Circular dichroism of DNA

mRNA Lipoplexes with Cationic and Ionizable α-Amino-lipophosphonates: Membrane Fusion, Transfection, mRNA Translation and Conformation

Cationic liposomes are attractive carriers for mRNA delivery. Here, mRNA lipoplexes (LX) were prepared with the cationic lipids α-aminolipophosphonate (3b) or imidazolium lipophosphoramidate (2) associated with various α-aminolipophosphonates co-lipids comprising protonable groups (imidazole or pyridine) and DOPE. Physicochemical parameters of liposomes and their membrane fusion activity were measured. LXs comprising either 3b- or 2- allowed transfection of ~25% and 40% of dendritic cells with low cytotoxicity, respectively; the efficiency increased up to 80% when 2 was combined with the imidazole-based co-lipid 1. The transfections were high with 3b/1, 3b/DOPE, 2/1 and 2/DOPE LXs. We observed that the transfection level was not well correlated with the acid-mediated membrane fusion activity of liposomes supposed to destabilize endosomes. The mRNA release from LXs and its translation capacity after release were studied for the most efficient LXs. The results showed that the more mRNA was condensed, the poorer the translation efficiency after release was. In contrast to DNA, circular dichroism performed on mRNA complexed with 2/DOPE revealed the presence of denatured mRNA in LXs explaining this lack of translation efficiency. This is an important parameter that should be stressed for the preparation of mRNA LXs with a conserved mRNA translation activity.

Simultaneously monitoring UVC-induced DNA damage and photoenzymatic repair of cyclobutane pyrimidine dimers by electrochemical impedance spectroscopy

Cyclobutane pyrimidine dimers (CPDs) are the major DNA photoproducts of thymine-thymine dinucleotides upon ultraviolet (UV) irradiation. Failure in the repair of damaged DNA may lead to DNA replication errors, DNA mutations, and even cell death. Photoreactivation can mediate the repair of UV-induced DNA lesions by photolyases upon UVA (315-400 nm) or blue light (400-500 nm) irradiation. Herein, the UVC (254 nm)-induced DNA damage and photoenzymatic repair of the CPD products were simultaneously monitored by electrochemical impedance spectroscopy (EIS). The UVC-damaged dT₂₀ was first immobilized on the gold electrode, and the specific recognition by the anti-CPD antibody leads to significantly increased EIS signals. The electron transfer resistance (R_et) values were linearly proportional to the concentrations of damaged dT₂₀ ranging from 0.005 to 0.1 μM, and a detection limit of 3.06 nM was achieved. Using surface plasmon resonance, the equilibrium dissociation constant (K_D) between the CPDs in dT₂₀ and anti-CPD antibody was estimated to be (3.32 ± 0.31) × 10^-12 M, indicating the strong binding affinity. Evidenced by EIS, the CPDs in the damaged dT₂₀ could be repaired by the attached DNA photolyase under UVA (365 nm) photoexcitation, and the detachment of the photolyase from the DNA strand was accomplished after completion of the repair process. The repair efficiency was calculated to be 70.0% by EIS, being consistent with that of 71.4% by UV spectroscopy. The electrochemical method is simple, sensitive and straightforward, holding great potential for assaying other types of DNA lesions and their repair processes.

Application of spectral methods for studying DNA damage induced by gamma-radiation

Spectral methods can provide a variety of possibilities to determine several types of radiation-induced DNA damage, such as nucleobase destruction and local denaturation. DNA UV absorption and CD spectra measured at room temperature undergo noticeable alteration under the action of γ-radiation. We have applied the Spirin method of total nucleobases determination, and have measured the molar extinction coefficient of DNA and DNA CD spectra for solutions with different NaCl concentrations (3mM-3.2M) and containing MgCl₂, exposed to γ-radiation with the doses of 0-10³Gy. The melting temperatures of DNA in irradiated solutions at the doses of 0-50Gy were obtained with the help of spectrophotometric melting. It was found that the amount of destructed nucleobases and radiation-induced loss of DNA helicity significantly decreases with the rise of the ionic strength of the irradiated solution. Substitution of a portion of Na⁺ ions on Mg²⁺ while keeping the total ionic strength constant (μ=5mM) does not affect the considered radiation effects. The role of the structure and composition of the DNA secondary hydration layer in the radiation-induced damages is discussed.

Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory

It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles.

On the interplay between chirality and exciton coupling: a DFT calculation of the circular dichroism in π-stacked ethylene

The chirality of stacked weakly interacting π-systems was interpreted in terms of Frenkel exciton states and the formation of excitonic circular dichroism (CD) bands was monitored for ethylene stacks of varying sizes. Convergence of CD bands with respect to the system size was observed for stacks involving around 10 molecules. By means of rotation around the C-C double bond in ethylene, chirality was induced in the monomeric system and which was shown to dominate the spectral responses, even for polymer aggregates. In helical assemblies of chiral entities, there will always be a mix of excitonic and monomeric contributions to the CD signal and it is demonstrated that the complex polarization propagator approach in combination with Density Functional Theory is a suitable method to address this situation.

Metal-enhanced fluorescence-based core-shell Ag@SiO₂ nanoflares for affinity biosensing via target-induced structure switching of aptamer

One of the great challenges in metal-enhanced fluorescence (MEF) technology is the achievement of distance modulation with nanometer accuracy between the fluorophore and metal surface to obtain maximum enhancement. We propose an MEF-based core-shell Ag@SiO2 nanoflare for distance control via the thickness of silica shell with cooperation of DNA hybridization. The nanoflare contains a 50 nm spherical silver nanoparticle (Ag NP) core, a 8 nm silica shell, and cyanine (Cy5)-labeled aptamer hybridized with a complementary DNA (cDNA) immobilized onto the shell surface. The formation of the Cy5-labeled aptamer/cDNA duplex on the Ag@SiO2 NP surface results in the confinement of Cy5 to the shell surface and an increase in the fluorescence of Cy5 with a 32-fold enhancement factor in bulk solution (signal-on). In the presence of affinity-binding targets, the Cy5-labeled aptamers confined onto the Ag@SiO2 NP surface dissociate from their cDNA into the solution because of structure switching. The target-induced release of aptamer leads to a reduction in the enhanced fluorescence signal of the labeled Cy5 moiety (signal-off). Thus, the nanoflare can be used as a sensor for target recognition. Using adenosine-5'-triphosphate (ATP) aptamer, detection of ATP has a linear response from 0 to 0.5 mM and a detection limit of 8 μM. With various types of DNA probes immobilized onto the core-shell Ag@SiO2 NPs, the MEF-based nanoflare has provided an effective platform for the detection and quantification of a broad range of analytes, such as mRNA regulation and detection, cell sorting, and gene profiling.

A highly sensitive sensor for Cu2+ with unmodified gold nanoparticles and DNAzyme by using the dynamic light scattering technique

Copper ion (Cu(2+)) plays an important role in many biological reactions, and a suitable level of Cu(2+) is necessary for the regular metabolism of life. Thus developing a sensitive and simple method for determination of Cu(2+) is essential. Here, a novel and sensitive Cu(2+) sensor was developed based on detecting the average hydrodynamic diameter of AuNPs by using dynamic light scattering (DLS). Cu(2+)-specific DNAzyme was double-strand and could not adsorb on the surface of AuNPs, accordingly AuNPs aggregation would occur with the addition of NaCl. However, Cu(2+) could cleave DNAzyme and release single-stranded DNA (ssDNA) fragments, which could adsorb on the surface of AuNPs and prevent them from aggregation. Such differences in DNA adsorption ability on AuNPs before and after the addition of Cu(2+) affected the disperse state of AuNPs directly, and then affected their average hydrodynamic diameter, which could be detected with the DLS technique. Based upon the above mentioned principle, detection of Cu(2+) could be realized over the range from 100 pM to 2.0 nM, with a linear regression equation of D = 306.73 - 89.66C (C: nM, R = 0.9953) and a detection limit of 60 pM (3δ/slope). Moreover, satisfactory results were obtained when the assay was applied in the detection of Cu(2+) in water samples.

