Denaturation: Denaturation,, in biology, process modifying the molecular structure of a protein. Denaturation involves the breaking of many of the weak linkages, or bonds (e.g., hydrogen
The denaturation of proteins occurs when high temperatures or chemical interactions destroy both their secondary and tertiary structures. Denaturation processes are not actually strong enough to...
I think I can respond to that challenge given a more realistic starting point. Lets say I isolate a protein and have some amino acids sequenced. Say it is known to be associated with a certain biological function say heat shock response (you know the process by which living organisms are able to survive stress when they normally wouldnt due to the protection from protein denaturation). Lets say I have no idea what my protein is. Could alternatively be an interesting mRNA or genomic DNA or a candidate gene in a QTL region - doesnt matter - just something that I know is associated with a process of interest. Lets say I get this protein sequence data, and probe a cDNA library (or do a northern or southern in the other cases) now I have the DNA sequence from which my gene/sequence is transcribed from. I may know how many copies the gene has etc...Lastly, I do a database search and get a set of homologous genes and their alignment. 1) I now know what species the gene is most closely related to, ...
Bendazac, as such or in the form of its l-lysine salt, has a protective effect against lens protein denaturation both in vitro… Expand ...
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TY - GEN. T1 - Sensitivity enhancement of leakage current microsensor for detection of target protein by using protein denaturant. AU - Lorchirachoonkul, P.. AU - Yamashita, K.. AU - Noda, M.. AU - Shimanouchi, Toshinori. AU - Umakoshi, H.. AU - Kuboi, R.. PY - 2010. Y1 - 2010. N2 - We have developed a highly-sensitive leakage current microsensor by using 1,2-dipalmitoyl-sn-glycero-3-phosphocholline (DPPC) liposome entrapping K 4[Fe(CN)6] solution to detect existence of biomolecules especially proteins and their dynamic conditions. In this work, the addition of guanidinium hydrochloride (GuHCl) as protein denaturant successfully leads a prominent improvement in sensitivity by 129-fold of magnitude, although target protein, which is carbonic anhydrase from bovine (CAB), weakly interacts with liposome under the normal condition. Moreover, we can use it to evaluate the conformation state of CAB protein such as Native, Molten-Globule and Unfold states and we can use this leakage current ...
Cyclic PNAs targeting the HIV-1 TAR RNA loop have been synthesized following a convenient solid-phase strategy which allows on-resin cyclisation. UV-monitored thermal denaturation studies demonstrate that these cyclic PNAs are able to strongly interact with their TAR RNA target, very likely through the formation of a six-base pair stable complex, involving the TAR RNA loop.
article{59bb1196-24eb-433d-9855-9f47e2375da3, abstract = {Unlike most ordered molecular systems, globular proteins exhibit a temperature of maximum stability, implying that the structure can be disrupted by cooling. This cold denaturation phenomenon is usually linked to the temperature-dependent hydrophobic driving force for protein folding. Yet, despite the key role played by protein−water interactions, hydration changes during cold denaturation have not been investigated experimentally. Here, we use water−17O spin relaxation to monitor the hydration dynamics of the proteins BPTI, ubiquitin, apomyoglobin, and β-lactoglobulin in aqueous solution from room temperature down to −35 °C. To access this temperature range without ice formation, we contained the protein solution in nonperturbing picoliter emulsion droplets. Among the four proteins, only the destabilized apomyoglobin was observed to cold denature. Ubiquitin was found to be thermodynamically stable at least down to −32 °C, ...
The denaturation of bovine serum albumin (BSA) by guanidine hydrochloride (GdnHC1) showed a single-step, two-state transition, when monitored by different probes such as intrinsic fluorescence at 338 and 333 nm after excitation at 280 and 295 nm respectively, UV difference spectral signal at 288 nm, 1-anilinonaphthalene-8-sulphonate (ANS) fluorescence at 470 nm after excitation at 380 nm, bromophenol blue (BPB)-induced difference spectral signal at 619 nm and A.,„„ of positive difference spectral signal of BPB-BSA complex. A comparison of the denaturation curves obtained with the above mentioned probes showed differences in the requirement of GdnHC1 concentration• for the transition to start and complete. The values for the mid-point of denaturation transition and free energy change associated with GdnHC1 denaturation (AG Du2o.) also varied from each other, using different probes ...
Proteins are stable in their compact, folded structures only in a narrow range of physiological conditions. Deviation from these conditions, such as changes in temperature and salt concentrations, can destabilize the folded structures. Investigating the mechanism(s) of protein denaturation induced by these extreme conditions has a fundamental importance in understanding of the evolution of organisms with extreme habitats and formulating effective long-term preservation strategies for biological therapeutics. Using replica-exchange molecular dynamics simulations, we examine the mechanisms of cold- and salt-induced denaturation of a fully-atomistic model of the Trp-cage miniprotein, and we make direct comparison with the unfolding behavior at high temperatures. In contrast to the complete unraveling of the secondary and tertiary structures observed during heat denaturation, the cold-denatured structure of the Trp-cage is compact and partially folded with stable alpha-helix, despite the loss of ...
Using a newly developed microsecond pressure-jump apparatus, we monitor the refolding kinetics of the helix-stabilized five-helix bundle protein λ*YA, the Y22W/Q33Y/G46,48A mutant of λ-repressor fragment 6-85, from 3 μs to 5 ms after a 1,200-bar P-drop. In addition to a microsecond phase, we observe a slower 1.4-ms phase during refolding to the native state. Unlike temperature denaturation, pressure denaturation produces a highly reversible helix-coil-rich state. This difference highlights the importance of the denatured initial condition in folding experiments and leads us to assign a compact nonnative helical trap as the reason for slower P-jump-induced refolding. To complement the experiments, we performed over 50 μs of all-atom molecular dynamics P-drop refolding simulations with four different force fields. Two of the force fields yield compact nonnative states with misplaced α-helix content within a few microseconds of the P-drop. Our overall conclusion from experiment and simulation ...
Double stranded nucleic acid is denatured by subjecting a solution thereof to a voltage applied between electrodes spaced by no more than 1.5 mm in a time not previously achievable in electrochemical denaturation. PCR is practiced isothermally by periodic application of voltage to produce denaturation. Electrochemical cells and kits for use in the process are provided.
Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomis 2017 PCCP HOT Articles
ICS-3 Group seminar Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation ...
Callupeel is used for the effective removal of the feets thick outer layer and stubborn calluses through protein denaturation. The skin may produce excessive k
Denaturation Protein molecules carry out many important tasks in living systems. Most important, the majority of proteins are quite specific about which task they perform.
On 25 Oct 93 22:25:12 GMT, Dave Knecht writes: ,Hi Netters- I have read recently several times about denaturation of dsDNA wit ,h NaOH and reference is made to the fact that the hybrids do not reform. Does ,anyone know the basis of this statement. I am particularly confused because we , have always base denatured DNA before transfer to Nylon for Southerns and then , base denatured the probe for the hybridization. According to this dogma, the ,blot should not work, but of course it does! Dave Maybe there is a confusion here as to the modes of action: NaOH is used: (1) to denature plasmids for sequencing. I always understood that this was iriversible since by pulling apart the strands somewhere in a supercoil you get even more extensive coiling elsewhere and the plasmid basically tied itself into an untangleable knot with some accessible single stranded bits and other inaccesible hyperknotted bits. This would affect different regions on different plasmid molecules, hence there would always be ...
The three-state model of Dunham et al. 1993 is among the simplest mechanisms containing more than one event in the activation-inactivation process. However, m
This is a 9 level Heretic wad designed for single/cooperative play. Have fun, and be sure to use the proper DMFLAGs listed below if you are playing on cooperative mode. 1-6 players should be the limit. Story: IN AN EPIC TURN OF EVENTS, the Overlords of Fruit have rallied their unequaled forces of...
Intrinsically disordered proteins (IDPs) lack stable structures under physiological conditions but often fold into stable structures upon specific binding. These coupled binding and folding processes underlie the organization ...
The guanidinium chloride (GdmCl) denaturation of RNAase A, lysozyme and metmyoglobin was investigated at several pH values by using absorbance measurements at 287, 300 and 409 nm respectively. From these measurements the free-energy change on denaturation, delta Gapp., was calculated, assuming a two-state mechanism, and values of delta Gapp. at zero concentration of the denaturant were measured. For each protein all delta Gapp. values were adjusted to pH 7.00 by using the appropriate relationship between delta Gapp. and pH. Dependence of the adjusted delta Gapp. value on GdmCl concentration increases for metmyoglobin and decreases for the other two proteins as the denaturant concentration decreases. It has been shown that these are expected results if the presence of the acid-denatured state during the GdmCl denaturation of proteins is considered. ...
The chaperone-like protein alpha-crystallin is a approximately 35 subunit hetero-oligomer consisting of alphaA and alphaB subunits in a 3:1 molar ratio and has the function of maintaining eye lens transparency. We studied the thermal denaturation of alpha-crystallin by differential scanning calorimetry (DSC), circular dichroism (CD), and dynamic light scattering (DLS) as a function of pH. Our results show that between pH 7 and 10 the protein undergoes a reversible thermal transition. However, the thermodynamic parameters obtained by DSC are inconsistent with the complete denaturation of an oligomeric protein of the size of alpha-crystallin. Accordingly, the CD data suggest the presence of extensive residual secondary structure above the transition temperature. Within the pH range from 4 to 7 the increased aggregation propensity around the isoelectric point (pI approximately 6) precludes observation of a thermal transition. As pH decreases below 4 the protein undergoes a substantial unfolding. ...
High sensitivity differential scanning calorimetry (d.s.c.) and uv-visible spectrophotometry have been used to study the thermal unfolding of alpha-chymotrypsin in presence of calcium chloride at pH = 2.8, 3.4, 5.0, 7.0, and 8.2. Quantitative thermodynamic parameters accompanying the thermal transitions have been evaluated. In the absence of calcium ions, the thermal denaturation of a-chymotrypsin is a reversible process giving a ratio of the vant Hoff to calorimetric enthalpy of 0.92 at pH = 2.8. At pH values higher than 5.0, the thermal denaturations in the absence of calcium chloride were observed to be completely irreversible. In the presence of calcium chloride, alpha-chymotrypsin undergoes irreversible thermal denaturation and its thermal transitions are found to be scan-rate dependent fitting to the model N-2 --, I, yielding an average activation energy of (419 +/- 16) kJ (.) mol(-1) using different approaches at pH = 2.8. It is also observed that at pH 2.8 and 3.4, calcium reduces the ...
Transmembrane α-helical proteins are unusually stable judging from thermal denaturation studies, because they do not unfold completely within the membranes (the complete unfolding would require breaking down too many α-helical H-bonds in the nonpolar media). On the other hand, these proteins easily misfold, due to non-native aggregation in membranes, transition to the molten globule states, formation of non-native disulfide bonds, or unfolding of peripheral regions and nonregular loops that are locally less stable. It is also important to properly define the unfolded state. The unfolded state of membrane proteins in detergent micelles is different from that in the thermal denaturation experiments. This state represents a combination of folded hydrophobic α-helices and partially unfolded segments covered by the detergent. For example, the "unfolded" bacteriorhodopsin in SDS micelles has four transmembrane α-helices folded, while the rest of the protein is situated at the micelle-water ...
Refolding of proteins is traditionally carried out either by diluting the denaturant-unfolded protein into buffer (GdmCl-jump) or by mixing the acid-denatured protein with strong buffer (pH-jump). The first method does not allow direct measurement of folding rates in water since the GdmCl cannot be infinitely diluted, and the second method suffers from the limitation that many proteins cannot be pH-denatured. Further, some proteins do not refold reversibly from low pH where they get trapped as aggregation prone intermediates. Here, we present an alternative approach for direct measurement of refolding rates in water, which does not rely on extrapolation. The protein is denatured in SDS, and is then mixed with -cyclodextrin, which rapidly strips SDS molecules from the protein, leaving the naked unfolded protein to refold.. ...
