An infrared study of the influence of growth media and myo-inositol on structural changes in DNA induced by dehydration and ultraviolet light

1968 ◽  
Vol 14 (8) ◽  
pp. 841-852 ◽  
Author(s):  
S. J. Webb ◽  
M. D. Dumasia
Keyword(s):  
Structural Changes ◽  
Bound Water ◽  
Helical Structure ◽  
Growth Media ◽  
Minimal Salt Medium ◽  
Infrared Study ◽  
Bacterial Dna ◽  
Double Helical Structure ◽  
Spectral Shifts ◽  
Absorption Frequencies

The infrared spectra of films of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and synthetic polynucleotides have been studied under varying degrees of relative humidity (R.H.) in the presence and absence of myo-inositol. In addition the effect of 2537 Å light (ultraviolet) on the hydration of DNA has been investigated. As other researchers have shown, when the R.H. is lowered shifts in the P=O and C=O absorption frequencies occur. These shifts seem to be associated with the removal of approximately 12 molecules of water/nucleotide and all are prevented by the presence of 2 molecules of inositol/nucleotide during desiccation. The irradiation of DNA at 75% R.H. with ultraviolet also produces spectral shifts which appear to arise as a result of bound water molecules moving from P=O and C=O groups.The response of bacterial DNA to desiccation appears to depend on the medium in which the cells are grown. The DNA from cells grown in a minimal salts medium is less hydrated at a given R.H. level than the DNA from cells grown in an enriched medium. This loss of water-adsorbing sites is considered to be due to a physiological replacement of water on the DNA of cells grown on minimal salt medium by amino acids or proteins. RNA and polynucleotides are less hydrated than DNA, which is assumed to be due to their lack of an ordered double helical structure. Of the synthetic polynucleotides poly-I was found to most closely resemble the behavior of DNA. The ability of inositol to prevent spectral shifts in DNA caused by desiccation and irradiation tends to substantiate the suggestion that it preserves the biological integrity of cells and viruses during stress by combining with DNA.

scholarly journals The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

2020 ◽  
Vol 48 (4) ◽  
pp. 1748-1763 ◽  
Author(s):  
Jack W Shepherd ◽  
Robert J Greenall ◽  
Matt I J Probert ◽  
Agnes Noy ◽  
Mark C Leake
Keyword(s):  
Structural Changes ◽  
Periodic Structures ◽  
Helical Structure ◽  
Specific Response ◽  
Base Pairs ◽  
Structural Motifs ◽  
Double Helical Structure ◽  
Physiological Relevance ◽  
Stable Periodic ◽  
Dynamics Simulations

Abstract The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20–30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.

Computational determination of radiation damage effects on DNA structure

Open Physics ◽  
2003 ◽  
Vol 1 (1) ◽  
Author(s):  
Miroslav Pinak
Keyword(s):  
Structural Changes ◽  
Double Helix ◽  
Helical Structure ◽  
Electrostatic Energy ◽  
Necessary Condition ◽  
Enzyme Complex ◽  
Repair Enzyme ◽  
Thymine Dimer ◽  
Thymine Glycol ◽  
Double Helical Structure

AbstractMolecular dynamics (MD) studies of several radiation originated lesions on the DNA molecules are presented. The pyrimidine lesions (cytosinyl radical, thymine dimer, thymine glycol) and purine lesion (8-oxoguanine) were subjected to the MD simulations for several hundred picoseconds using MD simulation code AMBER 5.0 (4.0). The simulations were performed for fully dissolved solute molecules in water. Significant structural changes in the DNA double helical structure were observed in all cases which may be categorized as: a) the breaking of hydrogen bonds network between complementary bases and resulted opening of the double helix (cytosinyl, radical, 8-oxoguanine); b) the sharp bending of the DNA helix centered at the lesion site (thymine dimer, thymine glycol); and c) the flippingout of adenine on the strand complementary to the lesion (8-oxoguanine). These changes related to the overall collapsing of the double helical structure around the lesion, are expected to facilitate the docking of the repair enzyme into the DNA in the formation of DNA-enzyme complex. The stable DNA-enzyme complex is a necessary condition for the onset of the enzymatic repair process. In addition to structural changes, specific values of electrostatic interaction energy were determined at several lesion sites (thymine dimer, thymine glycol and 8-oxoguanine). This lesion-specific electrostatic energy is a factor that enables repair enzyme to discriminate lesion from the native site during the scanning of the DNA surface.

scholarly journals The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

2019 ◽  
Author(s):  
Jack W Shepherd ◽  
R J Greenall ◽  
M I J Probert ◽  
Agnes Noy ◽  
Mark C. Leake
Keyword(s):  
Structural Changes ◽  
Periodic Structures ◽  
Helical Structure ◽  
Specific Response ◽  
Base Pairs ◽  
Structural Motifs ◽  
Double Helical Structure ◽  
Physiological Relevance ◽  
Stable Periodic ◽  
Dynamics Simulations

ABSTRACTThe double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations to show that sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulated overextension on four different sequences of DNA ((AA)12, (AT)12, (GG)12and (GC)12) with supercoiling densities within the physiological range. We found that DNA denatures in the majority of stretching simulations, surprisingly including those with overtwisted DNA. GC-rich sequences were observed to be more stable than AT-rich, with the specific response dependent on base pair ordering. Furthermore, we found that (AT)12forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (GC)12forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.