An aptamer based resonance light scattering assay of prostate specific antigen

Prostate specific antigen (PSA) is a valuable tumor marker for prostate cancer screening. In this work, a novel and sensitive resonance light scattering (RLS) spectral assay of PSA was proposed based on PSA aptamer modified gold nanoparticles (AuNPs). The sulfhydryl modified single-strand aptamer could interact with AuNPs, which made the AuNPs stable in high concentration of salt. In pH 7.0 BR buffer solution, the highly selective combination of PSA and AuNPs-labeling aptamer resulted in the aggregation of AuNPs which showed high RLS intensity. Under the optimal conditions, the magnitude of enhanced RLS intensity (ΔI(RLS)) was proportional to the concentration of PSA in the range from 0.13 to 110 ng/mL, with a detection limit (LOD, 3σ) of 0.032 ng/mL. This developed RLS assay as well as a commercially available enzyme-linked immunosorbent assay (ELISA) kit was successfully applied to the detection of PSA in 15 serum samples, and an excellent correlation of the levels of PSA measured was obtained. This is the first report of the aptamer based RLS assay for PSA and it is also a significant application of instrumental analysis technique.

Stable secondary structure near the nicking site for adeno-associated virus type 2 Rep proteins on human chromosome 19

Adeno-associated virus serotype 2 (AAV-2) can preferentially integrate its DNA into a 4-kb region of human chromosome 19, designated AAVS1. The nicking activity of AAV-2's Rep68 or Rep78 proteins is essential for preferential integration. These proteins nick at the viral origin of DNA replication and at a similar site within AAVS1. The current nicking model suggests that the strand containing the nicking site is separated from its complementary strand prior to nicking. In AAV serotypes 1 through 6, the nicking site is flanked by a sequence that is predicted to form a stem-loop with standard Watson-Crick base pairing. The region flanking the nicking site in AAVS1 (5'-GGCGGCGGT/TGGGGCTCG-3' [the slash indicates the nicking site]) lacks extensive potential for Watson-Crick base pairing. We therefore performed an empirical search for a stable secondary structure. By comparing the migration of radiolabeled oligonucleotides containing wild-type or mutated sequences from the AAVS1 nicking site to appropriate standards, on native and denaturing polyacrylamide gels, we have found evidence that this region forms a stable secondary structure. Further confirmation was provided by circular dichroism analyses. We identified six bases that appear to be important in forming this putative secondary structure. Mutation of five of these bases, within the context of a double-stranded nicking substrate, reduces the ability of the substrate to be nicked by Rep78 in vitro. Four of these five bases are outside the previously recognized GTTGG nicking site motif and include parts of the CTC motif that has been demonstrated to be important for integration targeting.

Polyamines permit the preparation of stable Physarum core particles which have a structure similar to those from higher eukaryotes

The inherent instability of Physarum nucleosome core particles prepared by micrococcal nuclease digestion in Na+/Ca2+ buffers can be overcome by the addition of 0.15 mM spermine and 0.5 mM spermidine. Neutron scattering, circular dichroism, nuclease digestion and thermal denaturation studies carried out on these stable monosomes show them to be very similar to those obtained from higher eukaryotes.

CAP binding to B and Z forms of DNA

We have examined the interaction between the cyclic AMP receptor protein (CAP) and a small DNA fragment containing its specific recognition sequence by circular dichroism spectroscopy. The binding of CAP to this fragment induces a B to "C-like" change in the CD spectrum, which is different from that observed for non-specific binding. A one-to-one (CAP dimer to DNA) binding stoichiometry was deduced from spectroscopic titration data, as was a non-specific binding site size of 17 bp/dimer. In addition, we have compared the non-specific binding affinity of CAP for the B and Z forms of synthetic DNA copolymers. A slight preference for the B form was found. These results do not support the recent specific suggestion that CAP binds to a left-handed form of DNA (1), but indicate more generally that an optically detectable conformational change takes place in DNA on binding CAP.

Lac repressor - lac operator interaction. Circular dichroism study

The interaction between lac repressor and a small operator DNA fragment have been examined by circular dichroism spectroscopy. The binding of lac repressor on the operator induces a conformation change of the DNA which is different from that observed upon non specific binding on non operator DNA. The CD titration curve indicates that the stoechiometry of interaction is complex. A two operators-one repressor complex was found. This result was confirmed by a gel filtration experiment.