Within the framework of the Peyrard-Bishop model for DNA melting, sharp denaturation temperature profiles can currently be obtained only if anharmonic base-pair stacking interactions are considered. We show that, when solvent interactions are included, a sharp denaturation of the DNA double helix is obtained without the need for anharmonic nearest-neighbor interactions. Using the concept of pseudo-Schrodinger equations we discuss the analogy of these transition to quantum-mechanical tunneling, and in particular we show that the sharp transitions are similar to resonant tunneling.. Full text not available from this repository.. ...
... , the crystalline compound of strong alkalinity formed by the oxidation of guanine, is a normal product of protein metabolism and a protein denaturant.
Certain bacterial species produce extracellular enzymes that lyse red blood cells in the blood agar (hemolysis). These hemolysins (extotoxin) radially diffuses outwards from the colony (or colonies) causing complete or partial destruction of the red cells (RBC) in the medium and complete denaturation of hemoglobin within the cells to colorless products.. Four types of hemolysis are produced in sheep blood agar by Streptococci namely; alpha hemolysis, beta hemolysis, gamma hemolysis and alpha prime or wide zone alpha hemolysis.. Hemolysis is best observed by examining colonies grown under anaerobic conditions or inspecting sub-surface colonies.. ...
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Yadav, Subhash Chandra, Prasanna Kumari, N. K. and Jagannadham, Medicherla V. 2010, Deglycosylated milin unfolds via inactive monomeric intermediates, European biophysics journal, vol. 39, no. 12, pp. 1581-1588, doi: 10.1007/s00249-010-0615-x. ...
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थोक चीन से नाइट्रो Guanidine , लेकिन कम कीमत के अग्रणी निर्माताओं के रूप में सस्ते नाइट्रो Guanidine खोजने की आवश्यकता है। बस नाइट्रो Guanidine पर उच्च गुणवत्ता वाले ब्रांडों पा कारखाना उत्पादन, आप आप क्या चाहते हैं, बचत शुरू करते हैं और हमारे नाइट्रो Guanidine का पता लगाने के बारे में भी राय, आप में सबसे तेजी से उत्तर हम करूँगा कर सकते हैं ...
In its native state, which of the following elements has bonds between many cations and a sea of valence electrons? Cl He Zn...
usr/bin/env python import numpy import scipy from scipy import optimize wt_CD = scipy.array([-46.396, -46.43 , -46.082, -46.159, -46.169, -45.949, -45.896, -45.78 , -45.7 , -45.434, -45.19 , -45.084, -44.374, -43.963, -43.265, -42.12 , -40.694, -38.897, -36.468, -33.651, -30.485, -26.564, -23.369, -21.652, -20.149, -18.564, -17.223, -15.661, -14.473, -13.155, -12.688, -11.335, -11.297, -10.525, -10.013, -9.199, -8.816, -8.388, -8.499, -7.707, -7.329, -7.355, -6.688, -6.782, -6.789, -6.37 , -5.944, -5.817, -5.719, -5.545, -5.651, -5.692, -4.971, -5.184]) wt_m0 = scipy.array([ 0. , 0.3, 0.6, 0.9, 1.2, 1.5, 1.8, 2. , 2.2, 2.4, 2.6, 2.8, 3. , 3.2, 3.4, 3.6, 3.8, 4. , 4.2, 4.4, 4.6, 4.8, 5. , 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6. , 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, 7. , 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8. , 8.1]) def denmeltfit(CDsignal, m0): import numpy import scipy from scipy import optimize # define equation for denaturant melt fit # m0 = denaturant ...
The 3M Value Index Score (VIS) is a population-centric value measure that complements existing quality and total cost-of-care (TCC) metrics.
Background: Champedak galactose-binding (CGB) lectin is a tetrameric protein with noncovalently bound monomers, isolated from Artocarpus integer fruit seeds. We had previously reported existence of a structured monomer and an unfolded monomer of CGB lectin at pH 2.5 and pH 1.5, respectively. Polyols are known to induce significant refolding in denatured proteins and stabilize proteins against environmental stresses. Studies on the effect of various polyols on the acid-denatured states of CGB lectin are lacking. Objective: The objective of this study was to investigate the effects of four different polyols, namely, ethylene glycol, erythritol, xylitol and sorbitol on the acid-denatured states of CGB lectin. Methods: CGB lectin was subjected to acid denaturation at pH 2.5 and pH 1.5, both in the absence and presence of 30% (w/v) polyols, i.e. ethylene glycol, erythritol, xylitol and sorbitol. Thermal denaturation of the acid-denatured states was also studied in the absence and presence of these ...
The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was studied using differential scanning calorimetry and circular dichroism spectroscopy. Analytical ultracentrifugation and gel filtration showed that Ssh10b is a stable dimer in the pH range 2.5-7.0. Thermal denaturation data fit into a two-state unfolding model, suggesting that the Ssh10 dimer unfolds as a single cooperative unit with a maximal melting temperature of 99.9 degrees C and an enthalpy change of 134 kcal/mol at pH 7.0. The heat capacity change upon unfolding determined from linear fits of the temperature dependence of DeltaH(cal) is 2.55 kcal/(mol K). The low specific heat capacity change of 13 cal/(mol K residue) leads to a considerable flattening of the protein stability curve (DeltaG (T)) and results in a maximal DeltaG of only 9.5 kcal/mol at 320 K and a DeltaG of only 6.0 kcal/mol at the optimal growth temperature of Sulfolobus.
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Population fI of the molten globule state of apomyoglobin mutants.Dependency of the population fI of the molten globule state versus urea concentration for apom
Ebook How To Avoid Protein Aggregation :: Figure 1 cellular strategies for controlling protein, Evolutionary selection for protein aggregation, Lea proteins prevent protein aggregation due to water, Refolding of inclusion body proteins from e coli, Protein aggregation which method of detection do you prefer, Er stress causes widespread protein aggregation and prion, Protein aggregation in neurodegenerative disease to be, Amyotrophic lateral sclerosis ppt video online download, Protein aggregation urea all about ketogenic diet, Physical and chemical properties of proteins denaturation
Lydias main research interests are directed at improving functional properties of food proteins and proteins derived from food waste. There is a demand in the food industry for protein-based fat replacers as well as replacement of costly dairy-based protein ingredients by low cost plant-based proteins. Lydia is in involved in modifying functional properties such as solubility, binding, foaming, thickening and gelling properties by heat-induced denaturation and/or glycation with sugars and oligosaccharides via the Maillard reaction. Nano-particles are generated by denaturation and polymerisation/aggregation and particle size is controlled by technology based on monitoring of light scattering. Soluble fibres (oligosaccharides) extracted from pulses, dates and seeds are extracted and characterised by HPLC and protein-fiber conjugates are formed by controlled denaturation and glycation. The physicochemical properties of the compounds are studied using proteomic techniques such as SDS PAGE and ...
