Parallel self-associated structures formed by T,C-rich sequences at acidic pH

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs

The dynamics of excited electronic states in self-assembled structures formed between silver(I) ions and cytosine-containing DNA strands or monomeric cytosine derivatives were investigated by time-resolved infrared (TRIR) spectroscopy and quantum mechanical calculations. The steady-state and time-resolved spectra depend sensitively on the underlying structures, which change with pH and the nucleobase and silver ion concentrations. At pH ∼ 4 and low dC20 strand concentration, an intramolecularly folded i-motif is observed, in which protons, and not silver ions, mediate C-C base pairing. However, at the higher strand concentrations used in the TRIR measurements, dC20 strands associate pairwise to yield duplex structures containing C-Ag+-C base pairs with a high degree of propeller twisting. UV excitation of the silver ion-mediated duplex produces a long-lived excited state, which we assign to a triplet excimer state localized on a pair of stacked cytosines. The computational results indicate that the propeller-twisted motifs induced by metal-ion binding are responsible for the enhanced intersystem crossing that populates the triplet state and not a generic heavy atom effect. Although triplet excimer states have been discussed frequently as intermediates in the formation of cyclobutane pyrimidine dimers, we find neither computational nor experimental evidence for cytosine-cytosine photoproduct formation in the systems studied. These findings provide a rare demonstration of a long-lived triplet excited state that is formed in a significant yield in a DNA duplex, demonstrating that supramolecular structural changes induced by metal ion binding profoundly affect DNA photophysics.

Toward Complete Resolution of DNA/Carbon Nanotube Hybrids by Aqueous Two-Phase Systems

Sequence-dependent interactions between DNA and single-wall carbon nanotubes (SWCNTs) are shown to provide resolution for the atomic-structure-based sorting of DNA-wrapped SWCNTs. Previous studies have demonstrated that aqueous two-phase (ATP) systems are very effective for sorting DNA-wrapped SWCNTs (DNA-SWCNTs). However, most separations have been carried out with a polyethylene glycol (PEG)/polyacrylamide (PAM) ATP system, which shows severe interfacial trapping for many DNA-SWCNT dispersions, resulting in significant material loss and limiting multistage extraction. Here, we report a study of several new ATP systems for sorting DNA-SWCNTs. We have developed a convenient method to explore these systems without knowledge of the corresponding phase diagram. We further show that the molecular weight of the polymer strongly affects the partition behavior and separation results for DNA-SWCNTs in PEG/dextran (DX) ATP systems. This leads to the identification of the PEG1.5kDa/DX250kDa ATP system as an effective vehicle for the chirality separation of DNA-SWCNTs. Additionally, this ATP system exhibits greatly reduced interfacial trapping, enabling for the first time continuous multistep sorting of four species of SWCNTs from a single dispersion. Enhanced stability of DNA-SWCNTs in the PEG1.5kDa/DX250kDa ATP system also allows us to investigate pH dependent sorting of SWCNTs wrapped by C-rich sequences. Our observations suggest that hydrogen bonding may form between the DNA bases at lower pH, enabling a more ordered wrapping structure on the SWCNTs and improvement in sorting (11,0). Together, these findings reveal that the new ATP system is suitable for searching DNA sequences leading toward more complete resolution of DNA-SWCNTs. A new concept of "resolving sequences", evolved from the old notion of "recognition sequences", is proposed to describe a broader range of behaviors of DNA/SWCNT interactions and sorting.

G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool

We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.

Inhibition of HBsAg secretion by nucleic acid polymers in HepG2.2.15 cells

More than 290 million people have chronic HBV infection and are at risk of developing cirrhosis and hepatocellular carcinoma. HBV subviral particles are produced in large excess over virions in infected patients and are the primary source of HBsAg, which is postulated to be important in allowing HBV to chronically persist by interfering with immune function. Nucleic acid polymers (NAPs) have been shown to result in clearance of HBsAg from the blood in pre-clinical and clinical studies. In this study, we show for the first time the recapitulation of NAP- induced inhibition of secretion of HBsAg in vitro using the human HepG2.2.15 cell line. With the restoration of endosomal release of NAPs in vitro using the UNC7938 compound, NAPs were observed to selectively impair the secretion of HBsAg without any intracellular HBsAg accumulation. Additionally, the structure-activity relationship of NAPs for this antiviral activity is similar to that previously reported in other infectious diseases and identifies an exposed hydrophobic protein domain as the target interface for this antiviral effect. The presented in vitro model, the first one to be based on a human derived cell line that constitutively expresses HBV, is a very promising tool for the identification of the host proteins(s) targeted by NAPs.

Study of light-induced formation of photodimers in the i-motif nucleic acid structure by rapid-scan FTIR difference spectroscopy and hybrid hard- and soft-modelling

The i-motif is a DNA structure formed by cytosine-rich sequences, very relevant from a biochemical point of view and potentially useful in nanotechnology as pH-sensitive nanodevices or nanomotors. To provide a different view on the structural changes and dynamics of direct excitation processes involving i-motif structures, the use of rapid-scan FTIR spectroscopy is proposed. Hybrid hard- and soft-modelling based on the Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) algorithm has been used for the resolution of rapid-scan FTIR spectra and the interpretation of the photochemically induced time-dependent conformational changes of i-motif structures. The hybrid hard- and soft-modelling version of MCR-ALS (HS-MCR), which allows the introduction of kinetic models to describe process behavior, provides also rate constants associated with the transitions modeled. The results show that UV irradiation does not produce degradation of the studied sequences but induces the formation of photodimers. The presence of these affect much more the stability of i-motif structures formed by short sequences than that of those formed by longer sequences containing additional structural stabilizing elements, such as hairpins.

