scholarly journals A Review on the Thermodynamics of Denaturation Transition of DNA Duplex Oligomers in the Context of Nearest-Neighbor Models

10.5772/62574 ◽  
2016 ◽  
Author(s):  
João C. O. Guerra
Keyword(s):  
Nearest Neighbor ◽  
Dna Duplex

scholarly journals Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes

1996 ◽  
Vol 24 (22) ◽  
pp. 4501-4505 ◽  
Author(s):  
Naoki Sugimoto ◽  
Shu-ich Nakano ◽  
Mari Yoneyama ◽  
Kei-ich Honda
Keyword(s):  
Thermodynamic Parameters ◽  
Nearest Neighbor ◽  
Enthalpy Change ◽  
Initiation Factor ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Dna And Rna ◽  
Sequence Dependent ◽  
Experimental Values

Abstract To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (Δ H °, Δ S ° and Δ G °) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (ΔG° 37 = 3.4 kcal/mol). The improved nearest-neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing Δ G ° 37 values of DNA/DNA nearest-neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.

scholarly journals Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions

2020 ◽  
Vol 117 (25) ◽  
pp. 14194-14201 ◽  
Author(s):  
Saptarshi Ghosh ◽  
Shuntaro Takahashi ◽  
Tatsuya Ohyama ◽  
Tamaki Endoh ◽  
Hisae Tateishi-Karimata ◽  
...  
Keyword(s):  
Nearest Neighbor ◽  
Average Molecular Weight ◽  
Molecular Crowding ◽  
Dna Duplexes ◽  
Dna Duplex ◽  
Intracellular Environment ◽  
Duplex Stability ◽  
Key Factor ◽  
The Stability ◽  
Duplex Formation

The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.

Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†

Biochemistry ◽  
1996 ◽  
Vol 35 (11) ◽  
pp. 3555-3562 ◽  
Author(s):  
John SantaLucia, ◽  
Hatim T. Allawi ◽  
P. Ananda Seneviratne
Keyword(s):  
Nearest Neighbor ◽  
Dna Duplex ◽  
Duplex Stability

Observation of Superlattice Dislocations on Cube Planes in Ni3Al

1973 ◽  
Vol 31 ◽  
pp. 174-175 ◽  
Author(s):  
J. M. Oblak ◽  
W. H. Rand
Keyword(s):  
Nearest Neighbor ◽  
Antiphase Boundary ◽  
Nearest Neighbors ◽  
High Energy ◽  
Cross Slip ◽  
Octahedral Plane ◽  
Trapping Mechanism ◽  
Slip Traces

The energy of an a/2 <110> shear antiphase. boundary in the Ll2 expected to be at a minimum on {100} cube planes because here strue ture is there is no violation of nearest-neighbor order. The latter however does involve the disruption of second nearest neighbors. It has been suggested that cross slip of paired a/2 <110> dislocations from octahedral onto cube planes is an important dislocation trapping mechanism in Ni3Al; furthermore, slip traces consistent with cube slip are observed above 920°K.Due to the high energy of the {111} antiphase boundary (> 200 mJ/m2), paired a/2 <110> dislocations are tightly constricted on the octahedral plane and cannot be individually resolved.

Application of Lattice Imaging Techniques to Amorphous Films

1975 ◽  
Vol 33 ◽  
pp. 8-9
Author(s):  
S. R. Herd ◽  
P. Chaudhari
Keyword(s):  
Nearest Neighbor ◽  
Random Network ◽  
Imaging Techniques ◽  
Network Models ◽  
Accurate Method ◽  
Direct Transmission ◽  
Lattice Imaging ◽  
Transmission Electron ◽  
Lattice Planes ◽  
Nearest Neighbor Distances

Electron diffraction and direct transmission have been used extensively to study the local atomic arrangement in amorphous solids and in particular Ge. Nearest neighbor distances had been calculated from E.D. profiles and the results have been interpreted in terms of the microcrystalline or the random network models. Direct transmission electron microscopy appears the most direct and accurate method to resolve this issue since the spacial resolution of the better instruments are of the order of 3Å. In particular the tilted beam interference method is used regularly to show fringes corresponding to 1.5 to 3Å lattice planes in crystals as resolution tests.

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