Effect of tetramethylammonium ions on conformational changes of DNA in the premelting temperature range

Fast and precise detection of DNA methylation with tetramethylammonium-filled nanopore

The tremendous demand for detecting methylated DNA has stimulated intensive studies on developing fast single-molecule techniques with excellent sensitivity, reliability, and selectivity. However, most of these methods cannot directly detect DNA methylation at single-molecule level, which need either special recognizing elements or chemical modification of DNA. Here, we report a tetramethylammonium-based nanopore (termed TMA-NP) sensor that can quickly and accurately detect locus-specific DNA methylation, without bisulfite conversion, chemical modification or enzyme amplification. In the TMA-NP sensor, TMA-Cl is utilized as a nanopore-filling electrolyte to record the ion current change in a single nanopore triggered by methylated DNA translocation through the pore. Because of its methyl-philic nature, TMA can insert into the methylcytosine-guanine (mC-G) bond and then effectively unfasten and reduce the mC-G strength by 2.24 times. Simultaneously, TMA can increase the stability of A-T to the same level as C-G. The abilities of TMA (removing the base pair composition dependence of DNA strands, yet highly sensing for methylated base sites) endow the TMA-NP sensor with high selectivity and high precision. Using nanopore to detect dsDNA stability, the methylated and unmethylated bases are easily distinguished. This simple single-molecule technique should be applicable to the rapid analysis in epigenetic research.

The B-DNA to Z-DNA transition in alkali and tetraalkylammonium salts correlated with cation effects on solvent structure

The B-to-Z transition in DNA with alternating purine and pyrimidine sequences is driven by high concentrations of monovalent cations. In addition to screening of phosphate repulsion, an important factor may be the influence of ions on DNA hydration. The relative efficiencies of tetraalkylammonium and alkali metal salts in promoting the formation of Z-DNA, monitored by CD, in poly[d(G-C)] and poly[d(G-m5C)] was correlated with the degree to which the cations tie up water molecules in ordered arrangements and therefore decrease the availability of the solvent to hydrate DNA.

Circular dichroism study of stacking properties of oligodeoxyadenylates and polydeoxyadenylate. A three-state conformational model

The temperature dependence of the circular dichroism (CD) spectra of a series of deoxyadenylates (dA)n, n = 2, 3, 6, 9, 12, infinity, in aqueous solution was studied. The data were interpreted on the basis of a new conformational model for the stacked state suggested by our previous proton NMR studies on (dA)2 and (dA)3 [C. S. M. Olsthoorn, L. J. Bostelaar, J. H. van Boom & C. Altona (1980) Eur. J. biochem. 112, 95-110]. In this model the stacked regions of the single-stranded oligomers consist of residues taking up a geometry resembling that of the B-DNA genus of structures (all sugars S or C2'-endo) except those residues at the 3' end that do not 'feel' a following stacking interaction. The deoxyribose rings in the latter residues retain (or regain when melting out removes a stacking interaction somewhere along the chain) the conformational freedom (S in equilibrium N, N = C3'-endo) that these rings possess in the monomers 2'-deoxyadenosine 5'-methylphosphate or in 2'-deoxyadenosine 3',5'-bis(methylphosphate), as the case may be. It is shown that this model allows (a) construction of the CD spectra of (dA)n, n = 3, 6, 9, 12, from those of the dimer and the polymer; (b) the separation of the weak CD displayed by the regular S-S stacking mode and the far stronger CD exhibited by the 3'-end S-N stacking (the latter CD resembles that of the A-DNA genus of structures); (c) delineation of the thermodynamics of stacking. The melting temperature remains constant and independent of chain length (about 50 degrees C) whereas delta H degrees and delta S degrees show a slight increase in absolute values on increasing n from 2 to infinity owing to small cooperativity effects. Near 0 degrees C the dimer occurs for about 90% in the stacked form, the oligomers attain even higher conformational purities. It is suggested that premelting phenomena observed in the CD spectra of double-helical DNAs may also involve local transitions from the normal B-like ----S-S-s---- stacking mode to an A-like ----S-S-N---- stacking geometry.