The genome of Mycobacterium tuberculosis encodes for 11 pairs of Esx family proteins such as EsxA/EsxB and EsxO/EsxP that are located in pairs within the genome. Despite the clear importance of the Esx family proteins in mycobacterial virulence and pathogenesis, the precise molecular functions and mechanisms of action for these proteins remain unknown. Initially expression vectors carrying EsxO and EsxP were constructed and used to express these proteins as inclusion products. The inclusion bodies of both proteins were successfully resolubilized and co-refolded. The final purification step by gel filtration chromatography shows that these proteins form a tight 1:1 heterodimeric complex. Analysis using circular dichroism (CD) spectroscopy of the purified refolded complex showed that it contained a high helical content (53%). The complex showed a significant resistance to heat-induced denaturation with co-operative denaturation observed that indicates a stable folded structure. In addition, ...
This is because the Gibbs free energy also depends on the concentration of the reactants and products. Hence, for a reaction, if the energy change is negative it moves forwards, forming more product, which also changes the concentrations of the species involved. The Gibbs energy change at this new concentration will be less negative than that in the initial case, but the reaction still proceeds since the reaction is accompanied by a negative change of free energy.. A point comes, where the concentrations of the reactions and the products is such, that the Gibbs energy change now becomes zero for the particular reaction. This is the equilibrium condition (minimum free energy, maximum entropy). If the energy change is positive, the reverse reaction becomes favorable, again inching towards the zero energy change condition, i.e. equilibrium. So, the reaction is already at the minimum Gibbs energy when it is at equilibrium. Further proceeding of the reaction will be accompanied by a positive change, ...
Ken Houk has produced a very nice minireview on bifurcations in organic reactions.1 This article is a great introduction to a topic that has broad implication for mechanistic concepts. Bifurcations result when a valley-ridge inflection point occurs on or near the intrinsic reaction coordinate. This inflection point allows trajectories to split into neighboring basins (to proceed to different products) without crossing a second transition state. In the examples discussed, the reactant crosses a single transition state and then leads to two different products. This is the so-called "two-step no intermediate" process.. I discuss the implications of these kinds of potential energy surfaces, and other ones of a pathological nature, in the last chapter of my book. Very interesting reaction dynamics often are the result, leading to a mechanistic understanding far from the ordinary!. ...
DTT or Clelands Reagent reduces disulfides to their corresponding thiols. It is used at low concentrations to stabilize enzymes containing free sulphydryl groups. Higher concentrations of DTT are used to cleave disulphide linkages in polypeptides and to facilitate protein denaturation by detergents or chaotropic agents. ...
A commercially available zooblot containing 8 μg of EcoRI-digested genomic DNA isolated from various species (human, monkey, rat, mouse, dog, cow, rabbit, chicken, and yeast) was purchased (BD Biosciences-Clontech, Palo Alto, CA). A 376-bp DNA probe corresponding to exon 6 of the human ELOVL4 gene was generated from a genomic DNA template by polymerase chain reaction (PCR), with primers 5′-GAAGATGCCGATGTTGTTAAAAG-3′ and 5′-GTCAACAACAGTTAAGGCCCA-3′. PCR cycling parameters used were as follows: 1 cycle of denaturation at 94°C for 3 minutes; 30 cycles of denaturation at 94°C for 30 seconds, primer annealing at 55°C for 30 seconds, primer extension at 72°C for 40 seconds; and 1 cycle of extension at 72°C for 3 minutes. A probe corresponding to ELOVL4 coding regions was also generated by total cDNA synthesis with a commercial kit (Invitrogen Canada, Inc., Burlington, Ontario, Canada) and 5 μg of human retina total RNA as template, followed by PCR using 100 ng total cDNA template with ...
Despite the emerging importance of human P450 2B6 in xenobiotic metabolism, thorough biochemical and biophysical characterization has been impeded as a result of low expression in Escherichia coli. Comparison with similar N-terminal truncated and C-terminal His-tagged constructs (rat P450 2B1dH, rabbit 2B4dH, and dog 2B11dH) revealed that P450 2B6dH showed the lowest thermal stability, catalytic tolerance to temperature, and chemical stability against guanidinium chloride-induced denaturation. Eleven P450 2B6dH mutants were rationally engineered based on sequence comparison with the three other P450 2B enzymes and the solvent accessibility of residues in the ligand-free crystal structure of P450 2B4dH. L198M, L264F, and L390P showed ∼3-fold higher expression than P450 2B6dH. L264F alone showed enhanced stability against thermal and chemical denaturation compared with P450 2B6dH and was characterized further functionally. L264F showed similar preferential inhibition by pyridine over imidazole ...
For more than fifty-five years the air in a comparatively quiet but progressively decaying area of Queens just outside Jamaica, reverberated to the thunder of horses hooves as they beat around an elliptical course known as the Jamaica Race Track. Then progress in the form of a population-explosion out stripped the facilities of the Jamaica track, and on August 1, 1959 the last race was run at Jamaica. The possibilities of erecting a large housing development on the 170 acre site of the Jamaica track was the vision of Robert Moses, the then Chairman of the Slum Clearance Committee and City Construction Coordinator. The Jamaica Race Track was demolished in 1960 to make way for the complex, which was built for $ 86 million as a middle income cooperative.. Since Rochdale Village was to be the largest single cooperative housing community ever to be undertaken at that time, considerable thought was given to endowing it with an appropriate name. Because it was expected that the development would set a ...
