Random Coil Transition Research Articles

Alternative S2 Hinge Regions of the Myosin Rod Differentially Affect Muscle Function, Myofibril Dimensions and Myosin Tail Length

Muscle myosin heavy chain (MHC) rod domains intertwine to form alpha-helical coiled-coil dimers; these subsequently multimerize into thick filaments via electrostatic interactions. The subfragment 2/light meromyosin “hinge” region of the MHC rod, located in the C-terminal third of heavy meromyosin, may form a less stable coiled-coil than flanking regions. Partial “melting” of this region has been proposed to result in a helix to random-coil transition. A portion of the Drosophila melanogaster MHC hinge is encoded by mutually exclusive alternative exons 15a and 15b, the use of which correlates with fast (hinge A) or slow (hinge B) muscle physiological properties. To test the functional significance of alternative hinge regions, we constructed transgenic fly lines in which fast muscle isovariant hinge A was switched for slow muscle hinge B in the MHC isoforms of indirect flight and jump muscles. Substitution of the slow muscle hinge B impaired flight ability, increased sarcomere lengths by approximately 13% and resulted in minor disruption to indirect flight muscle sarcomeric structure compared with a transgenic control. With age, residual flight ability decreased rapidly and myofibrils developed peripheral defects. Computational analysis indicates that hinge B has a greater coiled-coil propensity and thus reduced flexibility compared to hinge A. Intriguingly, the MHC rod with hinge B was ∼5 nm longer than myosin with hinge A, consistent with the more rigid coiled-coil conformation predicted for hinge B. Our study demonstrates that hinge B cannot functionally substitute for hinge A in fast muscle types, likely as a result of differences in the molecular structure of the rod, subtle changes in myofibril structure and decreased ability to maintain sarcomere structure in indirect flight muscle myofibrils. Thus, alternative hinges are important in dictating the distinct functional properties of myosin isoforms and the muscles in which they are expressed.

What's so special about polymers? A little known organizing principle gives rise to an abundance of polymer phase transitions

AbstractWe argue that if an organizing principle exists it must have to do with the linear connectivity of the monomers since this feature is what distinguishes polymers from all other materials. We then compare a linear polymer threading a pore in a membrane (PTM) with an equal number of unconnected monomers which are also allowed to transit through a pore in a membrane. The crucial difference between the two cases is that the connected monomers are distinguishable from one another by virtue of their location along the polymer chain whereas the disconnected monomers are indistinguishable. Because of this, the disconnected monomers obey the ideal gas laws while the connected monomers undergo a first‐order thermodynamic phase transition! Four other phase transitions occurring in isolated linear polymer molecules are known. They are the helix to random coil (HR) transitions in biological polymers, surface adsorption (SA), polymer collapse (C), and a model of polymerization (P). These five kinds of transitions can be coupled to one another resulting in a sizable number of exactly solvable minimal models of phase transitions. There are also five classes of phase transitions in many polymers systems. The coupling of these 10 classes of transitions to each‐other results in a plethora of phases. These in turn provide the basis for the many polymer structures observed in the world about us. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2612–2620, 2006

The membrane-induced structure of melittin is correlated with the fluidity of the lipids

The effect of the bee toxin melittin on DMPC dynamics in fast-tumbling bicelles has been investigated. The 13C R 1 and 13C– 1H NOE relaxation parameters for DMPC were used to monitor the effect of melittin and cholesterol on lipid dynamics. It was found that melittin has the largest effect on the DMPC mobility in DMPC/DHPC bicelles, while less effect was observed in cholesterol-doped bicelles, or in bicelles made with CHAPS, indicating that the rigidity of the membrane affects the melittin–membrane interaction. CD spectra were analysed in terms of cooperativity of the α-helix to random coil transition in melittin, and these results also indicated similar differences between the bicelles. The study shows that bicelles can be used to investigate lipid dynamics by spin relaxation, and in particular of peptide-induced changes in membrane fluidity.

Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions.

Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004) Science 303, 1674-1678] show that refolding, monitored by the end-to-end distance, occurs in distinct multiple stages. To clarify the molecular nature of folding starting from stretched conformations, we have probed the folding dynamics, upon force quench, for the single I27 domain from the muscle protein titin by using a C(alpha)-Go model. Upon temperature quench, collapse and folding of I27 are synchronous. In contrast, refolding from stretched initial structures not only increases the folding and collapse time scales but also decouples the two kinetic processes. The increase in the folding times is associated primarily with the stretched state to compact random coil transition. Surprisingly, force quench does not alter the nature of the refolding kinetics, but merely increases the height of the free-energy folding barrier. Force quench refolding times scale as tau(F) approximately tau(F)(0)exp(f(q)Deltax(f)/k(B)T), where Deltax(f) approximately 0.6 nm is the location of the average transition state along the reaction coordinate given by end-to-end distance. We predict that tau(F) and the folding mechanism can be dramatically altered by the initial and/or final values of force. The implications of our results for design and analysis of experiments are discussed.