Effect of tetramethylammonium ion on the helix-to-coil transition of poly(deoxyadenylylthymidine): a nuclear magnetic resonance and calorimetric investigation

Differential scanning calorimetry, temperature-dependent NMR, and UV spectroscopy are used to investigate the helix-to-coil transition of poly(deoxyadenylylthymidine) [poly(dA-dT)] in 1 M NaCl and 1 M Me4NCl (tetramethylammonium chloride). All three methods reveal that the polymer has a melting temperature, tm, that is approximately 6 degree C higher in 1 M Me4NCl than in 1 M NaCl. The NMR data show that this increased stability does not result from fundamental changes in base stacking or base pairing in going from 1 M NaCl to 1 M Me4NCl. Consistent with this observation, the calorimetric measurements yield essentially equal enthalpies for the helix-to-coil transition under the two salt conditions (6.8 kcal per base pair in 1 M NaCl and 7.0 kcal per base pair in M Me4NCl). Analysis of the shapes of the calorimetric curves shows that the transition is more cooperative in Me4NCl than in NaCl. Comparison of the calorimetric and van't Hoff enthalpies allows specification of the size of the cooperative unit: 27 base pairs in 1 M NaCl and 32 base pairs in 1 M Me4NCl. The NMR data reveal that the major Me4NCl-induced structural alterations (relative to NaCl) are a change in one glycosidic torison angle and a partial resolution of the two phosphates. The calorimetric experiments indicate that in the absence of fortuitous compensation these conformational changes are not accompanied by a significant enthalpy effect. On the basis of these data, we suggest that in 1 M NaCl poly(dA-dT) assumes predominantly a B-DNA-like conformation where the symmetry repeat occurs every base pair. By contrast, in 1 M Me4NCl the predominant conformation exhibits a dinucleotide repeat consistent with a right-handed alternating B-DNA structure.

The effects of tetraalkylammonium salts on helix-coil transition parameters in natural and synthetic ribo- and deoxyribo-polynucleotides

Thermal transition profiles were recorded for a variety of natural and synthetic DNA and double-stranded RNA preparations in the presence of tetramethylammonium (TMA+) and tetraethylammonium (TEA+) cations. Double-stranded RNAs of natural origin, with GC contents of 50% exhibited the same profiles and Tm values as native DNA containing normal bases. Hence the tetraalkylammonium cations liquidate not only the effects of base composition, and the difference in stability between A-T and A-U base pairs (further confirmed by measurements with uracil-containing DNA from phage PBS-2), but also that of the 2'OH. In the presence of TMA+ cations, there is very marked enhancement of the stability of U-U base pairs in poly(rU) and poly(Um). In 2.4 M TEA, the 1:1 complex of poly(G) with poly (C) formed readily and melted reversibly with a Tm as low as 87 degrees C. At concentrations of TMA and TEA for which dTm/dXGC = 0, the Tm values for various phage DNA preparations containing atypical bases (phages T2, T4, phi e, phi W-14, PBS-2) differ appreciably from those with 'normal bases'. Analysis of these findings indicates that the selective interaction of TMA and TEA cations with A-T base pairs occurs in the minor groove of the DNA helix. The overall results show that the action of these quaternary ammonium cations is not due exclusively to preferential binding to A-T base pairs, but must involve other factors, including modifications of solvent structure. They also underline the utility of TMA and TEA solvent systems for placing in evidence transition profiles not accessible in other solvent systems.

Thermal transition of core particle is not a two-state process

Thermal transition of core particle which occurs before melting of DNA and can be followed by circular dichroism is not a two-state process; it is the result of two processes which cannot be dissociated in static experiments: unfolding of core particles is immediately followed by their aggregation. It is thus impossible to get thermodynamic parameters of core particle unfolding from its thermal transition monitored by circular dichroism. Thermal denaturation kinetics of core particles gives some information about their stability. Finally core particle structure is more stable in chromatin than in its isolated state.