Circular Dichroism Spectropolarimetry Research Articles

Interactions of Archaeal Chromatin Proteins Alba1 and Alba2 with Nucleic Acids

BackgroundArchitectural proteins have important roles in compacting and organising chromosomal DNA. There are two potential histone counterpart peptide sequences (Alba1 and Alba2) in the Aeropyrum pernix genome (APE1832.1 and APE1823).Methodology/Principal FindingsThese two peptides were expressed and their interactions with various DNAs were studied using a combination of various experimental techniques: surface plasmon resonance, UV spectrophotometry, circular dichroism–spectropolarimetry, gel-shift assays, and isothermal titration calorimetry.Conclusions/SignificanceOur data indicate that there are significant differences in the properties of the Alba1 and Alba2 proteins. Both of these Alba proteins can thermally stabilise DNA polynucleotides, as seen from UV melting curves. Alba2 and equimolar mixtures of Alba1/Alba2 have greater effects on the thermal stability of poly(dA-dT).poly(dA-dT). Surface plasmon resonance sensorgrams for binding of Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 to DNA oligonucleotides show different binding patterns. Circular dichroism indicates that Alba2 has a less-ordered secondary structure than Alba1. The secondary structures of the Alba proteins are not significantly influenced by DNA binding, even at high temperatures. Based on these data, we conclude that Alba1, Alba2, and equimolar mixtures of Alba1/Alba2 show different properties in their binding to various DNAs.

Utility of standard pharmacopeial and nonpharmacopeial methods in distinguishing folded, unfolded, and process variant forms of interferon α-2

Standard pharmacopeial test methods for biologics broadly focus on identity (active substance and impurities) and function (activity and toxicity). However, it is less clear which, if any, of the methods can identify a subtle change in protein therapeutics such as misfolding, unusual product-related impurities, or sequence or folding variants that may result from differences in manufacturing processes. In this study, we test the ability of standard pharmacopeia monograph methods and other common physicochemical methods (including circular dichroism spectropolarimetry, fluorescence spectroscopy, thermal denaturation, mass spectrometry, and capillary electrophoresis) to differentiate folding variants [purposely denatured interferon (IFN) α-2] and sequence variants (deliberately truncated, or truncated and chemically modified) from the IFN α-2 reference standards. The results show that the standard pharmacopeial methods are of limited utility in detecting alterations in protein structure, even when those alterations include changes in primary structure. None of the pharmacopeial methods were clear probes of higher order structure. The nonpharmacopeial methods were somewhat more successful but not a single method was able to distinguish all variants tested from the authentic standard. Taken together, the data underscore the requirement to use several different and complementary methods and stress conditions to assess primary and higher order structure when assessing the comparability in potential biosimilar protein products.

Structural characterization of an intrinsically unfolded mini-HBX protein from hepatitis B virus.

The hepatitis B virus x protein (HBX) is expressed in HBV-infected liver cells and can interact with a wide range of cellular proteins. In order to understand such promiscuous behavior of HBX we expressed a truncated mini-HBX protein (named Tr-HBX) (residues 18-142) with 5 Cys → Ser mutations and characterized its structural features using circular dichroism (CD) spectropolarimetry, NMR spectroscopy as well as bioinformatics tools for predicting disorder in intrinsically unstructured proteins (IUPs). The secondary structural content of Tr-HBX from CD data suggests that Tr-HBX is only partially folded. The protein disorder prediction by IUPred reveals that the unstructured region encompasses its N-terminal ~30 residues of Tr-HBX. A two-dimensional (1)H-(15)N HSQC NMR spectrum exhibits fewer number of resonances than expected, suggesting that Tr-HBX is a hybrid type IUP where its folded C-terminal half coexists with a disordered N-terminal region. Many IUPs are known to be capable of having promiscuous interactions with a multitude of target proteins. Therefore the intrinsically disordered nature of Tr-HBX revealed in this study provides a partial structural basis for the promiscuous structure-function behavior of HBX.

