bluuebunny/crossref_metadata_2025_split huggingface dataset:
PNAand Its Applications
Authors: Ray Arghya , Nordén Bengt 
Published: September 2006

AbstractIn recent years, there has been considerable interest in developing gene‐targeting drugs. Synthetic molecules that bind effectively with high sequence specificity to a desired target in a particular “destined” gene sequence are of major interest in medicine and molecular biotechnological research. They show hope for the development of gene therapeutic agents, high‐precision diagnostic devices for genetic analysis and convenient tools for nucleic acid manipulations. Peptide nucleic acid (PNA) is a nucleic acid analog in which the sugar–phosphate backbone of natural nucleic acid has been replaced by a synthetic peptide backbone usually formed from N‐(2‐aminoethyl)glycine units resulting in an achiral and uncharged mimic. It is chemically stable and, in contrast to nucleic acids and peptides, is naturally resistant to hydrolytic (enzymatic) cleavage and thereby not expected to be degraded by cell extracts or inside a living cell. It is capable of sequence‐specific recognition of DNA and RNA obeying a Watson–Crick hydrogen bonding scheme and the hybrid complexes exhibit extraordinary thermal stability and unique ionic strength effects. It also recognizes duplex homopurine sequences of DNA to which it binds by strand invasion, forming a stable PNA·DNA–PNA triplex with a looped‐out DNA strand. This potential synthetic mimic of DNA, since its discovery in 1991, has attracted great attention within medicinal chemistry and molecular biology and also various other fields such as organic and physical chemistry because of its interesting chemical and physical properties. It has been regarded to have great potential for both diagnostic and pharmaceutical applications. In vitro studies have shown successful attempts to use PNA as an inhibitor for both transcription and translation of specific genes. This holds promise for using PNA for antigene and antisense therapy. However, the most exciting use of PNA, as an antisense or antigene drug, requires an efficient and safe method to deliver PNA into living cells, a problem that still remains to be solved.
Polycyclic Aromatic Compounds Mapping
Authors: Chakravarti Dhrubajyoti 
Published: September 2006

AbstractPolycyclic aromatic compounds (PACs) induce tumors by reacting with specific sequences of the initiating oncogene. The resulting DNA damage is converted into oncogenic mutation by in situ mutagenesis during repair or replication. The analysis of PAC/DNA reaction specificity is crucial for understanding the molecular biology of tumor initiation.The sequence specificity of PAC/DNA reactions has been analyzed by various methods. These methods detect different types of DNA‐damage lesions. For example, alkali‐labile lesions can be mapped by a chemical procedure (piperidine treatment) and bulky stable adducts can be mapped by a photochemical method (laser‐induced strand scission). Biochemical studies have identified several enzymes that act on damaged DNA and can be used for mapping the location of PAC/DNA reactions. For example, DNA lesions block the processive bypass of various enzymes (DNA polymerases, RNA polymerases and exonucleases), whereas some endonucleases (UvrABC exinuclease, S1 nuclease and apurinic/apyrimidinic (AP) endonuclease) make lesion‐specific incisions. Therefore, the sites of PAC reactions with DNA are mapped by treating PAC‐damaged DNA with these enzymes to generate lesion‐specific DNA strand breaks that are resolved by denaturing polyacrylamide gel electrophoresis. More recently, various polymerase chain reactions (PCRs) have been developed for mapping the sequence preferences of PAC/DNA reactions in vivo. These techniques include ligation‐mediated polymerase chain reactions (LMPCRs), single‐strand ligation polymerase chain reactions (SSLPCRs) and terminal transferase‐dependent polymerase chain reactions (TTDPCRs). In these methods, the PCR is used to amplify gene‐specific DNA fragments generated by chemical or enzymatic DNA lesion processing.
Restriction Landmark Genomic andcDNAScanning
Authors: Kawai Jun , Hayashizaki Yoshihide , Okazaki Yasushi , Suzuki Harukazu , Watanabe Sachihiko 
Published: September 2006

