discovery of mutation agents, which are presented in a variety of cells. The ability of DNA to complementary bind is one of the main principles in every method used in ISH. From the first use of in situ techniques, scientists paid attention to the improvement of the probe design and detection, to enhance the fluorescent signal intensity and inhibition of cross-hybrid presence. This article discusses the individual types and modifications, and is focused on explaining the principles and limitations of ISH division on different types of probes. The article describes a design of probes for individual types of in situ hybridization (ISH), as well as the gradual combination of several laboratory procedures to achieve the highest possible sensitivity and to prevent undesirable events accompanying hybridization. The article also informs about applications of the methodology, in practice and in research, to detect cell to cell communication and principles of gene silencing, process of oncogenesis, and many other unknown processes taking place in organisms at the DNA/RNA level.

Designer Anticancer Nanoprodrugs with Self-Toxification Activity Realized by Acid-triggered Biodegradation and In Situ Fragment Complexation

Prodrugs that allow in situ chemical conversion of less toxic precursors into active drugs in response to certain stimuli are promising anticancer candidates. Herein, we present a novel design of nanoprodrugs with a "degradation-mediated self-toxification" strategy, which realizes intracellular synthesis of anticancer agents using the nanoparticles' own degradation fragments as the precursors. To fulfill this concept, a metal complexing dicyclohexylphosphine (DCP) organosilane is carefully screened out from various ligands to conjugate onto Pd(OH)₂ nanodots confined hollow silica nanospheres (PD-HSN). This constructed nanoprodrug shows acid-triggered degradation in lysosomes and neutralizes protons to induce lysosomes rupturing, generating predesigned less toxic fragments (Pd²⁺ and DCP-silicates) that complex into DCP/Pd complex in situ for inducing DNA damage, leading to enhanced anticancer activity against various cancer cell lines as well as in a xenograft tumour model.

Insight into the binding mechanism of macrolide antibiotic; erythromycin to calf thymus DNA by multispectroscopic and computational approaches

In the present study, the interactions between Erythromycin drug and calf thymus deoxyribonucleic acid (ct-DNA) were explored by multi spectroscopic techniques (UV-Visible, fluorescence, circular dichroism spectroscopies), viscosity, molecular docking simulation, and atomic force microscopy (AFM). In addition, the values of binding constant were calculated by the UV-Visible and fluorescence spectroscopy. Competitive fluorescence study with methylene blue (MB), acridine orange (AO), and Hoechst 33258 were indicated that the Erythromycin drug could displace the DNA-bound Hoechst, which displays the strong competition of Erythromycin with Hoechst to interact with the groove binding site of DNA. In addition, the observed complexes in AFM analysis comprise the chains of ct-DNA and Erythromycin with an average size of 314.05 nm. The results of thermodynamic parameter calculations (ΔS° = -332.103 ± 14 J mol^-1 K^-1 and ΔH° = -115.839 ± 0.02 kJ mol^-1) approved the critical role of van der Waals forces and hydrogen bonds in the complexation of Erythromycin-DNA. Fluorescence spectroscopy results demonstrate the existence of a static enhancement mechanism in the interaction of Erythromycin-DNA. According to the obtained results, Erythromycin drug interacts with the major groove of ct-DNA. These consequences were further supported by the molecular docking study, and it could be determined that DNA-Erythromycin docked model was in a rough correlation with our experimental results.Communicated by Ramaswamy H. Sarma.

Synthesis and properties of helically-folded poly(arylenediethynylene)s

Three arylenediethnylene-based helical foldamers having pyridine, naphthaleneimide and pyrene cores show unique conformational changes and photophysical properties in various organic solvents.

Engineering Supramolecular Polymer Conformation for Efficient Carbon Nanotube Sorting

Supramolecular polymer sorting is a promising approach to separating single-walled carbon nanotubes (CNTs) by electronic type. Unlike conjugated polymers, they can be easily removed from the CNTs after sorting by breaking the supramolecular bonds, allowing for isolation of electronically pristine CNTs as well as facile recycling of the sorting polymer. However, little is understood about how supramolecular polymer properties affect CNT sorting. Herein, chain stoppers are used to engineer the conformation of a supramolecular sorting polymer, thereby elucidating the relationship between sorting efficacy and polymer conformation. Through NMR and UV-vis spectroscopy, small-angle X-ray scattering (SAXS), and thermodynamic modeling, it is shown that this supramolecular polymer exhibits ring-chain equilibrium, and that this equilibrium can be skewed toward chains by the addition of chain stoppers. Furthermore, by controlling the stopper-monomer ratio, the sorting yield can be doubled from 7% to 14% without compromising the semiconducting purity (>99%) or properties of sorted CNTs.