Nanocrystalline cellulose for covert optical encryption

Nanocrystalline cellulose (NCC) solid films derived from spruce pulp exhibit iridescence when cast from chiral nematic aqueous phase suspensions of the nanocrystals. The iridescence has potential for overt encryption as an anti-counterfeiting measure and also offers an intrinsic level of covert encryption since films of NCC reflect left-circularly polarized light. Addition of TINOPAL, an optical brightening agent (OBA), adds a third level of (covert) encryption potential since the chromophore exhibits strong fluorescence when excited with ultraviolet (UV) light. The overall result is a selectively polarizing fluorescent iridescent film. We examined the impact of additions of OBA on NCC iridescence, optical activity, and physical structure variation with polarized optical microscopy, circular dichroism (CD) spectropolarimetry, and zeta potential analysis. Increasing OBA additions increase the chiral nematic pitch of NCC films and alter chiral nematic domain structure in the solid film. Under low-concentration conditions, OBA yields intense UV fluorescence without compromising the visible light iridescent properties of the film. The potential security offered by the NCC film can be authenticated using a UV light source, a circular polarizer in conjunction with an iridescent feature that can be verified by the eye or by chiral spectrometry.

Physicochemical Characterization of Complex Drug Substances: Evaluation of Structural Similarities and Differences of Protamine Sulfate from Various Sources

The purpose of this study was to characterize and evaluate differences of protamine sulfate, a highly basic peptide drug, obtained from five different sources, using orthogonal thermal and spectroscopic analytical methods. Thermogravimetric analysis and modulated differential scanning calorimetry showed that all five protamine sulfate samples had different moisture contents and glass transition and melting temperatures when temperature was modulated from 25 to 270°C. Protamine sulfate from source III had the highest residual moisture content (4.7 ± 0.2%) at 105°C, resulting in the lowest glass transition (109.7°C) and melting (184.2°C) temperatures compared with the other four sources. By Fourier-transform infrared (FTIR) spectroscopy, the five sources of protamine sulfate had indistinguishable spectra, and the spectra were consistent with a predominantly random coil conformation in solution and a minor population in a β-sheet conformation (~12%). Circular dichroism spectropolarimetry confirmed the FTIR results with prominent minima at 206 nm observed for all five sources. Finally, proton ((1)H) nuclear magnetic resonance spectroscopy showed that all five protamine sulfate sources had identical spectra with backbone amide chemical shifts between 8.20 and 8.80 ppm, consistent with proteins with predominantly random coil conformation. In conclusion, thermal analyses showed differences in the thermal behavior of the five sources of protamine sulfate, while spectroscopic analyses showed the samples had a predominantly random coil conformation with a small amount of β-sheet present.

Investigation of the Differences in Thermal Stability of Two Recombinant Human Serum Albumins with 1,2-Dipalmitoyl-sn-glycero-3-phosphocholine Liposomes by UV Circular Dichroism Spectropolarimetry

Previous studies have demonstrated that liposome-protein interactions can result in changes to the thermal stability of the protein. We utilized far-UV circular dichroism spectropolarimetry and fluorescence spectroscopy to investigate the interaction of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes with two recombinant human serum albumins (rHSA). We demonstrate that rHSA expressed in Oryza sativa (OsrHSA) has improved secondary structure thermal stability compared to rHSA expressed in Pichia pastoris (PprHSA). A similar stability profile was observed when comparing bovine serum albumin (BSA) and defatted bovine serum albumin (dfBSA), suggesting the presence of fatty acids may be responsible for the improved stability of OsrHSA. Addition of DPPC liposomes reduced the thermal stability of both OsrHSA and BSA, but not of PprHSA or dfBSA. DPPC liposomes may disrupt stabilizing native fatty acids on OsrHSA and BSA.

Spectroscopic analysis of small multidrug resistance protein EmrE in the presence of various quaternary cation compounds

Escherichia coli EmrE protein is the archetypical member of the small multidrug resistance protein family in bacteria and confers host resistance to a wide assortment of toxic quaternary cation compounds by secondary active efflux. This protein can form a variety of multimers under various membrane mimetic conditions, and the consensus of most biochemical and biophysical studies indicate that the active form is a dimer. The purpose of this study is to characterize the conformation of organically extracted detergent solubilized EmrE protein known to predominate as monomer yet demonstrates ligand binding ability. Active site EmrE-E14 replacements were also examined as functionally inactive controls for this study. EmrE was solubilized in detergents, sodium dodecyl sulfate (SDS) and dodecyl maltoside (DDM), and protein conformation was examined in the presence of four known quaternary cation compound (QCC) substrates, tetraphenyl phosphonium (TPP), methyl viologen, cetylpyridinium, and ethidium. SDS-Tricine PAGE analysis of both detergent solubilized proteins revealed that DDM-EmrE preparations enhanced the formation of dimer (and in some cases trimer) forms in the presence of all four QCC above 25 QCC:1 EmrE molar ratios. Examination of EmrE and its active site variant tertiary structures in DDM by circular dichroism spectropolarimetry, intrinsic Trp fluorescence quenching and second order derivative ultraviolet absorbance revealed that the variant fails to bind TPP but interacts with all other compounds. The results of this study show that monomeric detergent solubilized EmrE is capable of forming multimeric complexes that are enhanced by chemically diverse QCCs.

