An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechannics

Biopolymers ◽  
1983 ◽  
Vol 22 (3) ◽  
pp. 969-1002 ◽  
Author(s):  
Robert F. Tilton ◽  
Paul K. Weiner ◽  
Peter A. Kollman
Keyword(s):  
Sequence Dependence ◽  
Dna Models

scholarly journals Electrical characteristics of amyloid beta peptides in vertical junctions

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sohyeon Seo ◽  
Jinju Lee ◽  
Jungsue Choi ◽  
G. Hwan Park ◽  
Yeseul Hong ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electron Transport ◽  
Amyloid Beta ◽  
Field Effect Transistors ◽  
Brain Diseases ◽  
Electrical Characteristics ◽  
Transport Pathway ◽  
Sequence Dependence ◽  
Aβ Oligomers ◽  
Aβ Peptides

AbstractAssembled amyloid beta (Aβ) peptides have been considered pathological assemblies involved in human brain diseases, and the electron transfer or electron transport characteristics of Aβ are important for the formation of structured assemblies. Here, we report the electrical characteristics of surface-assembled Aβ peptides similar to those observed in Alzheimer’s patients. These characteristics correlate to their electron transfer characteristics. Electrical current–voltage plots of Aβ vertical junction devices show the Aβ sequence dependence of the current densities at both Aβ monomers (mono-Aβs) and Aβ oligomers (oli-Aβs), while Aβ sequence dependence is not clearly observed in the electrical characteristics of Aβ planar field effect transistors (FETs). In particular, surface oligomerization of Aβ peptides drastically decreases the activity of electron transfer, which presents a change in the electron transport pathway in the Aβ vertical junctions. Electron transport at oli-Aβ junctions is symmetric (tunneling/tunneling) due to the weak and voltage-independent coupling of the less redox-reactive oli-Aβ to the contacts, while that at mono-Aβ junctions is asymmetric (hopping/tunneling) due to redox levels of mono-Aβ voltage-dependently coupled with contact electrodes. Consequently, through vertical junctions, the sequence- and conformation-dependent electrical characteristics of Aβs can reveal their electron transfer activities.

scholarly journals The effect of flanking bases on direct and triplet sensitized cyclobutane pyrimidine dimer formation in DNA depends on the dipyrimidine, wavelength and the photosensitizer

2021 ◽  
Author(s):  
Chen Lu ◽  
Natalia Eugenia Gutierrez-Bayona ◽  
John-Stephen Taylor
Keyword(s):  
Uv Light ◽  
Pyrimidine Dimer ◽  
Flanking Sequence ◽  
Quenching Mechanism ◽  
Cyclobutane Pyrimidine Dimers ◽  
Sequence Dependence ◽  
Pyrimidine Dimers ◽  
Skin Cancers ◽  
A Charge ◽  
C To T Mutations

Abstract Cyclobutane pyrimidine dimers (CPDs) are the major products of DNA produced by direct absorption of UV light, and result in C to T mutations linked to human skin cancers. Most recently a new pathway to CPDs in melanocytes has been discovered that has been proposed to arise from a chemisensitized pathway involving a triplet sensitizer that increases mutagenesis by increasing the percentage of C-containing CPDs. To investigate how triplet sensitization may differ from direct UV irradiation, CPD formation was quantified in a 129-mer DNA designed to contain all 64 possible NYYN sequences. CPD formation with UVB light varied about 2-fold between dipyrimidines and 12-fold with flanking sequence and was most frequent at YYYR and least frequent for GYYN sites in accord with a charge transfer quenching mechanism. In contrast, photosensitized CPD formation greatly favored TT over C-containing sites, more so for norfloxacin (NFX) than acetone, in accord with their differing triplet energies. While the sequence dependence for photosensitized TT CPD formation was similar to UVB light, there were significant differences, especially between NFX and acetone that could be largely explained by the ability of NFX to intercalate into DNA.

