Surface plasmon resonance (SPR) / DNA Hybridization / Localized Surface Plasmon Resonance Spectroscopy of Triangular Aluminum Nanoparticles / NASA Worldview Oct.14, 2017

South America, detail off coast of Chile (above – sepia & contrast enhanced) / Oct.14, 2017


VSF: How many of us have ever heard of “surface plasmon resonance”? In my research into geoengineering and plasma technology, I have read many actual textbooks. A recent text, “Plasmon Resonances in Nanoparticles” by Isaak D. Mayergoyz, led me to unexpected territory. Obviously there are many aspects to our current science that most of us are not informed about. What other uses can these technologies be applied to? There are over 66,000 links found on Google Scholar when I write “DNA hybridization plasmon resonance.”

Surface plasmon resonance (SPR) is the resonant oscillation of conduction electrons at the interface between negative and positive permittivity material stimulated by incident light. SPR is the basis of many standard tools for measuring adsorption of material onto planar metal (typically gold or silver) surfaces or onto the surface of metal nanoparticles. It is the fundamental principle behind many color-based biosensor applications and different lab-on-a-chip sensors.

South America, detail off coast of Chile (above – sepia & contrast enhanced) / Oct.14, 2017.

DNA-DNA hybridization: When DNA is heated to denaturation temperatures to form single strands and then cooled double helices will re-form (renaturation) at regions of sequence complementarity. This technique is useful for determining sequence similarity among DNAs of different origin and the amount of sequence repetition within one DNA.

DNA–DNA hybridization generally refers to a molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two organisms. This has been used extensively in phylogeny and taxonomy.
The DNA of one organism is labeled, then mixed with the unlabeled DNA to be compared against. The mixture is incubated to allow DNA strands to dissociate and renewal forming hybrid double-stranded DNA. Hybridized sequences with a high degree of similarity will bind more firmly, and require more energy to separate them: i.e. they separate when heated at a higher temperature than dissimilar sequences, a process known as “DNA melting”.
To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column and the mixture is heated in small steps. At each step, the column is washed; sequences that melt become single-stranded and wash off the column. The temperatures at which labeled DNA comes off the column reflects the amount of similarity between sequences (and the self-hybridization sample serves as a control). These results are combined to determine the degree of genetic similarity between organisms. WIKI.

South America, detail off coast of Ecuador & Peru (above – sepia & contrast enhanced) / Oct.14, 2017. I call these “drippers” like they are dripping down. What would make metalized plasma drip, ooze, like a slow slime…?                                      

Localized Surface Plasmon Resonance Spectroscopy of Triangular Aluminum Nanoparticles
George H. Chan †, Jing Zhao †, George C. Schatz*, and Richard P. Van Duyne*
Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113
August 15, 2008
Copyright © 2008 American Chemical Society
The localized surface plasmon resonance (LSPR) of Al nanoparticles fabricated by nanosphere lithography (NSL) was examined by UV−vis extinction spectroscopy and electrodynamics theory. Al (aluminum) triangular nanoparticle arrays can support LSP resonances that are tunable throughout the visible and into the UV portion of the spectrum. Scanning electron microscope and atomic force microscope studies point to the presence of a thin native Al2O3 layer on the surface of the Al triangular nanoparticles. The presence of the oxide layer, especially on the tips of the nanotriangles, results in a significant red shift in the LSPR λmax. The refractive index (RI) sensitivity of the Al triangular nanoparticle arrays in bulk solvents was determined to be 0.405 eV/RIU. Theoretical results show that the oxide layer leads to a significant decrease in this RI sensitivity compared to unoxidized triangular nanoparticles of similar size and geometry.

South America, detail off coast of Ecuador & Peru (above – sepia & contrast enhanced) / Oct.14, 2017. More unnatural “tufted” cloud forms.                                 

Building plasmonic nanostructures with DNA
Shawn J. Tan, Michael J. Campolongo, Dan Luo,  & Wenlong Cheng
April 17, 2011
Plasmonic structures can be constructed from precise numbers of well-defined metal nanoparticles that are held together with molecular linkers, templates or spacers. Such structures could be used to concentrate, guide and switch light on the nanoscale in sensors and various other devices.

DNA was first used to rationally design plasmonic structures in 1996, and more sophisticated motifs have since emerged as effective and versatile species for guiding the assembly of plasmonic nanoparticles into structures with useful properties. Here we review the design principles for plasmonic nanostructures, and discuss how DNA has been applied to build finite-number assemblies (plasmonic molecules), regularly spaced nanoparticle chains (plasmonic polymers) and extended two- and three-dimensional ordered arrays (plasmonic crystals).

South America, detail off coast of Ecuador & Peru (above – sepia & contrast enhanced) / Oct.14, 2017. More unnatural ‘tufted’ cloud forms.  Detail of radio-frequency/microwave radiation charging ‘erect tuft’ clouds.

Artificial DNA and surface plasmon resonance
Roberta D’Agata and Giuseppe Spoto
April 1, 2012
The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years.

