Conformational transitions and aggregation in poly(dA)-poly(dT) system induced by Na+ and Mg2+ ions

Pathway-controlled formation of mesostructured all-DNA colloids and superstructures

DNA has traditionally been used for the programmable design of nanostructures by exploiting its sequence-defined supramolecular recognition. However, control on larger length scales or even hierarchical materials that translate to the macroscale remain difficult to construct. Here, we show that the polymer character of single-stranded DNA (ssDNA) can be activated via a nucleobase-specific lower critical solution temperature, which provides a unique access to mesoscale structuring mechanisms on larger length scales. We integrate both effects into ssDNA multiblock copolymers that code sequences for phase separation, hybridization and functionalization. Kinetic pathway guidance using temperature ramps balances the counteracting mesoscale phase separation during heating with nanoscale duplex recognition during cooling to yield a diversity of complex all-DNA colloids with control over the internal dynamics and of their superstructures. Our approach provides a facile and versatile platform to add mesostructural layers into hierarchical all-DNA materials. The high density of addressable ssDNA blocks opens routes for applications such as gene delivery, artificial evolution or spatially encoded (bio)materials.

Spermine Condenses DNA, but Not RNA Duplexes

Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA. A comparison of wide-angle x-ray scattering profiles with simulation results suggests that spermine is sequestered deep within the major groove of mixed-sequence RNA. This prevents condensation by limiting opportunities to bridge to other molecules and stabilizes the RNA by locking it into a particular conformation. In contrast, for DNA, simulations suggest that spermine binds externally to the duplex, offering opportunities for intermolecular interaction. The goal of this study is to explain how RNA can remain soluble and available for interaction with other molecules in the cell despite the presence of spermine at concentrations high enough to precipitate DNA.

Effect of Ni2+ and Cd2+ ions on thermally induced conformational transitions in poly(dA)-poly(dT) system

Effects of Ni(2+) and Cd(2+) ions on thermally induced conformational transitions in the poly(dA)·poly(dT) polynucleotide duplex and poly(dA)·2poly(dT) triplex under near physiological ionic conditions were studied by measurement of UV absorption melting curves and static light scattering intensity. The diagrams of conformational transitions in poly(dA)-poly(dT)-Me(2+) systems were plotted. An aggregation in these polynucleotide systems arises at certain values of the metal ions concentration and the temperature after the polymer dissociation into single strands. The phenomenon is conditioned by the aggregation of poly(dA) via the interstrand cross-linking by the dication bridges. Unlike Ni(2+), Cd(2+) induces formation of very stable aggregates which did not disintegrate even upon cooling up to room temperature.

Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model

Curves of transitions in double (2-->1 transition) and triple (3-->2 transition) complexes of oligonucleotides dA(N1)with dT(N2) in solutions with Na(+) and Mg(2+) are calculated for the case of oligomer lengths from 10 to 500 nucleotides in the wide range of ion concentrations. The calculated curves of transitions and their differential analogs reflect rather exactly the position and form of experimental curves and describe dependences of transition temperatures on the length of molecules, their concentration, and ionic conditions. Values of the nucleation parameter beta for the systems studied are determined by comparison of the calculated and experimental data obtained in a number of works. The average beta value equal to 10(-3) l/mole is in an agreement with values reported for similar systems earlier. It is shown that disordering of duplex and triplex ends ("end fraying") has an essential influence on the form of melting curves, their asymmetry and the increase of the transition interval.

Phase equilibrium in poly(rA).poly(rU) complexes with Cd2+ and Mg2+ ions, studied by ultraviolet, infrared, and vibrational circular dichroism spectroscopy

Ultraviolet (UV) and infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy were used to study conformational transitions in the double-stranded poly(rA). poly(rU) and its components-single-stranded poly(rA) and poly(rU) in buffer solution (pH 6.5) with 0.1M Na+ and different Mg2+ and Cd2+ (10(-6) to 10(-2) M) concentrations. Transitions were induced by elevated temperature that changed from 10 up to 96 degrees C. IR absorption and VCD spectra in the base-stretching region were obtained for duplex, triplex, and single-stranded forms of poly(rA) . poly(rU) at [Mg2+],[Cd2+]/[P] = 0.3. For single-stranded polynucleotides, the kind of conformational transition (ordering --> disordering --> compaction, aggregation) is conditioned by the dominating type of Me2+-polymer complex that in turn depends on the ion concentration range. The phase diagram obtained for poly(rA) . poly(rU) has a triple point ([Cd2+] approximately 10(-4)M) at which the helix-coil (2 --> 1) transition is replaced with a disproportion transition 2AU --> A2U + poly(rA) (2 --> 3) and the subsequent destruction of the triple helix (3 --> 1). The 2 --> 1 transitions occur in the narrow temperature interval of 2 degrees -5 degrees . Unlike 2 --> 1 and 3 --> 1 melting, the disproportion 2 --> 3 transition is a slightly cooperative one and observed over a wide temperature range. At [Me2+] approximately 10(-3) M, the temperature interval of A2U stability is not less than 20 degrees C. In the case of Cd2+, it increases with the rise of ion concentration due to the decrease of T(m) (2-->3). The T(m) (3-->1) value is practically unchanged up to [Cd2+] approximately 10(-3)M. Differences between diagrams for Mg(2+) and Cd2+ result from the various kinds of ion binding to poly(rA).poly-(rU) and poly(rA).