The Order of Phase Transition of Solvable DNA Melting Models

2003 ◽  
Vol 17 (16) ◽  
pp. 885-896 ◽  
Author(s):  
Su-Long Nyeo ◽  
I-Ching Yang
Keyword(s):  
Phase Transition ◽  
Hydrogen Bonds ◽  
Short Range ◽  
Scaling Laws ◽  
Dna Melting ◽  
Thermodynamic Quantities ◽  
Base Pairs ◽  
Order Of Phase Transition ◽  
Exactly Solvable ◽  
Dna Models

The phase transition of DNA molecules is studied in an exactly solvable formalism with the Morse and Deng–Fan potentials for the interstrand hydrogen bonds of nucleotide base pairs. It is shown that although the two potentials have different short-range behaviors, the thermodynamic quantities of the DNA system in these potentials enjoy the same scaling laws with the associated critical exponents, which are explicitly calculated. These exactly solvable DNA models are shown to exhibit a phase transition of the second order and the results of the analysis agree with previous studies.

scholarly journals Recombination within the Y locus in Ascobolus immersus

1967 ◽  
Vol 9 (2) ◽  
pp. 159-177 ◽  
Author(s):  
A. Kruszewska ◽  
W. Gajewski
Keyword(s):  
Opposite Direction ◽  
Negative Correlation ◽  
Linear Order ◽  
Great Majority ◽  
Wild Type Allele ◽  
Wild Type ◽  
Marker Effect ◽  
Dna Models ◽  
Ascobolus Immersus ◽  
Hybrid Dna

Mutants of the Y locus differed appreciably in their basic conversion frequencies (frequencies of conversion in one-point crosses) to wild type. The differences in the basic conversion frequencies in the opposite direction, i.e. from corresponding wild-type allele to mutant, were in general not pronounced. For some alleles frequencies of conversion in both directions were similar, but for the others they differed markedly. No evident correlation between the position of mutants on the map and their basic conversion frequencies was observed.In two-point crosses in repulsion, the great majority of recombinant octads were of conversion type. In these crosses symmetry or asymmetry of conversion depended mainly on similarity or differences in basic conversion frequencies of mutants crossed. In crosses between mutants from different clusters the recombination frequencies were near to the sums of their basic conversion frequencies. Such ‘mutant specificity’ makes it impossible to establish the linear order of mutants on the basis of recombination frequencies in two-point crosses.The results of two-point crosses in repulsion between mutants within clusters pointed to the influence of one allele on the frequency of conversion of another one. This ‘marker effect’ was also evident in some three-point crosses.The frequencies of simultaneous conversions in two-point crosses in coupling did not show negative correlation with the distances between the mutants involved.It seems that many of the data presented here are most easily explained by recently developed hybrid DNA models.

DFT study of DNA sequence dependence at the level of dinucleoside monophosphates

2011 ◽  
Vol 975 (1-3) ◽  
pp. 69-75 ◽  
Author(s):  
V.I. Poltev ◽  
V.M. Anisimov ◽  
V.I. Danilov ◽  
D. Garcia ◽  
A. Deriabina ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dft Study ◽  
Sequence Dependence ◽  
Dinucleoside Monophosphates

Sequence Dependence of the Stability of RNA Hairpin Molecules with Six Nucleotide Loops†

Biochemistry ◽  
2006 ◽  
Vol 45 (5) ◽  
pp. 1400-1407 ◽  
Author(s):  
Christopher J. Vecenie ◽  
Catherine V. Morrow ◽  
Allison Zyra ◽  
Martin J. Serra
Keyword(s):  
Sequence Dependence ◽  
The Stability ◽  
Rna Hairpin

scholarly journals Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA

2018 ◽  
Author(s):  
Debayan Chakraborty ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Electrostatic Interactions ◽  
Persistence Length ◽  
Data Bank ◽  
Coarse Grained ◽  
Force Extension ◽  
Sequence Dependence ◽  
Coarse Grained Model ◽  
Interaction Sites ◽  
Double Stranded Dna ◽  
Centers Of Mass

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.

scholarly journals Gene conversion: observations on the DNA hybrid models

1970 ◽  
Vol 15 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Andrzej Paszewski
Keyword(s):  
Experimental Data ◽  
Gene Conversion ◽  
Hybrid Models ◽  
Crossing Over ◽  
Meiotic Segregation ◽  
Tetrad Analysis ◽  
Dna Models ◽  
Complex Picture ◽  
New Hypothesis ◽  
Hybrid Dna

SUMMARYSome features of gene conversion in fungi and their bearing on the hybrid DNA models are discussed. Available experimental data from tetrad analysis seem to give a more complex picture of polarity in intra-genic recombination and of the relations between conversion and post-meiotic segregation, and between conversion and crossing-over, than predicted by the models.A new hypothesis of the mechanism of gene conversion with special attention given to the aspect of asymmetry in this phenomenon is proposed as an alternative to the mechanism suggested by the DNA hybrid models.

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