For more than fifty-five years the air in a comparatively quiet but progressively decaying area of Queens just outside Jamaica, reverberated to the thunder of horses hooves as they beat around an elliptical course known as the Jamaica Race Track. Then progress in the form of a population-explosion out stripped the facilities of the Jamaica track, and on August 1, 1959 the last race was run at Jamaica. The possibilities of erecting a large housing development on the 170 acre site of the Jamaica track was the vision of Robert Moses, the then Chairman of the Slum Clearance Committee and City Construction Coordinator. The Jamaica Race Track was demolished in 1960 to make way for the complex, which was built for $ 86 million as a middle income cooperative.. Since Rochdale Village was to be the largest single cooperative housing community ever to be undertaken at that time, considerable thought was given to endowing it with an appropriate name. Because it was expected that the development would set a ...
The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding.s profile, publications, research topics, and co-authors
Temperature Controlled Demountable Liquid Cells are intended for transmission measurements of liquids and mulls at temperatures ranging from -80°C to 240°C. These leak-free transmission cells are designed for both static and flow operation. In addition, these 316 stainless steel transmission cells feature high chemical resistance and readily exchanged pathlength spacers.. The BioATRCell II is a micro-ATR unit that was specially developed in a partnership between Harrick Scientific and Bruker Optics. It is a powerful and sensitive tool for investigating temperature induced unfolding, refolding and denaturation processes of proteins in aqueous media and membrane-standing proteins. It can be applied for aqueous protein solutions and also for membrane-standing proteins. Available only through Bruker Optics. http://www.bruker.com/products/optical-spectroscopy/ft-ir-spectrometers-.... ...
The dimeric nature of triosephosphate isomerases (TIMs) is maintained by a thorough surface area interface of more than 1600 ?2. to dissociate the dimer. Herein we found that the character of residue I45 controls the dimer-monomer equilibrium in TvTIMs. Unfolding experiments employing monomeric and dimeric mutants led us to conclude that dimeric TvTIMs unfold following a four state model denaturation process whereas monomeric TvTIMs follow a three state model. In contrast to other monomeric TIMs monomeric variants of TvTIM1 are stable and unexpectedly one of them (I45A) is only 29-fold less active than wild-type TvTIM1. The high enzymatic activity of monomeric TvTIMs contrast with the marginal catalytic activity of diverse monomeric TIMs variants. The stability of the monomeric variants of TvTIM1 and the use of cross-linking and analytical ultracentrifugation experiments permit us to understand the differences between the catalytic activities of TvTIMs and other marginally active monomeric TIMs. ...
Students from Miami and Muldrow High Schools were the top winners in the Oklahoma State Science and Engineering Fair held March 25-27 at East Central University in Ada.. Miami High Schools Ban He, a senior, and Jennifer Spillars,a sophomore, received the $500 Best of Fair Award in the Senior High Division for their team project, "Evaluating Novel Methods for Reversing the Denaturation Process in Catalase." ...
Students from Miami and Muldrow High Schools were the top winners in the Oklahoma State Science and Engineering Fair held March 25-27 at East Central University in Ada.. Miami High Schools Ban He, a senior, and Jennifer Spillars,a sophomore, received the $500 Best of Fair Award in the Senior High Division for their team project, "Evaluating Novel Methods for Reversing the Denaturation Process in Catalase." ...
or denaturating conditions with a lysis buffer such as PBS containing guanidine hydrochloride 6M or urea 8M pH 8.0 for example, with or without beta-mercaptoethanol (approx. 1% v/v). In this case, the buffer A (step 1) can be replaced by PBS buffer containing guanidine hydrochloride 6M pH 8.0 and the steps 4, 6, 7 and 8 are not yet necessary. The buffers E & F can contain beta-mercaptoethanol. ...
Mines are man made and inherently a higher risk environment than the vast majority of natural caves. A cave is formed over a long period of time and its intrinsic stability is due to this. Mines are cavities excavated over a relatively short time period and not there because of any natural process. ...
Downloadable (with restrictions)! Investment is often irreversible: once installed, capital has little or no value unless used in production. This paper proposes and solves a model of sequential irreversible investment and characterizes the aggregate implications of microeconomic irreversibility and idiosyncratic uncertainty. If a large amount of idiosyncratic uncertainty is allowed for, the distributional dynamics induced by the nonlinear character of irreversible investment policies are capable of smoothing the dynamics of aggregate investment (relative to those of its forcing processes) to the extent required by U.S. data.
In a previous report (J. Fluoresc. 16, 153, 2006) we studied the chaotropiclly induced denaturation of Bovine Serum Albumin (BSA) using the fluorescence decay kinetics at different stages in the denaturation of BSA by ...
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Living beings are not isolated systems. Although apparently living organisms violate the second law of thermodynamics, they do not.
you can renature the protein (most of the time) by equilibrating the gel in buffer containing triton x-100 (it may also work on the protein bound to a membrane).. ...
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Guanidine exists protonated, as guanidinium, in solution at physiological pH. Guanidinium chloride (also known as guanidine hydrochloride) has chaotropic properties and is used to denature proteins. Guanidinium chloride is known to denature proteins with a linear relationship between concentration and free energy of unfolding. In aqueous solutions containing 6 M guanidinium chloride, almost all proteins lose their entire secondary structure and become randomly coiled peptide chains. Guanidinium thiocyanate is also used for its denaturing effect on various biological samples. Guanidinium chloride[9] is used as an adjuvant in treatment of botulism, introduced in 1968,[10] but now its role is considered controversial[11] - because in some patients there was no improvement after this drug administration. ...
Current models derived from in vitro studies propose that sHsps prevent irreversible substrate aggregation by binding heat-denatured substrates, and then present substrate to other cellular components for ATP-dependent refolding (Waters et al., 1996; Ehrnsperger et al., 1997;Lee et al., 1997; Veinger et al., 1998). Our data extend this model for sHsp chaperone activity in several important ways. First, we determined that the chaperones required for high levels of refolding of Hsp18.1-bound Luc were Hsp/Hsc70 plus DnaJ homologs. The addition of Hsp90 and Hop gave minimal or no further enhancement of refolding. Despite the eukaryotic origin of Hsp18.1, the highest Luc refolding rates were observed when Hsp18.1-bound Luc was reactivated in the presence of the prokaryotic DnaK system. These findings imply that the mechanism of sHsp action in conjunction with Hsp70 systems is universal among eukaryotes and prokaryotes, and suggest that sHsps may not physically interact with the Hsp70 systems. Also, ...