Nucleic acid polymers: Broad spectrum antiviral activity, antiviral mechanisms and optimization for the treatment of hepatitis B and hepatitis D infection

Antiviral polymers are a well-studied class of broad spectrum viral attachment/entry inhibitors whose activity increases with polymer length and with increased amphipathic (hydrophobic) character. The newest members of this class of compounds are nucleic acid polymers whose activity is derived from the sequence independent properties of phosphorothioated oligonucleotides as amphipathic polymers. Although the antiviral mechanisms and broad spectrum antiviral activity of nucleic acid polymers mirror the functionality of other members of this class, they exert in addition a unique post entry activity in hepatitis B infection which inhibits the release of HBsAg from infected hepatocytes. This review provides a general overview of the antiviral polymer class with a focus on nucleic acid polymers and their development as therapeutic agents for the treatment of hepatitis B/hepatitis D. This article forms part of a symposium in Antiviral Research on ''An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B.''.

Stabilization of i-motif structures by 2'-β-fluorination of DNA

i-Motifs are four-stranded DNA structures consisting of two parallel DNA duplexes held together by hemi-protonated and intercalated cytosine base pairs (C:CH⁺). They have attracted considerable research interest for their potential role in gene regulation and their use as pH responsive switches and building blocks in macromolecular assemblies. At neutral and basic pH values, the cytosine bases deprotonate and the structure unfolds into single strands. To avoid this limitation and expand the range of environmental conditions supporting i-motif folding, we replaced the sugar in DNA by 2-deoxy-2-fluoroarabinose. We demonstrate that such a modification significantly stabilizes i-motif formation over a wide pH range, including pH 7. Nuclear magnetic resonance experiments reveal that 2-deoxy-2-fluoroarabinose adopts a C2′-endo conformation, instead of the C3′-endo conformation usually found in unmodified i-motifs. Nevertheless, this substitution does not alter the overall i-motif structure. This conformational change, together with the changes in charge distribution in the sugar caused by the electronegative fluorine atoms, leads to a number of favorable sequential and inter-strand electrostatic interactions. The availability of folded i-motifs at neutral pH will aid investigations into the biological function of i-motifs in vitro, and will expand i-motif applications in nanotechnology.

Fundamental aspects of the nucleic acid i-motif structures

The latest research on fundamental aspects of i-motif structures is reviewed with special attention to their hypothetical rolein vivo.

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.

Calorimetric unfolding of the bimolecular and i-motif complexes of the human telomere complementary strand, d(C3TA2)4

A combination of spectroscopic and calorimetric techniques is used to determine the unfolding thermodynamics of the complexes formed by the complementary sequence of the human telomere, d(C(3)TA(2))(4), in the pH range of 4.2 to 6. Calorimetric melting curves show biphasic transitions; both transitions are shifted to higher temperatures as the pH is decreased, indicative of cytosine protonation, which favors the formation of C*C(+) base pairs. Furthermore, the transition temperature, T(M), of the lower transition depends on strand concentration, while the T(M) of the higher transition is independent of strand concentration, indicating the following sequential melting: bimolecular complex(s)-->intramolecular complex-->random coil. The thermodynamic profiles for the formation of each complex, bimolecular and i-motif reveals small favorable free energy terms resulting from favorable enthalpy-unfavorable entropy compensations, uptake of protons, marginal uptake of counterions (i-motif) and marginal release of water molecules (i-motif). Furthermore, an enthalpy of 3.2 kcal/mol (bimolecular complex) and 5.0 kcal/mol (i-motif) is estimated for a single C*C(+)/C*C(+) base-pair stack.

Vibrational circular dichroism signature of hemiprotonated intercalated four-stranded i-DNA

The four-stranded intercalated DNA structure exemplified by the oligonucleotide 5'-d(CCCCCCCCCCCC) (d(C)12) was studied at acidic pH by infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopy and compared with spectra of the same oligonucleotide at neutral pH to establish distinct VCD markers for the intercalation motif. The most striking feature is a new absorption at 1694 cm(-1) and its corresponding VCD couplet with reversed sign. These are unique for the intercalated structure and have not been observed for other parallel stranded duplexes. Significant characteristic features resulting from the spatial arrangement of the sugar-phosphate backbone are also clearly present for d(C)12 at acidic pH. An extensive network of CH...O bonds twists the backbone such that multiple through-space vibrational coupling occurs among neighbouring sugar-phosphate residues resulting in unusual VCD signals.

A library of IR bands of nucleic acids in solution

This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800-800 cm(-1) relevant for DNA/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base-sugar, sugar-phosphate and sugar moiety. The approach allows comparisons of information obtained from one spectral region with another. The IR band library should facilitate detailed and unambiguous assignment of structural changes, ligand binding, etc. in nucleic acids from IR spectra. is aimed at highlighting specific features that are useful for following major changes in nucleic acid structures. also concerns some recent results, where IR spectroscopy has been used to obtain semi-quantitative information on coexisting modes of sugar pucker in oligonucleotides.