The stability of helical polynucleotides: Base contributions

DeVoe, Howard; Tinoco, Ignacio

doi:10.1016/s0022-2836(62)80105-3

Cited by 483 publications

(154 citation statements)

References 31 publications

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“…If it is assumed that the increase in melting temperature is due solely to entropic effects, i.e. the enthalpy of the transition is the same for the intact and singly nicked forms, we find that entropy of unwinding and of strand separation accounts for about 5% of the total entropy of the transition, and 10 to 20% of the change in configurational entropy (28) that takes place during melting of DNA.…”

Section: I20mentioning

confidence: 81%

Physical and Topological Properties of Circular DNA

Vinograd

Lebowitz

1966

The Journal of General Physiology

326

102

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Several types of circular DNA molecules are now known. These are classified as single-stranded rings, covalently closed duplex rings, and weakly bonded duplex rings containing an interruption in one or both strands. Single rings are exemplified by the viral DNA from X174 bacteriophage. Duplex rings appear to exist in a twisted configuration in neutral salt solutions at room temperature. Examples of such molecules are the DNA's from the papova group of tumor viruses and certain intracellular forms of OX and X-DNA. These DNA's have several common properties which derive from the topological requirement that the winding number in such molecules is invariant. They sediment abnormally rapidly in alkaline (denaturing) solvents because of the topological barrier to unwinding. For the same basic reason these DNA's are thermodynamically more stable than the strand separable DNA's in thermal and alkaline melting experiments. The introduction of one single strand scission has a profound effect on the properties of closed circular duplex DNA's. In neutral solutions a scission appears to generate a swivel in the complementary strand at a site in the helix opposite to the scission. The twists are then released and a slower sedimenting, weakly closed circular duplex is formed. Such circular duplexes exhibit normal melting behavior, and in alkali dissociate to form circular and linear single strands which sediment at different velocities. Weakly closed circular duplexes containing an interruption in each strand are formed by intramolecular cyclization of viral X-DNA. A third kind of weakly closed circular duplex is formed by reannealing single strands derived from circularly permuted T2 DNA. These reconstituted duplexes again contain an interruption in each strand though not necessarily regularly spaced with respect to each other.In recent years it has become known that genes in chromosomes may be circularly arranged with respect to each other. Jacob and Wollman (1) in 1958 showed that distant markers in a donor strain of E. coli appeared in closely linked genes in a recipient strain after bacterial mating. Streisinger, Edgar, and Denhardt (2) in 1964 proved in genetic mapping experiments that the entire map of T4 bacteriophage is circular. It is not surprising therefore that DNA, the genetic macromolecule, should also occur in a circular form.Since the demonstration in 1962 by Fiers and Sinsheimer (3) that the singlei03

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Section: I20mentioning

confidence: 81%

Physical and Topological Properties of Circular DNA

Vinograd

Lebowitz

1966

The Journal of General Physiology

326

102

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“…In order to extend our knowledge of radiationinduced damage in biomolecular systems and provide relevant parameters for radiation-based biomedical applications, it is necessary to apply these models to increasingly more complicated biomolecules. It is important to note that the great majority of the molecules of biological interest have a considerably high permanent dipole moment, for example, H 2 O [10], the DNA and RNA bases [11][12][13], tetrahydrofuran * g.garcia@iff.csic.es (THF) [14], and the target molecule of the present study pyrimidine [15].…”

Section: Introductionmentioning

confidence: 99%

Cross-section calculations for positron scattering from pyrimidine over an energy range from 0.1 to 10000 eV

et al. 2013

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We report a computational investigation of positron scattering by pyrimidine (C 4 H 4 N 2 ) in the gas phase. Integral and differential cross sections have been calculated over a broad energy range by employing two distinct ab initio quantum scattering methods: the R-matrix method and a corrected form of the independent-atom representation, at low and high energies, respectively. Since pyrimidine is a strong polar molecule further dipole-induced excitations have been calculated in the framework of the first Born approximation. Good agreement is found between the different computational models and fair agreement is found with prior experimental results.

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“…T he nearest-neighbor (NN) model (1)(2)(3)(4) for DNA thermodynamics has been successfully applied to predict the free energy of formation of secondary structures in nucleic acids. The model estimates the free-energy change to form a double helix from independent strands as a sum over all of resulting bp and adjacent-bp stacks, depending on the constituent four bases of the stack, by using 10 nearest-neighbor base-pair (NNBP) energies.…”

mentioning

confidence: 99%

Single-molecule derivation of salt dependent base-pair free energies in DNA

Huguet

Bizarro

Forns

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

229

298

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Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which depend on several assumptions. Here we report measurements of the DNA base-pair free energies based on a simplified system, the mechanical unzipping of single DNA molecules. By combining experimental data with a physical model and an optimization algorithm for analysis, we measure the 10 unique nearest-neighbor base-pair free energies with 0.1 kcal mol −1 precision over two orders of magnitude of monovalent salt concentration. We find an improved set of standard energy values compared with Unified Oligonucleotide energies and a unique set of 10 base-pair-specific salt-correction values. The latter are found to be strongest for AA/TT and weakest for CC/GG. Our unique energy values and salt corrections improve predictions of DNA unzipping forces and are fully compatible with melting temperatures for oligos. The method should make it possible to obtain free energies, enthalpies, and entropies in conditions not accessible by bulk methodologies.DNA thermodynamics | DNA unzipping | nearest-neighbor model | optical tweezers T he nearest-neighbor (NN) model (1-4) for DNA thermodynamics has been successfully applied to predict the free energy of formation of secondary structures in nucleic acids. The model estimates the free-energy change to form a double helix from independent strands as a sum over all of resulting bp and adjacent-bp stacks, depending on the constituent four bases of the stack, by using 10 nearest-neighbor base-pair (NNBP) energies. These energies themselves contain contributions from stacking, hydrogen-bonding, and electrostatic interactions as well as configurational entropy loss. Accurately predicting free energies has many applications in biological science: to predict self-assembled structures in DNA origami (5, 6); achievement of high selectivity in the hybridization of synthetic DNAs (7); antigene targeting and siRNA design (8); characterization of translocating motion of enzymes that mechanically disrupt nucleic acids (9); prediction of nonnative states (e.g., RNA misfolding) (10); and DNA guided crystallization of colloids (11).Some of the most reliable estimates of the NNBP energies to date have been obtained from thermal denaturation studies of DNA oligos and polymers (2). Although early studies showed large discrepancies in the NNBP values, nowadays they are remarkably consistent among several groups. In these studies it is assumed that duplexes melt in a two-state fashion. However this assumption is not often the case and a discrepancy between the values obtained using oligomers vs. polymers remains a persistent problem that has been attributed to many factors such as the slow dissociation kinetics induced by a population of transient nondenatured intermediates that develop during thermal denaturation experiments (12). Single-molecule techniques (13) circ...

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The stability of helical polynucleotides: Base contributions

Cited by 483 publications

References 31 publications

Physical and Topological Properties of Circular DNA

Physical and Topological Properties of Circular DNA

Cross-section calculations for positron scattering from pyrimidine over an energy range from 0.1 to 10000 eV

Single-molecule derivation of salt dependent base-pair free energies in DNA

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