AbstractRestriction landmark genomic scanning (RLGS) is a method for the high‐speed survey of the presence or absence of restriction landmarks throughout a genome. RLGS also provides for the measurement of the copy number of restriction landmarks based on the concept that restriction enzyme sites can serve as landmarks. RLGS employs direct end‐labeling of the genomic DNA digested with a restriction enzyme and high‐resolution, two‐dimensional electrophoresis. Compared with the conventional technologies for detecting the genes, such as Southern blot analysis and polymerase chain reaction (PCR), RLGS has the following advantages even though it needs specially designed instruments: (1) high‐speed scanning ability – thousands of restriction landmarks can be scanned simultaneously; (2) applicability to any organism – RLGS employs direct labeling of restriction enzyme sites, not a hybridization procedure; (3) a spot intensity that reflects the copy number of the restriction landmarks; and (4) the ability, by using a methylation‐sensitive enzyme, to screen the methylated state of genomic DNA.RLGS is a very useful system not only for genome mapping, but also in a variety of biological and medical fields, such as cancer research and the growth and development of various organisms throughout all stages of the life cycle. RLGS can also be applied for the visualization of mRNAs [restriction landmark cDNA scanning (RLCS)]. In one procedure, RLCS can scan the expression of several hundred mRNAs.
RNA
Tertiary Structure
Authors: Westhof Eric , Auffinger Pascal 
Published: September 2006

Abstract
Ribonucleic acids are negatively charged polymers assembled from four different types of monomers. Each monomer is made of an invariant phosphorylated sugar to which is attached one of the four standard nucleic acid bases; the pyrimidines uracil and cytosine, and the purines guanine and adenine. The first level of organization is thus the sequence of bases attached to the sugar–phosphate backbone. In salty water, the RNA molecules fold back on themselves via Watson–Crick base pairing between the bases (A with U, G with C or U) leading to double‐stranded helices interrupted by single‐stranded regions in internal loops or hairpin loops. The enumeration of the base‐paired regions or helices constitutes a description of the second level of organization, the secondary structure. The methods available to deduce the secondary structure of an RNA molecule are mainly of three types: the phylogenetic approach, the theoretical prediction, and chemical/enzymatic methods. The secondary structure of an RNA molecule is experimentally accessible and its content measurable. Under appropriate conditions, structured RNA molecules undergo a transition to a three‐dimensional (3D) fold in which the helices and the unpaired regions are precisely organized in space. This folding process usually depends on the presence of divalent ions, such as magnesium ions, and on the temperature. The tertiary structure is the level of organization relevant for biological function of structured RNA molecules.
Sequencing Strategies and Tactics inDNAandRNAAnalysis
Authors: Azhikina Tatyana L. 
Published: September 2006

AbstractSequencing procedures are aimed at the determination of sequences of monomer units constituting linear biopolymer molecules. In the particular case of nucleic acids the monomer units are DNA or RNA residues. The present article reviews several sequencing strategies: different approaches (random or systematic sequencing) as well as their combinations giving the best results for long‐range sequencing applicable to long and unique DNA fragments, including entire genomes, up to the Homo sapiens genome size; massive sequencing of relatively short fragments such as RNAs, complementary DNAs (cDNAs), etc.; and comparative sequencing of related DNA fragments originating from various individuals or different species.Although particular sequencing approaches may involve different ways of DNA treatment (chemical, enzymatic, or physical), they are all based on the same idea: a labeled molecule is cut to obtain a set of fragments all having one common end, other ends being different owing to the statistical character of the nucleic acid chain cleavage. The fragments obtained are then separated according to their lengths.The primary structure of nucleic acids is a key not only to physical and chemical properties of the molecules but also to the biological (genetic) information therein, including structures of genes and proteins, the ways of gene regulation and cell response to different signals. This is a great advantage over other physical, chemical, or biological methods of DNA/RNA analysis. However, sequencing in itself is usually insufficient to predict unambiguously the biological properties and functions of the encoded products.
Diffraction in Particle Size Analysis
Authors: Novales Bruno 
Published: September 2006