Functional and conformationally restricted DNA analogs (e.g., aptamers and PNAs) when used as components of SPR biosensors contribute to enhance the biosensor sensitivity and selectivity. At the same time, the SPR technology brings advantages that allows for better exploration of underlying properties of non-natural nucleic acid structures such us DNAzymes, LNA and HNA.
Keywords: DNAzyme, LNA, PNA, SPR, aptamer, biosensors
The advent of click chemistry1 has led to the design of DNA analogs with modified nucleobases and backbones,2 thus allowing the development of a new generation of “smart” systems useful for chemical and biological applications.3 As a consequence of those synthetic efforts DNA analogs with improved stability, functionality and binding characteristics and with properties not present in natural nucleic acids have been produced.4 The new nucleic acid analogs have been also produced with the aim to develop innovative therapeutic agents5 or new tools for diagnostics.6
Aptamers7 and DNAzymes,8 collectively referred to as functional nucleic acids, are RNA or DNA structures with binding and catalytic properties respectively. These systems have sequence-specific folds9 that achieve their tertiary folds and activities through a combination of different molecular interactions and motifs.10 Unfortunately, the use of functional nucleic acids in therapeutics has been hampered by their denaturation and/or biodegradation in body fluids. In this perspective, artificial nucleosides with unusual structural features may offer improved half-life in vivo, better structural stability, and could represent innovative systems to be used as novel interacting groups. Examples of promising non-natural nucleosides include conformationally restricted oligonucleotides such as peptide nucleic acid (PNA),11 locked nucleic acid (LNA),12 hexitol nucleic acid (HNA)13 and phosphoramidates morpholino (MORFs)14 oligomers.
Specific properties of artificial nucleosides have contributed to the development of more efficient tools for bio-sensing. In fact, artificial nucleoside probes have been used in combination with a number of different transduction platforms in order to achieve an even more sensitive and selective detection of nucleic acids and proteins.
Among the different platforms for multiplexed detection of protein markers and nucleic acids available, SPR15 has the greatest potential.16 In fact, recent improvements in instrumental and experimental design17 together with important features such as being real-time, label-free and having sensitive detection, make SPR a key technology for a wide range of potential therapeutic and diagnostic applications.18,19

The SPR phenomenon20 occurs when a plane-polarized radiation interacts with a metal film under total internal reflection conditions. At a specific incidence angle of the incoming radiation the intensity of the reflected light is attenuated. The resonance angle is dependent on the thickness and dielectric constant of both the metal film as well as its interfacing region. Keeping all the other conditions constant, the binding of molecules to the metal surface modifies the dielectric constant of the interface region, thus changing incident light/surface plasmons coupling conditions and the resonance angle. SPR experiments involve immobilizing one reactant on a metal surface (typically gold) and monitoring the reactant interaction with a second component which is typically available as a solute in a solution that flows over the sensor surface through a microfluidic cell.21
full article:


The eastern Pacific Ocean off the west coast of the USA, California, etc. (above – not enhanced) / Oct.14, 2017.                                                                               

Local Electric Field and Scattering Cross Section of Ag Nanoparticles under Surface Plasmon Resonance by Finite Difference Time Domain Method
M. Futamata,*†Y. Maruyama,‡§ andM. Ishikawa§‖
Nanoarchitectonics Research Center and Nanotechnology Materials Program, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8562, Japan, Hamamatsu Photonics Co. Ltd., and Single-Molecule Bioanalysis Laboratory, National Institute of Advanced Industrial Science and Technology, Shikoku, Takamatsu 761-0395, Japan
July 4, 2003
Local electric field and scattering cross section on Ag nanoparticles were evaluated by the FDTD (finite difference time domain) method with respect to single-molecule sensitivity (SMS) in SERS (surface-enhanced Raman scattering). As a result, (1) vast enhancement of >300-fold (in amplitude enhancement) in the SMS level was obtained at a junction between two connecting Ag particles with various shapes and sizes in addition to an edge of isolated triangular cylinders. Other sites of the connecting particles and of isolated circular and ellipsoidal cylinders gave only modest enhancement of ca. 20−30-fold. (2) The enormously large electric field at the junction rapidly decays with increasing gap sizes <1 nm, irrespective of particle size or shape. In contrast, the LSP (localized surface plasmon) extinction spectra from connecting particles gradually shift toward those from isolated particles with the gap. Thus, in addition to the dipole LSP excitation, nanostructures such as sharp edges, which yield higher order surface modes, are crucial for the vast enhancement.

Two-dimensional ordered structures do not yield any additional enhancement concerning SMS−SERS. (3) A red shift of the LSP extinction peak with decreasing height of Ag particles was reproduced only by use of three-dimensional simulation, while broadening and larger extinction at longer wavelength are given by two-dimensional calculation. (4) Blinking of SERS signal observed for dye and DNA base is most probably due to thermal diffusion of adsorbates between the junction with vast enhancement and ordinary sites with modest enhancement, which was supported by the numerical simulation and also experimentally evidenced by suppression of the phenomena at low temperature.

The eastern Pacific Ocean off the west coast of the USA, California, etc. (above – not enhanced) / Oct.14, 2017.                                                                              

Off Baja CA in the eastern Pacific Ocean off the west coast of the USA, California, etc. (above – not enhanced) / Oct.14, 2017.                                                        

Detail off Baja California in the eastern Pacific Ocean, the west coast of the USA, California, etc. (above – sepia enhanced)/ Oct.14, 2017. Note the radiation ripples in the ’tufted’ cloud shapes – just show up better in sepia, also contrast enhanced a bit.






Caterpillar-Larva clouds. Detail off Baja California in the eastern Pacific Ocean – off the west coast of the USA, California, etc. (above – sepia enhanced)/ Oct.14, 2017.







Praying mantis ‘eggs’ nest. Detail off Baja California in the eastern Pacific Ocean – off the west coast of the USA, California, etc. (above – sepia enhanced)/ Oct.14, 2017.




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