A simple method for the computation of first neighbour frequencies of DNAs from CD spectra

A procedure for the computation of the first neighbour frequencies of DNA's is presented. This procedure is based on the first neighbour approximation of Gray and Tinoco. We show that the knowledge of all the ten elementary CD signals attached to the ten double stranded first neighbour configurations is not necessary. One can obtain the ten frequencies of an unknown DNA with the use of eight elementary CD signals corresponding to eight linearly independent polymer sequences. These signals can be extracted very simply from any eight or more CD spectra of double stranded DNA's of known frequencies. The ten frequencies of a DNA are obtained by least square fit of its CD spectrum with these elementary signals. One advantage of this procedure is that it does not necessitate linear programming, it can be used with CD data digitalized using a large number of wavelengths, thus permitting an accurate resolution of the CD spectra. Under favorable case, the ten frequencies of a DNA (not used as input data) can be determined with an average absolute error < 2%. We have also observed that certain satellite DNA's, those of Drosophila virilis and Callinectes sapidus have CD spectra compatible with those of DNA's of quasi random sequence; these satellite DNA's should adopt also the B-form in solution.

Poly(2-aminoadenylic acid): interaction with poly(uridylic acid)

Poly(2-aminoadenylic acid) forms both double and triple helices with poly(uridylic acid) [poly(U)]. The 2-amino group forms a third hydrogen bond, elevating the 2 leads to 1 transition temperature by 33 degrees C. The third strand, however, has about the same stability as poly(A)-2poly(U), as measured by Tm 3 leads to 2. This selective stabilization of the two-stranded helix results in a much greater resolution of the differnt thermal transitions than that observed in analogous polynucleotide systems. In contrast to other A, U systems 3 leads to 1 and 2 leads to 3 transitions are not observed under any conditions, and the triple helix always undergoes a 3 leads to 2 transition even at very high ionic strength. A 1:1 mixture of poly(2NH2A) and poly(U) exhibits no transient formation of 1:2 complex, unlike similar mixtures of poly(A) with poly(U) and poly(T). This difference is evidently due to a more rapid displacement reaction: [poly(2NH2A) + poly(2NH2A)-2poly(U) leads to 2 poly(2NH2A)-poly(U)] With poly(2NH2A) than with poly(A). We describe a method for establishing the combining ratios of polynucleotide complexes which used a computer to calculate the angles of intersection of mixing curves as explicit and continuous functions of the wavelength. The wavelength dispersions of the angles of intersection determine optimum wavelengths for establishing stoichiometry and can also provide reliable negative evidence that presumably plausible complexes are not formed. Analogous computer procedures have been developed to determine wavelengths which are selective for the formation of both 1:1 and 1:2 complexes. Infrared spectra of the 1:1 and 1:2 complexes resemble those of other A, U homoribopolynucleotide helices in having two and three strong bands, respectively, in the region of carbonyl stretching vibrations. CD spectra of the two complexes are unusual in having negative first extrema of moderate intensity. We attribute these extrema to intrastrand interactions of strong, well-resolved transitions at 278 nm (B2u) of the 2-aminoadenine residues. The CD spectra are correlated with those of other polynucleotide helices.

The sequence dependence of circular dichroism spectra of DNA duplexes

The three satellite DNAs of Drosophila virilis, that approximate to poly d(CAAACTA)-poly d(TAGTTTG), poly d(TAAACTA)-poly d(TAGTTTA), poly d(CAAATTA)-poly d(TAATTTG), the satellite DNA of Drosophila melanogaster that approximates to poly d(AATAT)-poly d(ATATT), the synthetic DNA duplexes, poly dG-poly dC, poly d(AT)-poly d(AT), poly d(AAT)-poly d(ATT), poly d(AAC)-poly d(GTT), poly d(TAC)-poly d(GTA) and the block copolymer d(C15A15)-d(T15G15) all have circular dichroism spectra consistent with the propositions that they have the same molecular geometry in solution and that it is the kind and frequency of nucleotide triplet sequences that determines their spectral characteristics. Poly dA-poly dT is apparently an exception.