Sharp melting in DNA-linked nanostructure systems: thermodynamic models of DNA-linked polymers

Sharp melting that has been found for DNA-linked nanostructure systems such as DNA-linked gold nanoparticles enhances the resolution of DNA sequence detection enough to distinguish between a perfect match and single base pair mismatches. One intriguing explanation of the sharp melting involves the cooperative dehybridization of DNA strands between the nanostructures. However, in the DNA-linked gold nanoparticle system, strong optical absorption by the gold nanoparticles hinders the direct observation of cooperativity. Here, with a combination of theory and experiment, we investigate a DNA-linked polymer system in which we can show that the optical profile of the system at 260 nm is directly related to the individual DNA dehybridization profile, providing a clear distinction from other possible mechanisms. We find that cooperativity plays a crucial role in determining both the value of the melting temperature and the shape of the melting profile well away from the melting temperature. Our analysis suggests that the dehybridization properties of DNA strands in confined or dense structures differ from DNA in solution.     

Modeling of particle‐dispersed melting mechanism and its application in corotating twin‐screw extrusion

Particle‐dispersed melting is a complex but important melting mechanism in the corotating twin‐screw extruder. In this study, the complex multi‐particle‐dispersed system was simplified into a single‐particle melting model. The finite‐difference method was introduced to solve this problem. The simulation results show that the melting of a particle may involve two steps: the heating stage and melting stage. The heating time and melting time depend on solid concentration, initial melt and solid temperature, and shear rate. Calculations indicate that high solid concentration and solid temperature, low melt temperature and shear rate will result in a more uniform temperature distribution after polymer melting. The model offers valuable information for designing the melting zone in a corotating twin‐screw extruder, especially at high screw speed. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2461–2468, 2001     

Thermodynamic cloud point assays

Analysis of cloud points and clouding curves by varying heating rates using a commercially available automated melting point apparatus is a method to obtain a corrected cloud point for polymers that have a lower critical solution temperature (LCST). Such assays also provide information about the effects of varying heating rates on LCSTs and similar stimuli‐responsive phase separation behavior. This melting point apparatus makes it experimentally simple to conduct such assays that probe the effect of varying heating rates, the effect of polymer structure, and the effect of solution components on the breadth and progress of the phase transition process over a wide temperature range. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 186–193, 2008     

Thermal analysis of the multiple melting behavior of poly(butylene succinate‐co‐adipate)

The melting behavior of poly(butylene succinate‐co‐adipate) (PBSA) isothermally crystallized from the melt was investigated by differential scanning calorimetry. Triple, double, or single melting endotherms were observed in subsequent heating scan for the samples isothermally crystallized at different temperatures. These endothermic peaks were labeled as I, II, and III for low‐, middle‐, and high‐temperature melting endotherms, respectively. The independence of endotherm III to the crystallization temperature, the existence of an exothermic crystallization peak just below the endotherm III, and the heating rate dependence of endotherm III indicated that endotherm III was due to the remelting of recrystallized lamellar during a heating scan. The influence of crystallization time on the melting behavior of PBSA showed that endotherms II and III developed prior to endotherm I; endotherm III developed rather simultaneously with endotherm II. Further investigation showed that the peak temperature of endotherm I increased linearly with the logarithm of the crystallization time. It suggested that endotherm II was attributed to the melting of the primary lamellae, while endotherm I was due to the melting of secondary lamellae. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3077–3082, 2005     

Sharp melting of polymer-DNA hybrids: an associative phase separation approach

An associative equilibrium theory describing the sharp melting behavior of polymer-DNA hybrids is developed. The theory considers linear polymers with attached DNAs on each polymer that serve as "stickers" and with a two-state model governing the DNA melting equilibrium. For three or more oligonucleotides on each polymer, solutions of polymer-DNA hybrids are found to undergo phase separation at sufficiently low temperatures. The dense phase dissolves as temperature increases, which leads to a sharp increase in the fraction of non-hybridized DNA near the phase transition temperature, in agreement with experimental absorbance profiles at 260 nm. The melting temperature is predicted to have the same dependence on salt concentration as a solution of unattached DNAs and be weakly sensitive to the concentration of DNA in solution. The melting temperature is predicted to be higher than that of unattached DNA in solution, with the magnitude of the increase sensitive to the DNA hybridization cooperativity. The theoretical predictions are generally in good quantitative agreement with new experimental data (also presented here), which show the effect of the polymer-DNA hybrid length and salt concentration on the melting profiles.     