Abstract
The diffraction techniques for particle size analysis are based on the measurement of the angular distribution of light diffracted by particles situated in the path of a light beam. These techniques have been used for many years to measure the size of small particulates but the calculation to generate a particle size distribution is so complex that it is only in the last 15 years with the development of small, inexpensive, and powerful computers that these techniques have become so popular. The complete theory describing the diffraction of light by a spherical particle was described by Mie in 1908 and is able to predict the electromagnetic field at any point in space. This theory is adequate for particles with diameters of the same order as the wavelength of the incident light. Some other models have been presented. The most commonly used are based on the Fraunhofer diffraction theory. Light‐scattering techniques have obvious advantages for particle size analysis as compared to other methods. They are faster than mechanical techniques, nonintrusive, nondestructive and do not require large amounts of sample. These techniques can be performed on dry powders or on suspended particles in a liquid or in a gas. The operating range of light diffraction techniques is from 20 µm to several millimeters. This article presents the main theoretical aspects of light diffraction by particles. Also, a brief description of a diffraction particle sizer is given with some practical recommendations. Problems related to particle size analysis by light diffraction are examined. Some other light‐scattering methods (photon correlation spectroscopy, single particle scattering, Doppler techniques) are also presented.
Electrozone Sensing in Particle Size Analysis
Authors: Figueiredo M. Margarida 
Published: September 2006

AbstractParticle sizing is a rapidly growing field, not only because of its importance in a great variety of technological applications but also due to its outstanding relevance to numerous areas of scientific research.The currently available instruments to measure particle‐size distributions are many and varied, the results often being dependent on the measuring technique used. It is thus essential to understand the physical principles behind each technique in order to make an adequate choice.Electrozone sensing, a widely used method of particle‐size analysis, constitutes the main topic of this paper. A general description of its operating principle is provided, followed by some practical considerations mainly concerning sample preparation and the selection of electrolyte solutions and aperture tubes. Being a technique that requires prior calibration, emphasis is placed on the calibration procedures. The section dedicated to the measurement of special materials also reviews some recent improvements of this technique. Finally, a list of commercially available equipment is supplied, together with its most relevant features.
Field‐Flow Fractionation in Particle Size Analysis
Authors: Janča Josef 
Published: September 2006

Abstract
Field‐flow fractionation (FFF) is an analytical methodology suitable for the separation and characterization of macromolecules within a wide range of molar masses, and for particles in submicrometer and micrometer ranges. The separation is based on the action of effective physical or chemical forces across the separation channel. The field forces interact with the separated species and concentrate them at the appropriate position inside the channel. The resulting concentration gradient induces an opposite diffusion flux. This process leads to a quasi‐steady‐state distribution of the affected sample components across the channel. The velocity of the longitudinal flow of the carrier liquid also varies across the channel. A parabolic flow velocity profile is usually established inside the channel. The components of the separated sample are transported in the longitudinal direction inside the channel at different velocities, depending on the transverse positions of the zones of the sample components within the flow of the carrier liquid.
The separation is performed in one liquid phase. This is of fundamental importance for the fractionation and particle size analysis of biological samples, which can be sensitive to the type and intensity of the interaction with the surfaces and can denaturate. Steady‐state inside the channel is usually reached within a short time due to a small channel thickness. The simplicity of the channel construction permits an accurate description of the separation processes.
The field strength can be controlled over a wide range. Many operational variables in FFF can be manipulated during the experiment by suitable programming.
Accurate analytical results can be obtained from FFF by correct treatment and interpretation of the experimental data. If the relationship between the retention parameters and the characteristics of the separated particles is known, or can be predetermined by using an appropriate calibration procedure, the characteristics of an unknown analyzed sample can be evaluated quantitatively. The particle size distribution (PSD) of the analyzed sample then is determined from a fractogram.
Light Scattering, Classical: Size and Size Distribution Characterization
Authors: Berry Guy C. 
Published: September 2006