Hyaluronic acid: a double-helical structure in the presence of potassium at low pH and found also with the cations ammonium, rubidium and caesium

1977 ◽  
Vol 117 (1) ◽  
pp. 113-135 ◽  
Author(s):  
J.K. Sheehan ◽  
K.H. Gardner ◽  
E.D.T. Atkins
Keyword(s):  
Hyaluronic Acid ◽  
Helical Structure ◽  
Low Ph ◽  
Double Helical Structure

Hydrogen Release and Si-N Bond-Healing Infrared Study of Rapid Thermal Annealed Amorphous Silicon Nitride Thin Films

1995 ◽  
Vol 398 ◽  
Author(s):  
P. Santos-Filho ◽  
G. Stevens ◽  
Z. Lu ◽  
K. Koh ◽  
G. Lucovsky
Keyword(s):  
Silicon Nitride ◽  
Amorphous Silicon ◽  
Gas Flow ◽  
Structural Changes ◽  
Thermal Dissociation ◽  
Chemical Vapor ◽  
Hydrogen Release ◽  
Ex Situ ◽  
Infrared Study ◽  
Amorphous Silicon Nitride

ABSTRACTWe address aspects of hydrogen bonding and its thermal evolution in amorphous Silicon nitride films grown by Remote Plasma Enhanced Chemical Vapor Deposition (RPECVD) from SiH4 and NH3 (or ND3) source gases. Rapid Thermal Annealing (RTA) decreases the Si-H(D) and SiN-H(D) bond populations. The hydrogen bonds break, and H2 (HD, D2) forms and evolves from the film with the heat treatment. This molecular hydrogen release is accompanied by Si- and N- bond healing as detected by a SiN infra red stretch mode signal gain. The ex-situ RTA experiment temperatures ranged from 400 °C to 1200 °C, in 100 °C steps and the film structural changes were monitored by Fourier Transform Infrared spectroscopy (FTIR) after each incremental anneal. Gas flow ratios R=NH3/SiH4 > 2 produced films in which SiN-H(D) bonds dissociated, and a gas desorption rate equation estimated an activation energy barrier of Ea = 0.3 eV. The release of hydrogen from the films in the form of H2 (D2) and ammonia radicals was detected by mass spectrometry and is shown here. The re-bonding of nitrogen to silicon upon thermal dissociation of hydrogen's is consistent with the improvement of the electrical properties of a-SiN:H films following RTA treatment.

scholarly journals Living supramolecular polymerization of fluorinated cyclohexanes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Oleksandr Shyshov ◽  
Shyamkumar Vadakket Haridas ◽  
Luca Pesce ◽  
Haoyuan Qi ◽  
Andrea Gardin ◽  
...  
Keyword(s):  
Dipole Moment ◽  
Self Assembly ◽  
Materials Science ◽  
Helical Structure ◽  
The Self ◽  
Supramolecular Polymers ◽  
Aliphatic Compound ◽  
Double Helical Structure ◽  
Key Driver ◽  
Supramolecular Polymerization

AbstractThe development of powerful methods for living covalent polymerization has been a key driver of progress in organic materials science. While there have been remarkable reports on living supramolecular polymerization recently, the scope of monomers is still narrow and a simple solution to the problem is elusive. Here we report a minimalistic molecular platform for living supramolecular polymerization that is based on the unique structure of all-cis 1,2,3,4,5,6-hexafluorocyclohexane, the most polar aliphatic compound reported to date. We use this large dipole moment (6.2 Debye) not only to thermodynamically drive the self-assembly of supramolecular polymers, but also to generate kinetically trapped monomeric states. Upon addition of well-defined seeds, we observed that the dormant monomers engage in a kinetically controlled supramolecular polymerization. The obtained nanofibers have an unusual double helical structure and their length can be controlled by the ratio between seeds and monomers. The successful preparation of supramolecular block copolymers demonstrates the versatility of the approach.

scholarly journals Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions

2002 ◽  
Vol 83 (1) ◽  
pp. 382-406 ◽  
Author(s):  
Lihua Wang ◽  
Brian E. Hingerty ◽  
A.R. Srinivasan ◽  
Wilma K. Olson ◽  
Suse Broyde
Keyword(s):  
Helical Structure ◽  
Implicit Solvent ◽  
Accurate Representation ◽  
Double Helical Structure