Homopurine RP-stereodefined phosphorothioate analogs of DNA with hampered Watson-Crick base pairings form Hoogsteen paired parallel duplexes with (2'-OMe)-RNAs

3'-O-(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of 5'-O-DMT-N6-methyl-deoxyadenosine and 5'-O-DMT-N2,N2-dimethyl-O6-diphenylcarbamoyl-deoxyguanosine (OTP-NY, NY = DMT-m6dA or DMT-m,m2dGDPC) were synthesized, resolved onto pure P-diastereomers, and used in P-stereocontrolled synthesis of dinucleoside 3',5,-phosphorothioates NXPST (NX = m6dA or m,m2dG), in which the absolute configuration of the stereogenic phosphorus atom was established enzymatically. Diastereomerically pure OTP-NY and standard OTP-N (N = DMT-dABz or DMT-dGBz,DPC) were used in the synthesis of chimeric RP-stereodefined phosphorothioate oligomers ((RP-PS)-DN(NX)A) with hampered Watson-Crick base pairings. It was found that the m6dA units slightly reduce the thermodynamic stability of antiparallel duplexes formed with RNA and (2'-OMe)-RNA matrices, whereas m,m2dG units prevent their formation. The m6dA units stabilize (by up to 4.5 °C per modified unit) the parallel duplexes formed by (RP-PS)-DN(NX)A with Hoogsteen-paired (2'-OMe)-RNA templates compared to the analogous reference duplex containing only unmodified nucleobases. In contrast, the m,m2dG units destabilize such duplexes by up to 3 °C per modified unit. Both units prevent the formation of the corresponding parallel triplexes.

Switchable conformational changes of DNA nanogel shells containing disulfide–DNA hybrids for controlled drug release and efficient anticancer action

Oligonucleotide strands containing dithiol (–SS–) groups were used as the co-crosslinkers in PNIPA–AAc based nanogels (NGs). They hybridized with PEG–oligonucleotides introduced into the gels. The specific DNA hybrid formed in the nanogel/nanocarrier was involved in highly efficient accumulation of intercalators. The presence of –SS– groups/bridges improved the storing efficiency of doxorubicin (Dox) in DNA hybrids by 53, 40 and 20% compared to regular, single stranded and regular double stranded DNA crosslinkers, respectively. The explicit arrangement of the hybrids in the carrier enabled their reduction by glutathione and an effective cancer treatment while the side toxicity could be reduced. Compared to the NGs with traditional crosslinkers and those containing typical dsDNA-based hybrids, an improved, switchable and controlled drug release occurred in the novel NGs. Since the novel NGs can release the oligonucleotide strands during their degradation, this gives an opportunity for a combined drug-gene therapy.

Switchable conformational changes of multiresponsive nanogels containing disulfide/DNA hybrid shells for pulsative drug release.

An Ultraviolet Resonance Raman Spectroscopic Study of Cisplatin and Transplatin Interactions with Genomic DNA

Ultraviolet resonance Raman (UVRR) spectroscopy is a label-free method to define biomacromolecular interactions with anticancer compounds. Using UVRR, we describe the binding interactions of two Pt(II) compounds, cisplatin (cis-diamminedichloroplatinum(II)) and its isomer, transplatin, with nucleotides and genomic DNA. Cisplatin binds to DNA and other cellular components and triggers apoptosis, whereas transplatin is clinically ineffective. Here, a 244 nm UVRR study shows that purine UVRR bands are altered in frequency and intensity when mononucleotides are treated with cisplatin. This result is consistent with previous suggestions that purine N7 provides the cisplatin-binding site. The addition of cisplatin to DNA also causes changes in the UVRR spectrum, consistent with binding of platinum to purine N7 and disruption of hydrogen-bonding interactions between base pairs. Equally important is that transplatin treatment of DNA generates similar UVRR spectral changes, when compared to cisplatin-treated samples. Kinetic analysis, performed by monitoring decreases of the 1492 cm^-1 band, reveals biphasic kinetics and is consistent with a two-step binding mechanism for both platinum compounds. For cisplatin-DNA, the rate constants (6.8 × 10^-5 and 6.5 × 10^-6 s^-1) are assigned to the formation of monofunctional adducts and to bifunctional, intrastrand cross-linking, respectively. In transplatin-DNA, there is a 3.4-fold decrease in the rate constant of the slow phase, compared with the cisplatin samples. This change is attributed to generation of interstrand, rather than intrastrand, adducts. This longer reaction time may result in increased competition in the cellular environment and account, at least in part, for the lower pharmacological efficacy of transplatin.

Light Absorption by Brown Carbon in the Southeastern United States is pH-dependent

Light-absorbing organic material, or "brown carbon" (BrC), can significantly influence the effect that aerosols have on climate. Here, we investigate how changing pH affects the absorption spectra of water-soluble BrC from ambient particulate matter smaller than 2.5 μm collected in Athens, Georgia, in the spring and fall of 2016, including samples from nearby wildfires. We find that absorption increases 10% per pH unit from pH 2 to pH 12 with a broad, featureless tail at visible wavelengths, where the largest fractional increase is also observed. The resulting change in the spectral shape causes the absorption Ångström exponent to decrease by 0.18 per unit increase in pH. Similar behavior with humic substances suggests that they and BrC share a common link between pH and absorption, which we propose could be a consequence of conformational changes in supramolecular assemblies thought to exist in humic substances. Specifically, we hypothesize that a wider variety and larger number of absorbing charge transfer complexes are formed as functional groups in these molecules, such as carboxylic acid and phenol moieties, become deprotonated. These findings suggest that (1) the pH of ambient particulate matter samples should be measured or controlled and (2) radiative forcing by BrC aerosols could be overestimated if their pH-dependent BrC absorption is not accounted for in models.