Abstract
The use of classical, or time‐averaged, light scattering methods to characterize the size and size distribution of macromolecules in dilute solutions or particles in dilute dispersions is discussed. The necessary scattering relations are presented systematically, starting with three cases at infinite dilution: the scattering extrapolated to zero angle, the scattering at small angle, and the scattering for arbitrary angle, including the inversion of the scattering data to estimate the size distribution. The relationships needed to effect an extrapolation to infinite dilution from data on dilute solutions are also discussed. These are followed by remarks on light scattering methods, and the concluding sections give examples for several applications. The Rayleigh–Gans–Debye (RGD) approximation is usually appropriate in the scattering from dilute polymer solutions and is also adequate for the scattering from dilute dispersions of small particles. The approximation is assumed when appropriate, but more complete theories are introduced where necessary, as in the use of the Mie–Lorentz theory for large spherical particles.
Sieving in Particle Size Analysis
Authors: Dishman Karla L. 
Published: September 2006

Abstract
Sieve analysis is used to obtain the particle size distribution of a solid material by determining the amount of powder retained on a series of sieves with different sized apertures. A sample is added to the top of a nest of sieves arranged in decreasing size from top to bottom. As the sieves are vibrated, the sample is segregated onto the different sized sieves. The weight of sample retained on each sieve is then used to determine the particle size distribution as well as the mean diameter of the sample.
Turbidimetry in Particle Size Analysis
Authors: Kourti Theodora 
Published: September 2006

AbstractThe size of particles in a suspension can be estimated by measuring the turbidity of the suspension. Turbidity measures the attenuation of a beam of light traveling through the suspension caused by the scattering and absorption of light by the particles. The amount of scattering and absorption depends on the size of the particles and their concentration in the suspension. Most of the reported applications in the literature use turbidimetry for the estimation of the particle size distribution (PSD) or an average size for particles with diameters ranging from 0.035 to 50 µm. Turbidimetric techniques are low cost, experimentally simple, fast, nondestructive and require no calibration. They are robust methods with very good reproducibility and can be used either off‐ or on‐line, in a laboratory or a plant environment. They have been used for particle or droplet size determination in a variety of diverse systems such as latex particles, silver bromide sols and cow's milk. Most of the time common ultraviolet/visible (UV/VIS) spectrophotometers are utilized for the turbidity measurements. Certain modifications may be necessary on these instruments depending on the size of the particles. The turbidity of the suspension is measured and the size of the particles or the PSD is estimated utilizing light scattering theory. For spherical isotropic homogeneous particles and absence of multiple scattering this theory is well established. The extension to nonspherical and inhomogeneous particles is a field of active research yielding numerous publications.A controversy existed in the literature regarding the capability of turbidimetry to provide the full PSD but has now been resolved. For polydisperse suspensions, for certain combinations of particle sizes and optical properties, the method cannot provide the full PSD, but only an average of the PSD. This limitation is simply a result of the light scattering patterns and it is expected theoretically. In some cases it can be overcome by simply altering the optical properties of the suspension (i.e. choosing the proper wavelengths for the turbidity measurements or a medium with a different refractive index to suspend the particles). To make the best use of the method and interpret the results in a meaningful way one should be aware of this limitation and work with it. When this is done, excellent results can be achieved. The advantages of the method and a good knowledge of its capabilities make it a very robust choice for many applications. The numerous reports from the successful application of the method are a testimony to this.
Velocimetry in Particle Size Analysis
Authors: Farrell Patrick V. 
Published: September 2006

