A unified view of polymer, dumbbell, and oligonucleotide nearest-neighbor (NN) thermodynamics is presented DNA NN DG° 37 parameters from seven laboratories are presented in the same format so that careful comparisons can be made The seven studies used data from natural polymers, synthetic polymers, oligonucleotide dumbbells, and oligonucleotide duplexes to derive NN parameters; used dif- ferent methods of data analysis; used different salt concen- trations; and presented the NN thermodynamics in different formats As a result of these differences, there has been much confusion regarding the NN thermodynamics of DNA poly- mers and oligomers Herein I show that six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies re- main Further, a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics Empirical salt dependencies are also derived for oligonucleotides and polymers

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A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

Critical phenomena and renormalization-group theory

Background: High-resolution amplicon melting analysis was recently introduced as a closed-tube method for genotyping and mutation scanning (Gundry et al. Clin Chem 2003;49:396–406). The technique required a fluorescently labeled primer and was limited to the detection of mutations residing in the melting domain of the labeled primer. Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides.

Methods: We studied polymorphisms in the hydroxytryptamine receptor 2A (HTR2A) gene (T102C), β-globin (hemoglobins S and C) gene, and cystic fibrosis (F508del, F508C, I507del) gene. PCR was performed in the presence of the double-stranded DNA dye LCGreen, and high-resolution amplicon melting curves were obtained. After fluorescence normalization, temperature adjustment, and/or difference analysis, sequence alterations were distinguished by curve shape and/or position. Heterozygous DNA was identified by the low-temperature melting of heteroduplexes not observed with other dyes commonly used in real-time PCR.

Results: The six common β-globin genotypes (AA, AS, AC, SS, CC, and SC) were all distinguished in a 110-bp amplicon. The HTR2A single-nucleotide polymorphism was genotyped in a 544-bp fragment that split into two melting domains. Because melting curve acquisition required only 1–2 min, amplification and analysis were achieved in 10–20 min with rapid cycling conditions.

Conclusions: High-resolution melting analysis of PCR products amplified in the presence of LCGreen can identify both heterozygous and homozygous sequence variants. The technique requires only the usual unlabeled primers and a generic double-stranded DNA dye added before PCR for amplicon genotyping, and is a promising method for mutation screening.

/pdf/high-resolution-genotyping-by-amplicon-melting-analysis-22h5fms78p.pdf

High-Resolution Genotyping by Amplicon Melting Analysis Using LCGreen

A mean-field phase diagram for conformationally symmetric diblock melts using the standard Gaussian polymer model is presented. Our calculation, which traverses the weak- to strong-segregation regimes, is free of traditional approximations. Regions of stability are determined for disordered (DIS) melts and for ordered structures including lamellae (L), hexagonally packed cylinders (H), body-centered cubic spheres (QIm3m), close-packed spheres (CPS), and the bicontinuous cubic network with Ia3d symmetry (QIa3d). The CPS phase exists in narrow regions along the order−disorder transition for χN ≥ 17.67. Results suggest that the QIa3d phase is not stable above χN ∼ 60. Along the L/QIa3d phase boundaries, a hexagonally perforated lamellar (HPL) phase is found to be nearly stable. Our results for the bicontinuous Pn3m cubic (QPn3m) phase, known as the OBDD, indicate that it is an unstable structure in diblock melts. Earlier approximation schemes used to examine mean-field behavior are reviewed, and compa...

Unifying Weak- and Strong-Segregation Block Copolymer Theories

http://static.sif.it/SIF/resources/public/files/va2012/likos_0710.pdf

Effective interactions in soft condensed matter physics

Exact algorithms for the calculation of melting curves of heterogeneous DNA with N base pairs apparently require computer time proportional to N2. However, it is shown that a decomposition of the loop entropy factor into a sum of I exponential functions (1) gives an extremely accurate approximation to the loop entropy factor for small values of I and (2) makes the computer time for the exact algorithms proportional to I·N. In effect, exact results for melting curves and lengths of helix or coil stretches are obtained with computer time comparable to that required for the Frank-Kamenetskii approximation. The remarkable accuracy of the latter for the fraction of helical content (errors of 0.01–0.05) is confirmed, but appreciably larger errors are found for the lengths of helix or coil stretches (typical errors of 30–100%).

Theory of DNA melting curves.

The prediction and interpretation of conformational properties of branched polymers is difficult, due to the complexity and variety of these structures. Numerical simulations are, consequently, very useful in the investigation of these systems. This review describes the application of numerical simulation techniques to relevant theoretical problems concerning branched polymer systems, taking also into account the related experimental data. Monte Carlo, Molecular Dynamics and Brownian Dynamics methods are employed to simulate the equilibrium and dynamic behavior, and also to reproduce hydrodynamic properties. The simulations are performed on several polymer models. Thus, different Monte Carlo algorithms have been devised for lattice and off-lattice models. Moreover, Molecular Dynamics and Brownian Dynamics can be carried out for detailed atomic or coarse-grained chains. A great amount of investigation has been engaged in the understanding of uniform homopolymer stars as single chains, or in non-diluted solutions and melts, employing this variety of techniques, models and properties. However, other important structures, such as stars with different types of monomer units, combs, brushes, dendrimers and absorbed branched polymers have also been the subject of specific simulation studies.

Conformational Properties of Branched Polymers: Theory and Simulations

Monte Carlo calculation of hydrodynamic properties of freely jointed, freely rotating, and real polymethylene chains

Using rigid-body Monte Carlo simulation coupled with rigorous treatment of hydrodynamic interaction, translational coefficients and intrinsic viscosities of linear and cyclic polymers with excluded volume interactions are calculated using two models: freely jointed chains with hard-sphere interactions and Gaussian chains with Lennard-Jones potential. The results are compared with literature experimental data

http://leonardo.inf.um.es/macromol/publications/070MAC91.pdf

Monte carlo calculation of hydrodynamic properties of linear and cyclic polymers in good solvents

Monte Carlo calculations for linear chains and star polymers with intermolecular interactions. 3. Dimensions and hydrodynamic properties in good solvent conditions

Juan J. Freire

Papers

Theory of DNA melting curves.

Conformational Properties of Branched Polymers: Theory and Simulations

Monte Carlo calculation of hydrodynamic properties of freely jointed, freely rotating, and real polymethylene chains

Monte carlo calculation of hydrodynamic properties of linear and cyclic polymers in good solvents

Monte Carlo calculations for linear chains and star polymers with intermolecular interactions. 3. Dimensions and hydrodynamic properties in good solvent conditions