Circular RNA (circRNA) is a novel class of noncoding RNAs, and the roles of circRNAs in the development of cardiac hypertrophy remain to be explored. Here, we investigate the potential roles of circRNAs in cardiac hypertrophy. By circRNA sequencing in left ventricular specimens collected from 8-week-old mice with isoproterenol hydrochloride-induced cardiac hypertrophy, we found 401 out of 3323 total circRNAs were dysregulated in the hypertrophic hearts compared with the controls. Of these, 303 circRNAs were upregulated and 98 were downregulated. Moreover, the GO and KEGG analyses revealed that the majority of parental gene of differentially expressed circRNAs were not only related to biological process such as metabolic process and response to stimulus, but also related to pathway such as circulatory system and cardiovascular diseases. On the other hand, total 1974 miRNAs were predicted to binding to these differentially expressed circRNAs, and the possible target mRNAs of those miRNAs were also
How is Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins abbreviated? MADGELAS stands for Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins. MADGELAS is defined as Molecular description of Aggregation, Denaturation, Gelation And Surface activity of whey proteins very frequently.
Bimolecular nucleophilic substitution (SN2) reactions are concerted, meaning they are a one step process. This means that the process whereby the nucleophile attacks and the leaving group leaves is simultaneous. Hence, the bond-making between the nucleophile and the electrophilic carbon occurs at the same time as the bond-breaking between the electophilic carbon and the halogen.. The potential energy diagram for an SN2 reaction is shown below. Upon nucleophilic attack, a single transition state is formed. A transition state, unlike a reaction intermediate, is a very short-lived species that cannot be isolated or directly observed. Again, this is a single-step, concerted process with the occurrence of a single transition state.. ...
TY - JOUR. T1 - Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. AU - Day, Ryan. AU - Bennion, Brian J.. AU - Ham, Sihyun. AU - Daggett, Valerie. PY - 2002. Y1 - 2002. N2 - We have traditionally relied on extremely elevated temperatures (498 K, 225°C) to investigate the unfolding process of proteins within the time-scale available to molecular dynamics simulations with explicit solvent. However, recent advances in computer hardware have allowed us to extend our thermal denaturation studies to much lower temperatures. Here we describe the results of simulations of chymotrypsin inhibitor 2 at seven temperatures, ranging from 298 K to 498 K. The simulation lengths vary from 94 ns to 20 ns, for a total simulation time of 344 ns, or 0.34 μs. At 298 K, the protein is very stable over the full 50 ns simulation. At 348 K, corresponding to the experimentally observed melting temperature of CI2, the protein unfolds over the first 25 ns, explores partially ...
Sterile α motif (SAM) domains are found in many different proteins and shown to play important roles in various biological processes. The N-terminal domain of deleted in liver cancer 1 (DLC1) protein is a SAM domain which exists in a monomeric form in aqueous solution and facilitates the distribution of EF1A1 to the membrane periphery and ruffles upon growth factor stimulation. Here, we report the structure of an N-terminal truncated DLC1 SAM domain (DLC1-SAM) and its urea-induced equilibrium unfolding investigated with various biophysical methods such as CD, fluorescence emission spectroscopy, and NMR. CD and tryptophan intrinsic fluorescence emission data imply that the unfolding of DLC1-SAM follows a simple two-state mechanism, yet the NMR data suggest the presence of at least one intermediate state. The intermediate cannot be detected by NMR, but it does not exist in large aggregates as shown by analytical ultracentrifugation experiments. Analysis of the free energy values for different ...
Yutani, K.; Ogasahara, K.; Suzuki, M.; Sugino, Y., 1979: Comparison of denaturation by guanidine hydro chloride of the wild type tryptophan synthase ec 4.2.1.20 alpha subunit of escherichia coli and 2 mutant proteins glutamic acid 49 replaced by methionine or glutamine
protein refolding - posted in Protein Expression and Purification: Hello everyone. Im trying to purify alkaline phosphatase enzyme that has been overexpressed in E. coli BL21DE3. The protein formed inclusion bodies upon IPTG induction. I was able to isolate and purify the protein in the inclusion bodies using denaturing Nickel affinity chromatography. Then i used dialysis to remove the denaturant (8 M urea) 1. After i dialysed the unfolded protein for 48 hrs in a cold room. next day i was...
High hydrostatic pressure (HHP) can cause a host of problems, including dissociation of multimeric proteins, shifts in reaction equilibria, loss of membrane integrity, and protein denaturation (reviewed in [1]). In some cases, changes in mechanical stress result in differential gene expression driven by mechanosensitive promoters or repressors. Genes that have increased expression might include cold- and heat-shock and other stress response proteins[2], barostable polymerases[3], or membrane proteins[4, 5]. Down-regulated genes might include nutrient transporters[6, 7]. In other cases, porin proteins which provide ion diffusion pathways are opened in response to osmotic stress across the membrane. In addition to pressure-sensing promoters, many organisms have mechanosensitive channels which are involved in changing metabolism more quickly than transcriptional changes allow. One example of well-studied mechanosensitive channel protein is MscS (summarized in [8]). This protein forms a non-specific ...
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We have applied rheological methods for the analysis of ethanol-lysozyme interaction during the process of denaturation and aggregation of the protein. At low concentration of ethanol a destruction of the hydration shell of lysozyme is observed. With the increase in the ethanol concentration a structural transformation takes place. It leads to the formation of a protein aggregate with an elongated structure. The rheological characteristics of lysozyme-water-ethanol solution changes from Newtonian to pseudoplastic ...