Single-crystalline gold microplates: synthesis, characterization, and thermal stability

Single-crystalline gold microplates of several 10 microm in lateral size, characterized by hexagonal, truncated triangular, and triangular shapes with (111) planes as two basal surfaces, have been synthesized in large quantities through a solution phase process. Significantly, such anisotropic Au nanostructures exhibit remarkable optical properties, in which the dipole plasmon resonance shifting in the NIR region and the quadrupole plasmon resonance at approximately 820 nm were observed. Fragmentation of Au microplates is found when the temperature is higher than 450 degrees C, indicating they are not thermodynamically stable structure at high temperature. Investigations on the Au microplates upon heating suggest that the melting and collapsing start mainly at the edges that should be Au (110) facets. This work is valuable for Au nanostructures applied at elevated temperatures.     

Toward room-temperature optical manipulation of small molecules

Room-temperature optical manipulation of small molecules is a challenging issue in the field of material science. To increase optical force for a single molecule trapping, it has been recognized that resonant excitation of molecules should be controlled under the light illumination. Strongly interacting molecules with solid surfaces at electrified interfaces show the exotic behavior of electronic excitation by localized surface plasmon. In this review, we emphases that surface-enhanced Raman scattering can be used to evaluate the resonant excitation of target molecules at interfaces. Under such excitation, the diffusion of small molecules can be controlled by the optical force generated by the intensity gradient of a highly localized electric field.     

Label-free characterisation of oligonucleotide hybridisation using reflectometric interference spectroscopy

The potential of a label-free detection method, reflectometric interference spectroscopy (RIfS), for temperature-dependent DNA hybridisation experiments (for example in single nucleotide polymorphism (SNP) analysis) is investigated. Hybridisations of DNA, peptide nucleic acid (PNA), and locked nucleic acid (LNA) to a single stranded DNA were measured for several temperatures, and the melting curves and temperatures were calculated from the changes in optical thickness obtained. These measurements were performed by hybridising surface-immobilised single stranded oligomers with their complementary ssDNA or with ssDNA containing SNPs at different temperatures. DNA was compared to its analogue oligomers PNA and LNA due to their stability against nuclease. A comparison of melting temperatures demonstrated the higher binding affinities of the DNA analogues. Moreover, a continuous melting curve was obtained by first hybridising the functionalised surface with its complementary DNA at room temperature and then heating up in-flow. Measurement of the continuous melting curve was only possible due to the insensitivity of the RIfS method towards temperature changes. This is an advantage over other label-free detection methods, which are based on determining the refractive index.Dedicated to the memory of Wilhelm Fresenius.     

Miscibility,melting, and crystallization of poly(butylene‐2,6‐naphthalate)/poly(ether imide) blends

We prepared blends of poly(butylene‐2,6‐naphthalate) (PBN) and poly(ether imide) (PEI) by solution‐casting from dichloroacetic acid solutions. The miscibility, crystallization, and melting behavior of the blends were investigated with differential scanning calorimetry (DSC) and dynamic mechanical analysis. PBN was miscible with PEI over the entire range of compositions, as shown by the existence of single composition‐dependent glass‐transition temperatures. In addition, a negative polymer–polymer interaction parameter was calculated, with the Nishi–Wang equation, based on the melting depression of PBN. In nonisothermal crystallization investigations, the depression of the crystallization temperature of PBN depended on the composition of the blend and the cooling rate; the presence of PEI reduced the number of PBN segments migrating to the crystallite/melt interface. Melting, recrystallization, and remelting processes occurring during the DSC heating scan caused the occurrence of multiple melting endotherms for PBN. We explored the effects of various experimental conditions on the melting behavior of PBN/PEI blends. The extent of recrystallization of the PBN component during DSC heating scans decreased as the PEI content, the heating rate, the crystallization temperature, and the crystallization time increased. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1694–1704, 2004     