Abstract
Velocimetry in particle size analysis encompasses the range of issues and methods used to measure particle velocities consistent with particle size measurement systems. Particle size may be measured simultaneously or consecutively with the velocity measurements described in this article. This article will present some issues that should be considered in selection of a velocity measurement technique. Three examples of commonly used particle velocity methods will be discussed as illustrations of possible approaches. For each of these examples, a brief discussion of advantages and limitations of the methods will also be presented.
Capillary Electrophoresis in Peptide and Protein Analysis, Detection Modes for
Authors: Weber Paul L. 
Published: September 2006

Abstract
Capillary electrophoresis (CE) is a highly efficient separation technique which achieves high resolution with low sample consumption. Crucial to any separation technique are detection modes capable of giving useful data about separated analytes, including both quantitative and qualitative information. A variety of general detection modes for CE have been developed, most based on similar systems used in high‐performance liquid chromatography (HPLC), but only some are useful in the analysis of peptides and proteins. Modes which are selective for certain spectral or chemical properties of these analytes are often employed. The absorption of ultraviolet/visible (UV/VIS) light as well as fluorescence (Fl) fit into the former category while electrochemical (EC) detection falls under the latter. The development of mass spectrometry (MS) as a detection mode for peptide and protein analysis may be the ideal choice since a great deal of qualitative information can be obtained and used for identification and structural characterization. By definition, CE involves separation in a “micro” environment, a capillary, and this places certain demands on the performance of the detection system and perhaps the greatest challenge is that of sensitivity.
Capillary Electrophoresis/Mass Spectrometry in Peptide and Protein Analysis
Authors: Tomlinson Andy J. , Naylor Stephen 
Published: September 2006

AbstractThe focus of this article is to describe the developments of capillary electrophoresis (CE) on‐line with detection by mass spectrometry (MS) for the analysis of peptides and proteins. Following a brief introduction in which we discuss the increasing role of the mass spectrometer for characterizing these important biomolecules, we present a historical overview of capillary electrophoresis/mass spectrometry (CE/MS). The latter discussion describes the experiments that allowed the connection of CE with MS, through developments to increase the volumes of analyte solutions that can be analyzed, to the current investigations of microfabricated chips that bring CE/MS towards a nano‐scale technology. We also consider the technical aspects of CE/MS, which include how to inject analyte mixtures into the capillary, ways to improve the concentration sensitivity of the technique, the optimal capillary surface technology to use, and considerations of buffer compositions that are compatible with on‐line MS detection. Other practical issues, including the physical connection between the CE and MS components, along with sample preparation and sequencing peptides by this technology are also reviewed. In the final section, the future of CE/MS is contemplated, with particular emphasis on the current developments of nanotechnologies that include the interfacing of microchip‐based CE with MS.
F
ourier Transform Infrared Spectroscopy in Peptide and Protein Analysis
Authors: Fabian Heinz , Schultz Christian P. 
Published: September 2006

Abstract
Infrared (IR) spectroscopy is one of the two forms of vibrational spectroscopy, the other being Raman spectroscopy. IR spectroscopy measures absorptions of vibrating molecules and yields information about molecular structures and structural interactions. The development of computerized Fourier transform infrared (FTIR) techniques has opened up new dimensions in biological IR spectroscopy owing to the increase in achievable signal‐to‐noise ratios, wavenumber accuracy, and data aquisition rates, and the ability to perform measurements with strongly absorbing samples. High‐quality FTIR spectra can be obtained with relative ease and rapidly with very small amounts of sample in a variety of environments. Measurements of proteins in aqueous solution are almost routine now, and can be performed under equilibrium and nonequilibrium conditions. There are many IR absorption bands characteristic of peptide groups and amino acid side‐chain groups from which information on protein structures can be obtained. The information provided by FTIR spectroscopy may be a global one or highly specific for a single vibrating chemical group. In some cases, the usefulness of the method is limited by difficulties in extracting the structural information contained in the IR absorption bands.