Mechanism of change in enantiomer migration order of enantioseparation of tartaric acid by ligand exchange capillary electrophoresis with Cu(II) and Ni(II)–D‐quinic acid systems

The mechanism of change in the enantiomer migration order (EMO) of tartarate on ligand exchange CE with Cu(II)- and Ni(II)-D-quinic acid systems was investigated thoroughly by circular dichroism (CD) spectropolarimetry. The (13) C NMR spectra of solutions containing D-quinate (pH 5.0) with Cu(II) or Ni(II) revealed the coordination of carboxylate and hydroxyl groups on D-quinate. The D-quinic acid concentration dependence of the CD spectra at a fixed Cu(II) concentration at pH 5.0 indicates that the 1:1, 1:2 and 1:3 Cu(II)-D-quinate complexes were formed with an increase in the concentration of D-quinic acid. The CD spectral behavior revealed that D-tartarate is selectively coordinated to the 1:1 complex to give the 1:1:1 Cu(II)-D-quinate-D-tartarate ternary complex while L-tartarate is selectively bound to the 1:2 and 1:3 complexes to form the 1:2:1 ternary complex. In the Ni(II)-D-quinic acid system, it became apparent that the 1:2 Ni(II)-D-quinate complex is mainly formed in the wide range of D-quinic acid concentration at pH 5.0 and D-tartarate is selectively coordinated to the 1:2 complex to form the 1:2:1 ternary complex. The change in EMO of tartarate on ligand exchange CE was explainable by the change in coordination selectivity for D- and L-tartarates in the Cu(II)- and Ni(II)-D-quinic acid systems depending on the compositions of the complexes formed in BGE.

Structure and function of proteins in hydrated choline dihydrogen phosphate ionic liquid

Ionic liquids are being intensely studied as promising media for the stabilization of proteins and other biomolecules. Choline dihydrogen phosphate (CDHP) has been identified as one of the most promising candidates for this application. In this work we have probed in more detail the effects that CDHP may have on the thermodynamics, structure, and stability of proteins, including one of therapeutic interest. Microcalorimetry and circular dichroism spectropolarimetry (CD) were used to assess the thermal stability of protein solutions in CDHP/water mixtures at various concentrations. Increasing thermal stability of lysozyme and interleukin-2 in proportion to CDHP concentration was observed. Isothermal titration calorimetry (ITC) was used to quantify binding interactions, and indicate that the mechanism for stability does not appear to be dependent upon CDHP binding to protein. CD and small angle X-ray scattering (SAXS) analyses were used to probe for structural changes due to the presence of CDHP. SAXS indicates charge effects on the surface of the protein play a role in protein stability in ionic liquids, and no significant alteration of the overall tertiary conformation of lysozyme was observed at 25 °C. However, after incubation at 37 °C or at higher concentrations of CDHP, small changes in protein structure were seen. Effects on protein activity were monitored using turbidity assays, and CDHP decreases protein activity but does not eliminate it. Protein solubility was also monitored using a turbidity assay and was found to be inversely proportional to the concentration of CDHP in solution.

Structure and hydrogel formation studies on homologs of a lactoglobulin-derived peptide

In order to study the impact of the amino acid sequence on the morphology of peptide-based nanostructures and their hydrogel formation, we designed a series of analogs of a milk-derived octapeptide (OP), mainly using strategic amino acid substitutions. Electronic transmission microscopy (TEM) and circular dichroism (CD) spectropolarimetry were used to analyze the nanostructures formed, and to characterize some structural features of the modified peptides. Further, the potential to form hydrogels was investigated for all of the analogous peptides. We learned that those able to undergo secondary structure transition to β-sheet conformation form strong gels. The results reported highlight some key structural properties that explain the self-assembly propensity of Peptide OP.

