Hypochromism in Polynucleotides1
01 Sep 1960-Journal of the American Chemical Society (American Chemical Society)-Vol. 82, Iss: 18, pp 4785-4790
About: This article is published in Journal of the American Chemical Society.The article was published on 1960-09-01. It has received 443 citations till now.
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TL;DR: A series of experiments and a theoretical model designed to systematically define and evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that contribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures are reported.
Abstract: We report a series of experiments and a theoretical model designed to systematically define and evaluate the relative importance of nanoparticle, oligonucleotide, and environmental variables that contribute to the observed sharp melting transitions associated with DNA-linked nanoparticle structures. These variables include the size of the nanoparticles, the surface density of the oligonucleotides on the nanoparticles, the dielectric constant of the surrounding medium, target concentration, and the position of the nanoparticles with respect to one another within the aggregate. The experimental data may be understood in terms of a thermodynamic model that attributes the sharp melting to a cooperative mechanism that results from two key factors: the presence of multiple DNA linkers between each pair of nanoparticles and a decrease in the melting temperature as DNA strands melt due to a concomitant reduction in local salt concentration. The cooperative melting effect, originating from short-range duplex-to-duplex interactions, is independent of DNA base sequences studied and should be universal for any type of nanostructured probe that is heavily functionalized with oligonucleotides. Understanding the fundamental origins of the melting properties of DNA-linked nanoparticle aggregates (or monolayers) is of paramount importance because these properties directly impact one's ability to formulate high sensitivity and selectivity DNA detection systems and construct materials from these novel nanoparticle materials.
1,420 citations
TL;DR: The nature and dynamics of the singlet excited electronic states created in nucleic acids and their constituents by UV light are reviewed, finding that these states are highly stable to photochemical decay, perhaps as a result of selection pressure during a long period of molecular evolution.
Abstract: The scope of this review is the nature and dynamics of the singlet excited electronic states created in nucleic acids and their constituents by UV light. Interest in the UV photochemistry of nucleic acids has long been the motivation for photophysical studies of the excited states, because these states are at the beginning of the complex chain of events that culminates in photodamage. UV-induced damage to DNA has profound biological consequences, including photocarcinogenesis, a growing human health problem.1-3 Sunlight, which is essential for life on earth, contains significant amounts of harmful UV (λ < 400 nm) radiation. These solar UV photons constitute one of the most ubiquitous and potent environmental carcinogens. This extraterrestrial threat is impressive for its long history; photodamage is as old as life itself. The genomic information encoded by these biopolymers has been under photochemical attack for billions of years. It is not surprising then that the excited states of the nucleic acid bases (see Chart 1), the most important UV chromophores of nucleic acids, are highly stable to photochemical decay, perhaps as a result of selection pressure during a long period of molecular evolution. This photostability is due to remarkably rapid decay pathways for electronic energy, which are only now coming into focus through femtosecond laser spectroscopy. The recently completed map of the human genome and the ever-expanding crystallographic database of nucleic acid structures are two examples that illustrate the richly detailed information currently available about the static properties of nucleic acids. In contrast, much less is known about the dynamics of these macromolecules. This is particularly true of the dynamics of the excited states that play a critical role in DNA photodamage. Efforts to study nucleic acids by time-resolved spectroscopy have been stymied by the apparent lack of suitable fluorophores. In contrast, dynamical spectroscopy of proteins has flourished thanks to intrinsically fluorescent amino acids such as tryptophan, tyrosine, and phenylalanine.4 The primary UVabsorbing constituents of nucleic acids, the nucleic acid bases, have vanishingly small fluorescence quantum yields under physiological conditions of temperature and pH.5 In fact, the bases were frequently described as “nonfluorescent” in the early literature. * To whom correspondence should be addressed. E-mail: kohler@ chemistry.ohio-state.edu. Phone: (614) 688-3944. Fax: (614) 2921685. 1977 Chem. Rev. 2004, 104, 1977−2019
1,115 citations
TL;DR: These calculations support the hypothesis that the change of Tm with salt concentration is due to changes in the screened interactions between the fixed phosphate charges, and indicate some of the limitations of the theoretical model.
Abstract: Data on the decrease of the DNA melting temperature Tm with the salt concentration M are reported and discussed. The electrostatic free energy change in the helix–coil transition, ΔFe is related to the potential, ψ, which represents the electrostatic repulsion between the phosphate charges; ψ is calculated as a function of M and of the distances between the charges of the two strands. The Debye-Huckel approximation is shown to overestimate ψ. It is suggested that the high local concentration of the counterions in the immediate vicinity of the fixed charges screen these charges from interacting with other fixed charges, to the extent that the system behaves as if the fixed ions carry a reduced charge. The notion of a reduced charge represents in a single parameter the deviation of the Debye-Huckel approximation from the true potential. A plot of Tm versus ΔFe gives a straight line as predicted. ΔH0 is calculated from the slope and found to be consistent with experimentally determined values. Our calculations support the hypothesis that the change of Tm with salt concentration is due to changes in the screened interactions between the fixed phosphate charges. In analyzing the results of these calculations, we are able on the one hand to indicate some of the limitations of the theoretical model and, on the other hand, draw some conclusions about the order of magnitude of the nonelectrostatic interaction energy of formation of the double helix.
658 citations
TL;DR: This chapter discusses the experimental methods needed to acquire a melting curve and the analysis and interpretation of the data, as well as comparing results with previously published data.
Abstract: Publisher Summary This chapter discusses the experimental methods needed to acquire a melting curve and the analysis and interpretation of the data. Any standard commercial UV spectrophotometer can be equipped to measure melting curves. A useful instrument is a single-beam Gilford (Oberlin, OH) spectrophotometer (Model 2530) with an automated reference compensator that allows melting curves to be obtained on three separate samples simultaneously. One major advantage of using UV spectroscopy is the high sensitivity of the method. Normally, the absorbance of the sample used should be between 0.2 and 2.0. Sample preparation for UV melting studies is straightforward. The RNA stock solution is prepared by dialysis against the desired buffer and different concentrations are made by dilution. The high salt concentration is chosen to minimize electrostatic repulsion between strands and to avoid divalent ions, which catalyze hydrolysis of RNA and favor triple-strand formation. This solvent provides a standard condition for measuring melting curves and for comparing results with previously published data.
613 citations
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01 Jan 1974TL;DR: This work has used bulk and single-molecule measurements of thermodynamics and kinetics, plus various spectroscopic methods (UV absorption, optical rotation, circular dichroism, circular intensity differential scattering, fluorescence, NMR) to approach this goal.
Abstract: ▪ Abstract The Watson-Crick double helix of DNA was first revealed in 1953. Since then a wide range of physical chemical methods have been applied to DNA and to its more versatile relative RNA to determine their structures and functions. My major goal is to predict the folded structure of any RNA from its sequence. We have used bulk and single-molecule measurements of thermodynamics and kinetics, plus various spectroscopic methods (UV absorption, optical rotation, circular dichroism, circular intensity differential scattering, fluorescence, NMR) to approach this goal.
581 citations
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