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Experiments with relatively high doses are often used to predict risks at appreciably lower doses. A point of departure (PoD) can be calculated as the dose associated with a specified moderate response level that is often in the range of experimental doses considered. A linear extrapolation to lower doses often follows. An alternative to the PoD method is to develop a model that accounts for the model uncertainty in the dose-response relationship and to use this model to estimate the risk at low doses. Two such approaches that account for model uncertainty are model averaging (MA) and semi-parametric methods. We use these methods, along with the PoD approach in the context of a large animal (40,000+ animal) bioassay that exhibited sub-linearity. When models are fit to high dose data and risks at low doses are predicted, the methods that account for model uncertainty produce dose estimates associated with an excess risk that are closer to the observed risk than the PoD linearization. This ...
0029]A data collection endpoint is selected, based on a predetermined percentage of the electrolyzed analyte. The predetermined percentage can be any percentage greater than 0 (zero) up to 100%. In some embodiments, however, the measured percentage of total charge is at least 40%, and in other embodiments, at least 50%. That is, in some embodiments, at least 40% of the analyte has been electrolyzed at the data collection endpoint, and in other embodiments, at least 50% of the analyte has been electrolyzed. The underlying premise of the calculation technique of the present disclosure is to use a data collection endpoint that balances between the speed and accuracy of measurement, and which is directly related to the percentage of analyte being electrolyzed. From the data collection endpoint, the subsequent current is extrapolated. Various different mathematic models can be used to provide the estimation. In one embodiment, a linear extrapolation, based on the measured current data and the data ...
The present invention relates to methods for pretreating biological samples for extraction of nucleic acid therefrom. The present invention employs a combination of at least one protein denaturant with one or more of the following elements to form a reaction mixture for extraction of nucleic acid: (1) at least one aprotic solvent, (2) stepwise heating, and (3) sample dilution.
Most proteins fold to specifi c native conformationsin order to function. Conformational stability is athermodynamic quantity which refl ects the populationof protein in its native, functional state. We reviewexperimental measurements of the stability of foldedconformations of proteins. Globular protein stability is animportant factor that can limit the usefulness of proteinsas pharmaceuticals or in biotechnology applications.. ...
1B5X: Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser Ala mutants.
1B5Z: Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser Ala mutants.
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Experimental thermodynamic data for aqueous biomolecules reported in the literature have been combined with group additivity equations of state to generate parameters which can be used to calculate the apparent standard molal Gibbs energies and enthalpies of formation (ΔG° and ΔH°, respectively) and the standard m
Supplement Biological proteins (such as enzymes) unfold and lose their active state when exposed to denaturing agents (e.g. strong acids or bases, heat, solvents, and salts). This is crucial especially when enzymes lose their structure and function as catalysts. The substrates can no longer bind to the active site, and biochemical process is therefore disrupted. The proteins can regain their natural active state if the denaturing agent is removed. However, there are instances in which the process is irreversible. ...
The explanation of aggregate and sectoral investment behavior has been one of the less successful endeavors in empirical economics. Existing econometric models have had little success in explaining or predicting investment spending. This may be because most such models fail to account for the irreversibility of most investment spending. With irreversibility, changes in the riskiness of future cash flows or interest rates should in theory dramatically affect the decision to invest - more so than, say, a change in the levels of interest rates. Here I survey some of the empirical support for this proposition, and discuss the implications for investment modelling ...
FAI uses thermal stability testing to collect certain data. For more information on this service, visit this page for the benefits.
The applicability of the conventional Hoffman-Weeks (HW) linear extrapolation for the determination of the equilibrium melting temperatures of semicrystalline polymers is critically reviewed. It is shown that the linear extrapolation of observed melting temperatures cannot, in general, provide a reliable estimate of the equilibrium melting temperature. A more rigorous nonlinear HW analysis is proposed in this dissertation, which yields more accurate estimates of the equilibrium melting temperatures for semicrystalline polymers. The proposed nonlinear HW analysis is successfully applied to the cases of isotactic polypropylene and poly(ethylene oxide). The predicted initial lamellar thickness as a function of the crystallization temperature matches well with experimental results and/or literature values. Results based on the nonlinear HW analysis are consistent with those obtained from the analysis of the temperature dependence of the crystal growth rates. The general applicability of the ...
A powerful tool used to monitor secondary structure is circular dichroism (CD), which is the differential absorbance of left and right circularly polarized light. Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the proteins secondary structure. This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software.. Protein secondary structure can also be used to monitor protein folding and unfolding. An equilibrium study consists of collection of CD spectra as a function of increasing temperature or chemical denaturant. As the protein unfolds, the CD spectrum reflects this. Fitting data at a single wavelength or the full spectral scans during this denaturation process provides thermodynamic information such as the melting temperature ...
Fourier transform infrared spectroscopy has been applied to study the thermal stability of multilayer Langmuir- Schaefer (LS) films of lysozyme deposited on silicon substrates. The study has confirmed previous structural findings that the LS protein films have a high thermal stability that is extended in a lysozyme multilayer up to 200 °C. 2D infrared analysis has been used here to identify the correlated molecular species during thermal denaturation. Asynchronous 2D spectra have shown that the two components of water, fully and not fully hydrogen bonded, in the high-wavenumber range (2800-3600 cm-1) are negatively correlated with the amine stretching band at 3300 cm-1. On the grounds of the 2D spectra the FTIR spectra have been deconvoluted using three main components, two for water and one for the amine. This analysis has shown that, at the first drying stage, up to 100 °C, only the water that is not fully hydrogen bonded is removed. Moreover, the amine intensity band does not change up to ...
It should be emphasized that the array of structures listed in Table 1 are but a point of departure. The competition dialysis method is completely general, and arrays of structures of particular interest can be designed as desired. The only limitations are that the structures be large enough to be retained by the dialysis tubing chosen for use, and that they are verified to be stable under the ionic conditions of the experiment. Essential quality control experiments to characterize nucleic acid samples were described in detail [41, 42] and include UV absorbance and circular dichroism spectroscopy, and thermal denaturation studies. Fig. 1 Schematic of the competition dialysis experiment. A schematic representation of the structures used is shown on the left. The center shows the simple experimental setup, a beaker containing the test ligand solution and the holder for the dialysis units. A schematic of the microdialysis unit is shown on the right Structural Selectivity of Drug-Nucleic Acid ...