Characterization of Mesoscale Coiled-Coil Peptide–Porphyrin Complexes

Photoelectronically conductive self-assembling peptide-porphyrin assemblies have great potential in their use as biomaterials, owing largely to their environmentally responsive properties. We have successfully designed a coiled-coil peptide that can self-assemble to form mesoscale filaments and serve as a scaffold for porphyrin interaction. In our earlier work, peptide-porphyrin-based biomaterials were formed at neutral pH, but the structures were irregular at the nano- to microscale size range, as judged by atomic force microscopy. We identified a pH in which mesoscale fibrils were formed, taking advantage of the types of porphyrin interactions that are present in well-characterized J-aggregates. We used UV-visible spectroscopy, circular dichroism spectropolarimetry, fluorescence spectroscopy, and atomic force microscopy to characterize these self-assembling biomaterials. We propose a new assembly paradigm that arises from a set of unique porphyrin-porphyrin and porphyrin-peptide interactions whose structure may be readily modulated by changes in pH or peptide concentration.

Thermodynamic Analysis of Self-Assembly in Coiled-Coil Biomaterials

Coiled-coil protein structural motifs have proven amenable to the design of structurally well-defined biomaterials. Mesoscale structural properties can be fairly well predicted based on rules governing the chemical interactions between the helices that define this structural motif. We explore the role of the hydrophobic core residues on the self-assembly of a coiled-coil polymer through a mutational analysis coupled with a salting-out procedure. Because the resultant polymers remain in solution, a thermodynamic approach is applied to characterize the polymer assembly using conventional equations from polymer theory to extract nucleation and elongation parameters. The stabilities and lengths of the polymers are measured using circular dichroism spectropolarimetry, sizing methods including dynamic light scattering and analytical ultracentrifugation, and atomic force microscopy to assess mesoscale morphology. Upon mutating isoleucines at two core positions to serines, we find that polymer stability is decreased while the degree of polymerization is about the same. Differences in results from circular dichroism and dynamic light scattering experiments suggest the presence of a stable intermediate state, and a scheme is proposed for how this intermediate might relate to the monomer and polymer states.

Biochemical Characterization of Hemoglobins from Caspian Sea Sturgeons (Acipenser persicus and Acipenser stellatus)

Hemoglobin (Hb) variability is a commonly used index of phylogenetic differentiation and molecular adaptation in fish enabling them to adapt to different ecological conditions. In this study, the characteristics of Hbs from two Sturgeon species of the Southern Caspian Sea Basin were investigated. After extraction and separation of hemoglobin from whole blood, the polyacrylamide gel electrophoresis (SDS-PAGE), cellulose acetate electrophoresis, and isoelectric focusing (IEF) were used to confirm Hb variabilities in these fishes. We showed that although both species have variable Hbs with different isoelectric points, their dominant Hbs can be identified. Ion exchange on CM-cellulose chromatography was used for purification of the dominant Hbs from these fishes. The accuracy of the methods was confirmed by IEF and SDS-PAGE. Spectral studies using fluorescence spectrophotometery indicated that although the Hbs from these fishes had similar properties they exhibited clear differences with human Hb. A comparative study of Hbs alpha-helix secondary substructures was performed by circular dichroism spectropolarimetry (CD) analysis. UV-vis spectrophotometery was also utilized to measure oxygen affinity of Hbs by sodium dithionite. Oxygen affinities of these Hbs were compared using Hb-oxygen dissociation curves. Together, these results demonstrate a significant relationship between oxygen affinity of fish hemoglobins and environmental partial pressure of oxygen.

In silico modeling of the staphylococcal bacteriophage-derived peptidase CHAPK

The aim of this study was to use comparative modeling to predict the three-dimensional structure of the CHAPK protein (cysteine, histidine-dependent amidohydrolase/peptidase domain of the LysK endolysin, derived from bacteriophage K). Iterative PSI-BLAST searches against the Protein Data Bank (PDB) and nonredundant (nr) databases were used to populate a multiple alignment for analysis using the T-Coffee Expresso server. A consensus Maximum Parsimony phylogenetic tree with a bootstrap analysis setting of 1,000 replicates was constructed using MEGA4. Structural templates relevant to our target (CHAPK) were identified, processed in Expresso and used to generate a 3D model in the alignment mode of SWISS-MODEL. These templates were also processed in the I-TASSER web server. A Staphylococcus saprophyticus CHAP domain protein, 2K3A, was identified as the structural template in both servers. The I-TASSER server generated the CHAPK model with the best bond geometries when analyzed using PROCHECK and the most logical organization of the structure. The predicted 3D model indicates that CHAPK has a papain-like fold. Circular dichroism spectropolarimetry also indicated that CHAPK has an αβ fold, which is consistent with the model presented. The putative active site maintained a highly conserved Cys54-His117-Glu134 charge relay and an oxyanion hole residue Asn136. The residue triplet, Cys-His-Glu, is known to be a viable proteolytic triad in which we predict the Cys residue is used in a nucleophilic attack on peptide bonds at a specific site in the pentaglycine cross bridge of staphylococcal cell wall peptidoglycan. Use of comparative modeling has allowed approximation of the 3D structure of CHAPK giving information on the structure and an insight into the binding and active site of the catalytic domain. This may facilitate its development as an alternative antibacterial agent.