Photolithographic Patterning of Dendrimer Monolayers and Pattern-Selective Adsorption of Linear Macromolecules

Alkyl groups of n-octadecyltrimethoxysilane (ODS) in a self-assembled monolayer on a silicon substrate were oxidized to carboxyl groups by partial irradiation of vacuum ultra-violet light under the photomask, producing a COOH/ODS line pattern. After active esterification of carboxyl groups, two kinds of amine-terminated dendrimers, poly(propyleneimine) and poly(amido amine) (PAMAM) dendrimers, were immobilized on a COOH line through amide-bond so that photolithographic dendrimer/ODS pattern was finally fabricated. Preparation was certified by atomic force microscopy (AFM) and surface-enhanced infrared absorption spectroscopy at transmission mode. Adsorption of linear macromolecules was examined on PAMAM dendrimer/ODS pattern. After adsorption of poly-L-glutamic acid (PGA) at a pH below alpha-helix--random coil transition, rod-shape texture was observed only on the dendrimer line in an AFM image. This texture is an aggregate of alpha-helical PGA. Sodium hyaluronate and DNA were also adsorbed selectively on the dendrimer line, keeping the line profile, although characteristic textures were not observed.

Energetic contributions for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks.

We used a combination of spectroscopic and calorimetric techniques to determine complete thermodynamic profiles accompanying the folding of a set of triple helices and control duplexes. Specifically, we studied the sequences: d(A(7)C(5)T(7)C(5)T(7)), d(A(6)C(5)T(6)C(5)T(6)), d(A(6)C(5)T(6)), d(AGAGAGAC(5)TCTCTCTC(5)TCTCTCT), d(AGAGAC(5)TCTCTC(5)TCTCT), d(AGAGAC(5)TCTCTC(2)), d(AAGGAC(5)TCCTTC(5)TTCCT), d(AGGAAC(5)TTCCTC(5)TCCTT), and d(GAAAGC(5)CTTTCC(5)CTTTC). Circular dichroism spectroscopy indicated that all triplexes and duplexes are in the "B" conformation. DSC melting experiments revealed that the formation of triplexes is accompanied by a favorable free energy change, which arises from the compensation of a large and favorable enthalpic contribution with an unfavorable entropic contribution. Comparison of the thermodynamic profiles of these triplexes yielded enthalpic contributions of -24 kcal/mol, -23 kcal/mol, and -22 kcal/mol for the formation of TAT/TAT, TAT/CGC(+), and CGC(+)/CGC(+) base triplet stacks, respectively. UV melts as a function of sodium concentration show sodium ions stabilize the triplexes that contain only TAT triplets but destabilize the triplexes that contain CGC(+) triplets. UV melts as a function of pH indicate that the protonation of the third strand and loop cytosines stabilizes the triplexes that contain CGC(+) and TAT triplets, respectively. Our overall results suggest that the triplex to duplex transition of triplexes that contain CGC(+) triplets is accompanied by a release of protons and an uptake of sodium, while their duplex to random coil transition is accompanied by a release of sodium ions. A consequence of this opposite sodium dependence is that their coupled transitions are nearly independent of sodium concentration but are dependent on the experimental pH.

The effect of helix-coil transition on backbone 15N NMR relaxation of isolated transmembrane segment (1–36)-bacteriorhodopsin

In this paper we develop a motional model of isolated transmembrane segment 1–36 bacteriorhodopsin (BR) in a weakly polar organic mixture. The model is based on the statistical mechanics theory [Lifson, S. and Roig, A. (1961) J. Chem. Phys., 34, 1963–1974] and represents the dynamics of 1–36BR as an interconversion between a limited number of intermediates of α-helix – random coil transition. The equilibrium parameters of helix-coil transition were selected by the comparison of calculated profiles of mean residual helicity of 1–36BR with the available experimental data. The kinetic modeling of the helix-coil transition was used for calculation of the correlation functions of internal motions of the backbone NH vectors. The calculated correlation functions are multiexponential and consist of two groups of exponential terms: ‘fast’ (pico–nanoseconds) and ‘slow’ (sub-microseconds). The decay of the correlation functions on the pico–nanosecond time-scale was used for qualitative estimates of NMR observable order parameters of the backbone NH vectors. The calculated order parameters are in good correspondence with the experimental values obtained from ‘model-free’ analysis of 1H-15N NMR relaxation data [Orekhov et al. (1999) J. Biomol. NMR, 14, 345–356]. Low and uniform (over the peptide) order parameters of nanosecond time-scale motions (Ss2 ∼ 0.5—0.6) are accounted for by the exchange between kinked states with several α-helical regions within 1–36BR. These states are caused by the presence of helix breaking residues Gly and Thr in the central part of 1–36BR.