All primer pairs are shown in Supplemental Table S1, along with annealing temperatures used for PCR. Amplification programs for Taq Polymerase (New England Biolabs) consisted of a 3-min denaturation at 94°C followed by 35 cycles of 15 s at 94°C, 30 s at the annealing temperature, and 1 min kb−1 at 72°C. Amplification programs for Phusion Polymerase (New England Biolabs) consisted of a 30-s denaturation at 98°C followed by 35 cycles of 7 s at 98°C, 7 s at the annealing temperature, and 30 s kb−1 at 72°C.. To construct the CESA8KO vector, a 3′ homologous region was amplified from Physcomitrella patens genomic DNA with primers 174JB and 193JB using Taq DNA polymerase, cut with SalI and BspDI, and cloned into the SalI/BstBI site of pBHSNR (a gift of Didier Schaefer, University of Neuchâtel). The resulting plasmid was cut with KasI and NsiI to accept the KasI/NsiI fragment of a 5′ homologous region amplified from P. patens genomic DNA with primers 203JB and 185JB (Supplemental Table ...
Elkordy, Amal, Forbes, Robert T and Barry, Brian W (2008) Study of protein conformational stability and integrity using calorimetry and FT-Raman spectroscopy correlated with enzymatic activity. European Journal of Pharmaceutical Sciences, 33 (2). pp. 177-190. ISSN 0928-0987 ...
ABSTRACT: Solubilization of membrane proteins by poly(styrene-co-maleic acid) salts (pSMA-S) has significant potential for membrane protein studies. This approach provides an opportunity to overcome many disadvantages associated with a traditional detergent-based technique including protein denaturation and displacement of boundary lipids which may offer both structural and functional stability to membrane proteins. Thylakoid membranes (TMs) from photosynthetic organisms are well studied protein-rich membranes that host several multi-subunit protein complexes associated with oxygenic photosynthesis. These protein complexes are important for applied photosynthesis and by being extracted and purified they can be used in the near future for direct energy conversion. In this study, we used spinach TMs isolated from purified intact chloroplasts to systematically test the solubilization efficacy of 12 commercially available styrene-maleic acid (SMA) copolymers that vary in size, styreneto-maleic acid ...
Various steps in the PMM procedure applied to canola meal were examined to optimize protein recovery. In the extraction step, solubilization was achieved with 0.5M NaCl. Using chromatographic and electrophoretic techniques, the predominant extracted protein identified was the 12S globulin under all salt conditions; there was no evidence to indicate the presence of dissociated 7S form. The impact of pH, NaCl concentration, protein concentration and dilution on protein conformation as well as the formation and interaction of protein micelles were evaluated using gel filtration chromatography, differential scanning calorimetry (DSC) and light microscopy. Variations in pH from 6 to 9 and salt concentrations between 0.1M and 0.5M resulted in no major conformational changes (similar enthalpies of denaturation) but higher pH values and salt concentrations were associated with increased denaturation temperatures reflecting increased molecular stability. At pH 4, however, the 12S globulin dissociated ...
Oxidative stress initiates harmful cellular responses, such as DNA damage and protein denaturation, triggering a series of cardiovascular disorders. Systematic investigations of the transcription factors (TFs) involved in oxidative stress can help reveal the underlying molecular mechanisms and facilitate the discovery of effective therapeutic targets in related diseases. In this study, an integrated strategy which integrated RNA-seq-based transcriptomics techniques and a newly developed concatenated tandem array of consensus TF response elements (catTFREs)-based proteomics approach and then combined with a network pharmacology analysis, was developed and this integrated strategy was used to investigate critical TFs in the protection of Yixin-shu (YXS), a standardized medical product used for ischaemic heart disease, against hydrogen peroxide (H2O2)-induced damage in cardiomyocytes ...
Supplementary Components1. interpretation of regression analyses can be stressed. Regions of additional research are talked about. Shown strategies and concepts are Flumazenil kinase activity assay illustrated through program to a little, wide data set of adults spanning a wide range in ages and multiple immunophenotypes that were assayed before and after immunization with inactivated influenza vaccine (IIV). Our regression modeling prescriptions identify some potentially important topics for future immunological research. 1) Immunologists may wish to distinguish differences in immune features from changes in immune features by aging. 2) A form of the bootstrap that employs linear extrapolation may prove to be an invaluable analytic tool because it allows the working immunologist to obtain accurate estimates of the stability of immune parameter estimates with a bare minimum of imposed assumptions. 3) Liberal inclusion of immune features in phenotyping panels can facilitate accurate separation of ...
Single-stranded DNA absorbs much more UV light than double-stranded DNA so you can follow denaturation and renaturation by simply measuring UV light absorbance in a spectrophotometer. The figure shows that the DNA molecules "melt," or denature, as the temperature is raised. When the temperature was lowered to 67°C they could follow the formation of double-standed DNA over time. For virus and bacteriophage DNA (solid triangles and circles) most of the DNA seemed to renature in about one hour. In the case of bacterial DNA (D. pneumoniae, open circles) the process was much slower and for cow DNA (open triangles) hardly any renaturation was seen in 100 minutes ...
Hare and Tantillo review the current understanding of post-transition state bifurcations (PTSB).3 This type of potential energy surface has been the subject of much of Chapter 8 of my book and many of my blog posts. What is becoming clear is the possibility of a transition state followed by a valley-ridge inflection leads to reaction dynamics where trajectories cross a single transition state but lead to two different products. This new review updates the state-of-the-art from Houks review4 of 2008 (see this post). Mentioned are a number of studies that I have included in this Blog, along with reactions involving metals, and biochemical systems (many of these examples come from the Tantillo lab). They close with the hope that their review might "inspire future studies aimed at controlling selectivity for reactions with PTSBs" (italics theirs). I might offer that controlling selectivity in these types of dynamical systems is another chemical Grail!. The Hase group has a long review of direct ...
Geometric Approaches to Gibbs Energy Landscapes and DNA Oligonucleotide Design: 10.4018/ijnmc.2011070104: DNA codeword design has been a fundamental problem since the early days of DNA computing. The problem calls for finding large sets of single DNA strands that