Mapping the IκB Kinase β (IKKβ)-binding Interface of the B14 Protein, a Vaccinia Virus Inhibitor of IKKβ-mediated Activation of Nuclear Factor κB

The IκB kinase (IKK) complex regulates activation of NF-κB, a critical transcription factor in mediating inflammatory and immune responses. Not surprisingly, therefore, many viruses seek to inhibit NF-κB activation. The vaccinia virus B14 protein contributes to virus virulence by binding to the IKKβ subunit of the IKK complex and preventing NF-κB activation in response to pro-inflammatory stimuli. Previous crystallographic studies showed that the B14 protein has a Bcl-2-like fold and forms homodimers in the crystal. However, multi-angle light scattering indicated that B14 is in monomer-dimer equilibrium in solution. This transient self-association suggested that the hydrophobic dimerization interface of B14 might also mediate its interaction with IKKβ, and this was investigated by introducing amino acid substitutions on the dimer interface. One mutant (Y35E) was entirely monomeric but still co-immunoprecipitated with IKKβ and blocked both NF-κB nuclear translocation and NF-κB-dependent gene expression. Therefore, B14 homodimerization is nonessential for binding and inhibition of IKKβ. In contrast, a second monomeric mutant (F130K) neither bound IKKβ nor inhibited NF-κB-dependent gene expression, demonstrating that this residue is required for the B14-IKKβ interaction. Thus, the dimerization and IKKβ-binding interfaces overlap and lie on a surface used for protein-protein interactions in many viral and cellular Bcl-2-like proteins.

The CLN025 Decapeptide Retains a β-Hairpin Conformation in Urea and Guanidinium Chloride

The conformational stability of the β-hairpin miniprotein, CLN025, a variant of chignolin in which the N- and C-terminal glycines are replaced by tyrosines, in various concentrations of guanidinium chloride (GdmCl) and urea was examined by molecular dynamics simulations and electronic circular dichroism (ECD) spectropolarimetry. The peptide maintains its β-hairpin conformation in GdmCl and urea solutions. In GdmCl, Gly7 influences the turn to reduce the number of Asp3-Gly7 H-bonds and the Tyr1-Trp9 H-bond is lost. The structure of the peptide is less stable in 3 M GdmCl than in water or 6 M GdmCl, because the number of Asp3-Thr8 and Tyr1-Tyr10 H-bonds are reduced and the Tyr2 side chain moves away from the Pro4 and Trp9 side chains and toward the Tyr10 side chain. This reduces the number of Tyr2-Pro4 CH-π interactions and Tyr2-Trp9 and Tyr1-Tyr10 aromatic-aromatic (Ar-Ar) interactions and increases the number of Tyr2-Tyr10 Ar-Ar interactions. In 6 M GdmCl at 300 and 333 K, the number of Tyr1-Tyr10 and Asp3-Thr8 H-bonds increases, but fewer structures have Tyr2-Pro4 CH-π and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In urea, Gly7 is in a mixture of β-turn and random meander structures and the number of Asp3-Thr6 and Tyr1-Tyr10 H-bonds are reduced as are the number of Tyr2-Pro4 CH-π interactions and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In 4 M urea, a shorter turn places Gly7 into the β-sheet region and Tyr10 is pushed out into the solvent. In 8 M urea, the number of Asp3-Glu5 H-bonds is increased and the β-sheet is lost, but the electrostatic interaction between the charged termini is restored and a cation-π interaction between the indolyl ring of Trp9 and the positively charged N-terminus is formed. In 8 M urea at 333 K, the β-hairpin conformation is almost lost. The structure of CLN025 is stable, because the weakly polar interactions and H-bonds maintain the β-hairpin conformation in the various environments. CLN025 should not be considered a miniprotein, because it lacks a well-defined tertiary structure, it is resistant to denaturation, it does not have an increased heat capacity near its melting temperature, and the structures near and above the melting temperature retain a β-hairpin conformation.