Synthesis of a series of novel chiral smectic C (Sc*) phase shish‐kebab type liquid crystalline polymers

A series of chiral smectic C phase shish‐kebab type liquid crystal polymers was synthesized by low‐temperature solution condensation polymerization from 2,5‐bis[4‐((S)‐alkoxyl)benzoyloxy]hydroquinone and aliphatic diacylchloride. The monomers and their precursors were identified by using elemental analysis, infrared spectrum, nuclear magnetic resonance and mass spectrometry. The polymers were characterized by gel permeation chromatography, differential scanning calorimetry, thermogravimetric analysis, temperature‐variable X‐ray diffraction, polarimeter and polarizing microscope (POM) with a heating stage. All the polymers entered into liquid crystal phase when heated to above their melting temperature. The Schlieren texture and sanded texture were observed on POM. All the chiral compounds and polymers showed high optical activity. Temperature‐variable, X‐ray diffraction study together with the POM and polarimetric analysis revealed that the polymers synthesized are chiral smectic C phase. Thus, the present report provides examples of shish‐kebab type polymers that form a chiral smectic C phase. The change of the melting temperature and isotropization temperature with the variation in molecular structure was also discussed. Copyright © 2000 John Wiley & Sons, Ltd.     

Yoctoliter Thermometry for Single‐Molecule Investigations: A Generic Bead‐on‐a‐Tip Temperature‐Control Module

A new temperature‐jump (T‐jump) strategy avoids photo‐damage of individual molecules by focusing a low‐intensity laser on a black microparticle at the tip of a capillary. The black particle produces an efficient photothermal effect that enables a wide selection of lasers with powers in the milliwatt range to achieve a T‐jump of 65 °C within milliseconds. To measure the temperature in situ in single‐molecule experiments, the temperature‐dependent mechanical unfolding of a single DNA hairpin molecule was monitored by optical tweezers within a yoctoliter volume. Using this bead‐on‐a‐tip module and the robust single‐molecule thermometer, full thermodynamic landscapes for the unfolding of this DNA hairpin were retrieved. These approaches are likely to provide powerful tools for the microanalytical investigation of dynamic processes with a combination of T‐jump and single‐molecule techniques.     

Analysis of the complex thermal behavior of poly(L‐lactic acid) film. II. Samples crystallized from the melt

The complex thermal behavior of poly(l ‐lactic acid) films crystallized from the melt, either isothermally or nonisothermally, was studied by differential scanning calorimetry (DSC), wide angle X‐ray diffraction, and small angle X‐ray scattering. The variation of the thermal behavior with crystallization temperature, time, and cooling rate was documented and analyzed. After nonisothermal crystallization at low cooling rates that develop high crystallinity, an obvious double melting peak appears at modest heating rates (e.g., 10 °C/min). At higher heating rates, these samples exhibit only single melting. However, an unusual form of double melting occurs under the majority of the conditions studied under either isothermal or nonisothermal conditions. In this case, double melting is marked by the appearance of a recrystallization exotherm just prior to the final melting that obscures the observation of the melting of the crystals formed during the initial crystallization process. The occurrence of double melting in melt‐crystallized samples was concluded to be the result of a melt‐recrystallization process occurring during the subsequent DSC heating scan; it is a function of crystalline perfection, not the initial crystallinity, nor whether or not the crystallization reached completion at the crystallization temperature. Many other very interesting observations are also discussed. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 3378–3391, 2006     

Unveiling the Hidden,Dark, and Short Life of a Vibronic State in a Boron Difluoride Formazanate Dye