Direct-to-Consumer Genetic Testing

2011 ◽  
pp. 51-84 ◽  
Author(s):  
Richard A. Stein
Keyword(s):  
Human Genome ◽  
Human Genome Project ◽  
Cost Effective ◽  
Helical Structure ◽  
Genome Project ◽  
Next Generation ◽  
Double Helical Structure ◽  
Sequencing Technologies ◽  
Human Genome Sequencing ◽  
The Human Genome Project

The 1953 discovery of the DNA double-helical structure by James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin, represented one of the most significant advances in the biomedical world (Watson and Crick 1953; Maddox 2003). Almost half a century after this landmark event, in February 2001, the initial draft sequences of the human genome were published (Lander et al., 2001; Venter et al., 2001) and, in April 2003, the International Human Genome Sequencing Consortium reported the completion of the Human Genome Project, a massive international collaborative endeavor that started in 1990 and is thought to represent the most ambitious undertaking in the history of biology (Collins et al., 2003; Thangadurai, 2004; National Human Genome Research Institute). The Human Genome Project provided a plethora of genetic and genomic information that significantly changed our perspectives on biomedical and social sciences. The sequencing of the first human genome was a 13-year, 2.7-billion-dollar effort that relied on the automated Sanger (dideoxy or chain termination) method, which was developed in 1977, around the same time as the Maxam-Gilbert (chemical) sequencing, and subsequently became the most frequently used approach for several decades (Sanger et al., 1975; Maxam & Gilbert, 1977; Sanger et al., 1977). The new generations of DNA sequencing technologies, known as next-generation (second generation) and next-next-generation (third generation) sequencing, which started to be commercialized in 2005, enabled the cost-effective sequencing of large chromosomal regions during progressively shorter time frames, and opened the possibility for new applications, such as the sequencing of single-cell genomes (Service, 2006; Blow, 2008; Morozova and Marra, 2008; Metzker, 2010).

scholarly journals Sensing Characteristics of Side-Polished Fiber Based on the Alterations in Helical Structure of Thermo-Sensitive Cholesteric Liquid Crystals

Crystals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 465
Author(s):  
Yuqi Han ◽  
Yan Jiang ◽  
Wei Guo
Keyword(s):  
Liquid Crystals ◽  
Structural Changes ◽  
Helical Structure ◽  
Polished Surface ◽  
Loss Peak ◽  
Cholesteric Liquid Crystals ◽  
Fiber Sensors ◽  
Temperature Changes ◽  
Solid Foundation ◽  
Transmitted Spectrum

Cholesteric liquid crystals (CLCs) are sensitive to environmental temperature changes, and have been employed as a specific intermediary for biosensors. Considering the temperature-dependent structural changes of CLCs, this study aimed to determine the sensing properties of side-polished fibers (SPFs) after coating with CLCs. The experimental results demonstrated that, with regard to the transmitted spectrum, the loss peak of CLC-coated SPFs exhibited a positive linear relationship with temperature changes over a range of 20 to 50 °C. The linear correlation coefficient achieved 97.8% when the temperature increased by 10 °C, and the loss peak drifted by 12.72 nm. The reflectance spectrum of CLCs coated on the polished surface were obtained using optical fiber sensors. The feasibility of measuring the helical structure of CLCs was further verified using SPF transmission spectroscopy. The findings indicated that the transmitted spectrum of SPFs could be adopted to characterize the helical structure of CLCs, which lays a solid foundation for further study on SPF-based biosensors.

scholarly journals Post-Mortem Chemical Changes in Poultry Breast Meat Monitored With Visible-Near Infrared Spectroscopy

2014 ◽  
Vol 3 (3) ◽  
pp. 57 ◽  
Author(s):  
Samantha A. Hawkins ◽  
Brian Bowker ◽  
Hong Zhuang ◽  
Gary Gamble ◽  
Ronald Holser
Keyword(s):  
Meat Quality ◽  
Structural Changes ◽  
Near Infrared ◽  
Muscle Protein ◽  
Visible Region ◽  
Bound Water ◽  
Nir Spectroscopy ◽  
Spectra Analysis ◽  
Freeze Dried ◽  
Postmortem Aging

<p>Chicken meat undergoes significant chemical and structural changes with postmortem time that influence meat quality characteristics. The objective of this study was to measure the visible-near infrared (vis-NIR) spectral differences in broiler breast fillets at 0.5, 4, 24, and 120 h postmortem. Muscle samples were flash frozen and freeze-dried prior to spectra analysis. In the visible region of the spectra (400-700 nm) changes in myoglobin protein peaks were observed with postmortem time. Freeze-drying muscle samples provided additional information from the NIR region of the spectra (800-2500 nm) on muscle protein changes during postmortem aging. Alterations to the b-sheet and a-helix structures of myofibrillar proteins and changes in the amount of bound water were observed in the NIR region with postmortem aging. Data from this study demonstrate that changes in breast fillets with postmortem time that are related to meat quality traits are detectable using vis-NIR spectroscopy.</p>

Sign in / Sign up

Export Citation Format

Share Document