Antigen Retrieval Causes Protein Unfolding

Antigen retrieval (AR), in which formalin-fixed paraffin-embedded tissue sections are briefly heated in buffers at high temperature, often greatly improves immunohistochemical staining. An important unresolved question regarding AR is how formalin treatment affects the conformation of protein epitopes and how heating unmasks these epitopes for subsequent antibody binding. The objective of the current study was to use model proteins to determine the effect of formalin treatment on protein conformation and thermal stability in relation to the mechanism of AR. Sodium dodecyl sulfate polyacrylamide gel electrophoresis was used to identify the presence of protein formaldehyde cross-links, and circular dichroism spectropolarimetry was used to determine the effect of formalin treatment and high-temperature incubation on the secondary and tertiary structure of the model proteins. Results revealed that for some proteins, formalin treatment left the native protein conformation unaltered, whereas for others, formalin denatured tertiary structure, yielding a molten globule protein. In either case, heating to temperatures used in AR methods led to irreversible protein unfolding, which supports a linear epitope model of recovered protein immunoreactivity. Consequently, the core mechanism of AR likely centers on the restoration of normal protein chemical composition coupled with improved accessibility to linear epitopes through protein unfolding.

Direct Calorimetric Determination of a Complete Polyproline II (pII) Propensity Scale Reveals PII Enhancement in Intrinsically Disordered Proteins

Circular dichroism spectropolarimetry experiments and other studies have suggested that the denatured states of polypeptides may comprise a smaller conformational space than previously thought, and that the polyproline II (PII) helix is one of the conformations that is highly populated in the denatured state. Src-homology 3 (SH3) is a modular domain that recognizes and binds peptide in the PII conformation, such as SosY, with high specificity. Our experimental strategy is to use isothermal titration calorimetry (ITC) to monitor the binding of SH3 to engineered SosY peptides, enabling the direct detection of ligand population that is in the PII conformation. Importantly, our model system allows direct access to free energy information concerning the context dependent PII propensity of amino acids at specific sites in the SosY peptide. Binding isotherms have been measured and quantitative estimates made for the PII propensity all twenty amino acids, developing a complete PII scale. Correlations of the calorimetrically determined scale to the GenomeNet database of amino acid physico-chemical property and secondary structure propensity scales revealed no significant correlations. An algorithm is developed to calculate the average PII propensities of different sequences, revealing that intrinsically disordered proteins have an enhancement of PII compared to sequences that fold. Upon random shuffling, the high PII regions within intrinsically disordered segments are lost, demonstrating local enrichment of high PII bias within these sequences.

The C-Terminus of Nucleolin Promotes the Formation of the c-MYC G-Quadruplex and Inhibits c-MYC Promoter Activity

Nucleolin, the most abundant nucleolar phosphoprotein of eukaryotic cells, is known primarily for its role in ribosome biogenesis and cell proliferation. It is, however, a multifunctional protein that, depending on the cellular context, can drive either cell proliferation or apoptosis. Our laboratory recently demonstrated that nucleolin can function as a repressor of c-MYC transcription by binding to and stabilizing the formation of a G-quadruplex structure in a region of the c-MYC promoter responsible for controlling 85-90% of c-MYC's transcriptional activity. In this study, we investigate the structural elements of nucleolin that are required for c-MYC repression. The effect of nucleolin deletion mutants on the formation and stability of the c-MYC G-quadruplex, as well as c-MYC transcriptional activity, was assessed by circular dichroism spectropolarimetry, thermal stability, and in vitro transcription. Here we report that nucleolin's RNA binding domains 3 and 4, as well as the arginine-glycine-glycine (RGG) domain, are required to repress c-MYC transcription.

Circular Dichroism Spectroscopy in the Undergraduate Curriculum

Circular dichroism spectropolarimetry (CD) is a method of optical spectroscopy that seems in most practical ways like UV−visible spectroscopy. The main difference between the two methods is that CD, instead of measuring the absorbance of light as a function of wavelength, measures the difference in absorbance of left versus right circularly polarized light as a function of wavelength. A CD spectrum is an observation of the structure of a chiral compound; it often serves as a “fingerprint” of the structure of biological molecules such as proteins and nucleic acids. For this reason, CD has been broadly applied in biochemistry and in many other areas ranging from organometallic to nanoscale chemistry. Despite its exceptional ease of use and connection to central topics in chemistry, however, CD remains rare in the undergraduate curriculum. This article briefly introduces the theory and practice of CD spectroscopy and a discussion of its advantages in the undergraduate curriculum and the required instrumentation.