Boron difluoride (BF₂) formazanate dyes are contenders for molecular species that exhibit a large Stokes shift and bright red emission. Excitation of 3‐cyanoformazanate complexes with 10 μs wide pulses of specific wavelengths resulted in strong luminescence at 663 nm at both room temperature in solution and at 77 K in a frozen solution. Analysis of the short‐lived excitation spectrum from this luminescence shows that it arises from a vibronic manifold of a higher‐lying excited state. This dark state relaxes to the emitting state over 10 μs. TD‐DFT calculations of the two lowest‐energy excited states show that the relaxed geometries are planar for S₁ but highly distorted in S₂. The specific time‐ and wavelength‐dependence of the excitation profile provides a unique optical encryption capability through the comparison of emission intensities between adjacent vibronic bands only accessible in the 0–12 μs time domain.     

Controlling Spatial Heat and Light Distribution by Using Photothermal Enhancing Auto‐Regulated Liposomes (PEARLs)

Photothermal therapy (PTT) is enhanced by the use of nanoparticles with a large optical absorption at the treatment wavelength. However, this comes at the cost of higher light attenuation that results in reduced depth of heating as well as larger thermal gradients, leading to potential over‐ and under‐treatment in the target tissue. These limitations can be overcome by using photothermal enhancing auto‐regulating liposomes (PEARLs), based on thermochromic J‐aggregate forming dye–lipid conjugates that reversibly alter their absorption above a predefined lipid phase‐transition temperature. Under irradiation by near‐infrared light, deeper layers of the target tissue revert to the intrinsic optical absorption, halting the temperature rise and enabling greater light penetration and heat generation at depth. This effect is demonstrated in both nanoparticle solutions and in gel phantoms containing the nanoparticles.     

Unveiling the Hidden,Dark, and Short Life of a Vibronic State in a Boron Difluoride Formazanate Dye

Boron difluoride (BF₂) formazanate dyes are contenders for molecular species that exhibit a large Stokes shift and bright red emission. Excitation of 3‐cyanoformazanate complexes with 10 μs wide pulses of specific wavelengths resulted in strong luminescence at 663 nm at both room temperature in solution and at 77 K in a frozen solution. Analysis of the short‐lived excitation spectrum from this luminescence shows that it arises from a vibronic manifold of a higher‐lying excited state. This dark state relaxes to the emitting state over 10 μs. TD‐DFT calculations of the two lowest‐energy excited states show that the relaxed geometries are planar for S₁ but highly distorted in S₂. The specific time‐ and wavelength‐dependence of the excitation profile provides a unique optical encryption capability through the comparison of emission intensities between adjacent vibronic bands only accessible in the 0–12 μs time domain.     

Osmolyte Effects on the Conformational Dynamics of a DNA Hairpin at Ambient and Extreme Environmental Conditions

The structural dynamics of a DNA hairpin (Hp) are studied in the absence and presence of the two natural osmolytes trimethylamine‐N‐oxide (TMAO) and urea at ambient and extreme environmental conditions, including high pressures and high temperatures, by using single‐molecule Förster resonance energy transfer and fluorescence correlation spectroscopy. The effect of pressure on the conformational dynamics of the DNA Hp is investigated on a single‐molecule level, providing novel mechanistic insights into its conformational conversions. Different from canonical DNA duplex structures of similar melting points, the DNA Hp is found to be rather pressure sensitive. The combined temperature and pressure dependent data allow dissection of the folding free energy into its enthalpic, entropic, and volumetric contributions. The folded conformation is effectively stabilized by the compatible osmolyte TMAO not only at high temperatures, but also at high pressures and in the presence of the destabilizing co‐solute urea.     