The effects of gallic/ferulic/caffeic acids on colour intensification and anthocyanin stability

The mechanism by which copigments stabilize colour, by protecting anthocyanin chromophores from nucleophilic attack, seems well accepted. This study was to determine effects of gallic/ferulic/caffeic acids on colour intensification and anthocyanin stability. Molecular dynamics simulations were applied to explore molecular interactions. Phenolic acids intensified the colour by 19%∼27%. Colour fading during heating followed first-order reactions with half-lives of 3.66, 9.64, 3.50, and 3.39h, whereas anthocyanin degradation, determined by the pH differential method (or HPLC-PDA), followed second-order reactions with half-lives of 3.29 (3.40), 3.43 (3.39), 2.29 (0.39), and 2.72 (0.32)h alone or with gallic/ferulic/caffeic acids, respectively, suggesting that anthocyanin degradation was faster than the colour fading. The strongest protection of gallic acids might be attributed to the shortest distance (4.37Å) of its aromatic ring to the anthocyanin (AC) panel. Hyperchromic effects induced by phenolic acids were pronounced and they obscured the accelerated anthocyanin degradation due to self-association interruption.

Characterization of the excited states of DNA building blocks: a coupled cluster computational study

DNA building blocks consisting of up to four nucleobases are investigated using the EOM-CCSD and CC2-LR methods in two B-DNA-like arrangements of a poly-adenine:poly-thymine (poly-A:poly-T) system. Excitation energies and oscillator strengths are presented and the characteristics of the excited states are discussed. Excited states of single-stranded poly-A systems are highly delocalized, especially the spectroscopically bright states, where delocalization over up to four fragments can be observed. In the case of poly-T systems, the states are somewhat less delocalized, extending to maximally about three fragments. A single A:T Watson-Crick pair has highly localized states, while delocalization over base pairs can be observed for some excited states of the (A)2:(T)2 system, but intrastrand delocalization is more pronounced in this case, as well. As for the characteristics of the simulated UV absorption spectra, a significant decrease of intensity can be observed in the case of single strands with increasing chain length; this is due to the stacking interactions and is in accordance with previous results. On the other hand, the breaking of H-bonds between the two strands does not alter the spectral intensity considerably, it only causes a redshift of the absorption band, thus it is unable to explain the experimentally observed DNA hyperchromism on its own, and stacking interactions need to be considered for the description of this effect as well.

Purification of Single-Stranded cDNA Based on RNA Degradation Treatment and Adsorption Chromatography

Analysis of gene expression is a common research tool to study networks controlling gene expression, the role of genes with unknown function, and environmentally induced responses of organisms. Most of the analytical tools used to analyze gene expression rely on accurate cDNA synthesis and quantification to obtain reproducible and quantifiable results. Thus far, most commercial kits for isolation and purification of cDNA target double-stranded molecules, which do not accurately represent the abundance of transcripts. In the present report, we provide a simple and fast method to purify single-stranded cDNA, exhibiting high purity and yield. This method is based on the treatment with RNase H and RNase A after cDNA synthesis, followed by separation in silica spin-columns and ethanol precipitation. In addition, our method avoids the use of DNase I to eliminate genomic DNA from RNA preparations, which improves cDNA yield. As a case report, our method proved to be useful in the purification of single-stranded cDNA from the pathogenic fungus Sporothrix schenckii.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

How Severely Is DNA Quantification Hampered by RNA Co-extraction?

The optional RNase digest that is part of many DNA extraction protocols is often omitted, either because RNase is not provided in the kit or because users do not want to risk contaminating their laboratory. Consequently, co-eluting RNA can become a "contaminant" of unknown magnitude in a DNA extraction. We extracted DNA from liver, lung, kidney, and heart tissues and established that 28-52% of the "DNA" as assessed by spectrophotometry is actually RNA (depending on tissue type). Including an RNase digest in the extraction protocol reduced 260:280 purity ratios. Co-eluting RNA drives an overestimation of DNA yield when quantification is carried out using OD 260 nm spectrophotometry, or becomes an unquantified contaminant when spectrofluorometry is used for DNA quantification. This situation is potentially incompatible with the best practice guidelines for biobanks issued by organizations such as the International Society for Biological and Environmental Repositories, which state that biospecimens should be accurately characterized in terms of their identity, purity, concentration, and integrity. Consequently, we conclude that an RNase digest must be included in DNA extractions if pure DNA is required. We also discuss the implications of unquantified RNA contamination in DNA samples in the context of laboratory accreditation schemes.

Computational modeling of photoexcitation in DNA single and double strands

The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.

Extracellularly synthesized ZnO nanoparticles interact with DNA and augment gamma radiation induced DNA damage through reactive oxygen species

ZnONPs were synthesized using ferulic acid as the reductant and the intricate twofold role as DNA binders and radio sensitizers was revealed, which can pave the way for anticancer therapy.

Photoinduced processes in nucleic acids

Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.