The effect of oxygen content on the melting of the eutectic of physiological salinity solution

The effect of oxygen concentration on the melting of this eutectic was investigated by DSC. In the deoxygenized solution, an endothermic peak attributed to the eutectic transition was observed in the course of heating, and its peak temperature is around ?21.5°C. Another endothermic peak appeared at lower temperature in the presence of oxygen. As the oxygen content in the solution increases, the temperature of this peak is shifted to lower temperature. The transition at the lower temperature are associated with the melting of eutectic carrying oxygen. The same results are given in the NMR data.     

Differential scanning calorimetry study on thermal behaviors of freeze‐dried poly(L‐lactide) from dilute solutions

Glass transition, cold crystallization, and melting of freeze‐dried poly(L‐lactide) (PLLA) prepared from dilute 1,4‐dioxane solutions were investigated by differential scanning calorimetry (DSC). Conventional DSC measurements of heating scans revealed that freeze‐dried PLLA prepared from a 0.07 wt % solution undergoes a two‐step cold crystallization (or reorganization) with a lower exotherm appearing at about 78 °C and with a higher broad exotherm between 110–155 °C. The peak temperature of the former exotherm is about 50 K lower than that observed for a reference bulk sample. Step‐scan mode DSC, which provides information essentially equivalent to that obtained from the temperature‐modulated DSC, revealed that the glass‐transition temperature is about 6 K lower than that of the reference bulk. These findings suggest enhanced chain mobility for freeze‐dried PLLA. Freeze‐dried PLLA that crystallized at 80 °C for 40 min was revealed to contain a rather large amount of rigid amorphous material (42%). © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 115–124, 2005     

Ion‐Mediated Polymerase Chain Reactions Performed with an Electronically Driven Microfluidic Device

The polymerase chain reaction (PCR) is a powerful method for exponentially amplifying very low amounts of target DNA from genetic, clinical, and forensic samples. However, the heating and cooling steps in PCR largely hamper the miniaturization of thermocyclers for on‐site detection of pathogens and point‐of‐care tests. Herein, we devise an ion‐mediated PCR (IM‐PCR) strategy by exploiting ion‐induced DNA denaturation/renaturation cycles. DNA duplexes are effectively denatured in alkaline solutions; whereas, the denatured single‐stranded DNA strands readily reform duplexes at neutral pH. By using an integrated microchip that can programmably control the solution pH simply switching the potential in a range of several hundred millivolts, we can trigger IM‐PCR at a constant temperature. Analogously to thermal cycling, 30 cycles of pH‐induced denaturation/renaturation were used to amplify protein DNA fragments as confirmed by DNA sequencing. We anticipate that this portable, low‐cost, and scalable IM‐PCR holds great promise for widespread biological, clinical, and environmental applications.     

An Optically and Thermally Switchable Electronic Structure Based on an Anthracene–BODIPY Conjugate

An optically and thermally responsive boron dipyrromethene (BODIPY) dye, namely, meso‐2‐(9,10‐dihydro‐9,10‐ethanoanthracene‐11,12‐dione) (DK)‐linked, bicyclo[2.2.2]octadiene (BCOD)‐fused BODIPY ( BCOD‐DK ), was synthesized. The weakly luminous structure of BCOD‐DK can be changed quantitatively to that of the strongly fluorescent BODIPY BCOD‐Ant by optical excitation at the DK unit, which induces double decarbonylation of the DK unit to give an anthracene unit. The solvent effect on the fluorescence properties of BCOD‐DK suggests that the dramatic change in fluorescence intensity is controlled by intramolecular electron transfer from the BODIPY moiety to the meso‐DK substituent. BCOD‐DK is converted to meso‐ DK benzene‐fused BODIPY ( Benzo‐DK ) by heating at 220 °C with 64–70 nm redshift of absorption and fluorescence peaks without changing the fluorescence quantum yield of Φ_F=0.08 in dichloromethane. Benzo‐DK can be converted to strongly fluorescent meso ‐ anthracene benzene‐fused BODIPY Benzo‐Ant by optical excitation. Thus, BCOD‐DK can show four different optical performances simply by irradiation and heating, and hence may be applicable for optical data storage and security data encryption.