Photochromic Polypeptides as Synthetic Models of Biological Photoreceptors: A Spectroscopic Study

l-Glutamic acid polypeptides containing photochromic nitrospiropyran bound to the side chains at various percentages (“local” concentration) have been synthesized and investigated as possible artificial models of biological photoreceptors. Absorption and fluorescence spectroscopy have been utilized to investigate the photophysical and photochemical properties of nitrospiropyrans, both inserted in the polypeptide chain and in solution as “free” dye. Conformational variations produced by dark storage and light exposure of the photochromic polypeptides have been studied by means of circular dichroism. Dark-kept “free” dyes in hexafluoro-2-propanol solution in the merocyanine form (“open” form) give rise to molecular aggregates, which have been characterized as merocyanine dimers. The equilibrium constant between the monomer and the dimer, K, and their molar extinction coefficients, ϵ, at several wavelengths have been determined. Fluorescence measurements on “free” and polypeptide-bound nitrospiropyrans suggest that the dimerization process between merocyanines is favored when the photochromic units are inserted in the polypeptide chain and that under these conditions an efficient energy transfer from the monomer (donor) to the dimer (acceptor) occurs. By varying “local” as well as total nitrospiropyran concentration, it has been shown that the dimeric species result from intermolecular interactions between photochromic groups inserted in the same polypeptide chain. The α-helix→random coil transition of the polypeptide structure after dark storage has eventually been shown to be the result of the dimerization process and not of the dark isomerization per se from the “closed” spiropyran form to the “open” merocyanine form of the dye.

Arabinogalactan from Western Larch, Part II; A Reversible Order-Disorder Transition

At the molecular level, larch arabinogalactan (AG) fragments into subunits when exposed to mild alkali or heat. This process is accompanied by a large increase in NMR spectral resolution, especially for NMR signals associated with main-chain units, and by the disappearance of 1H NMR signals probably due to persistent hydrogen bonds. Analysis by size-exclusion chromatography (SEC) shows that smaller AG species undergo the transition in preference to larger ones, and the transition can be reversed by drying from or freezing an aqueous solution of the “fragments” These observations indicate that the fragmentation is a dissociation of a molecular assembly accompanied by an order-disorder transition, analogous to the known triple helix → single-chain random coil transition of (1→6)-branched (1→3)-β-glucans. The small amount of uronic acid units in AG and the consequent ionexclusion effect in SEC provide a probe to study this transition, and results provide evidence in support of the concept that the transition involves dissociation of a triplex.

Kinetic study of conformational transition accompanied by isomerization of spiropyrans bound to poly(l-glutamic acid) side chains.

Kinetic studies have been made of the conformational transition of the backbone of spiropyran-modified poly(L-glutamic acid) (PSLG) from α-helix to random coil, accompanied by the isomerization of spiropyrans in the side chains from spiropyran form (SP) to merocyanine form (MC) in hexafluoro-2-propanol (HFP) in dark adaptation after visible light irradiation, by means of the measurements of absorption and circular dichroism spectra. The SP→ MC isomerization reaction of side-chain spiropyrans in PSLG deviated from first-order kinetics in the earlier stage, where the α-helix→ random coil transition of the backbone correlatively occurred. Then, the isomerization proceeded in first-order kinetics under the conformational state of the backbone merely in random coil. The kinetic analyses of the SP→MC isomerization were carried out on the basis of a binary competitive reaction kinetics, in which two species of SPs bound to the side chains of local PSLG in the backbone conformations of α-helix and random coil, respectively, are involved. As a result, it was derived that the rate of the SP→MC isomerization in the α-helix backbone was appreciably smaller than that in the random coil backbone, and depended on the spiropyran content in PSLG, indicating that the isomerization rate for PSLG with a low spiropyran content of 0.15 was considerably smaller than that for PSLGs with higher spiropyran contents above 0.25. Moreover, the solvent effect on the isomerization rates has been investigated, using the mixed solvent of HFP/MeOH. Consequently, the analytical results led to the inference that the isomerization rates of the spiropyran side chains are governed by molecular conformations of PSLG.

Solute Permeability Enhancement at a Specific pH by an Amphiphilic Copolypeptide Membrane

pH-Responsive polypeptide, poly(Leu-Gln(EtNH 2 )), membranes consisting of hydrophobic leucine (Leu) and hydrophilic N ω -β-(aminoethyl)-L-glutamine) (Gln(EtNH 2 )) residues have been prepared and pH-induced conformational changes of the polypeptide in membranes and their relation to membrane swelling and solute permeation properties were investigated. IR spectra of the membrane containing 31% Gln(EtNH 2 ) residues indicated an α-helix to random coil transition by decreasing pH with the midpoint of the transition at ca. pH 4.7

α‐helix to random coil transitions: Determination of peptide concentration from the CD at the isodichroic point

A method is presented for determining the concentrations of peptides and proteins having isodichroic points near 203 nm. The existence of an isodichroic point for a given substance indicates a local two-state (alpha-helix, random coil) population. The mean residue ellipticity at the isodichroic point, [theta lambda i], is, of course, independent of helix content. For a wide variety of synthetic and natural peptides, including both single helices and coiled coils, it is shown that [theta lambda i] is also essentially independent of substance and of whether the transition is induced by temperature, ionic strength, pH, chain length changes, amino acid substitution, or solvent perturbation. Averaging [theta lambda i] values culled from various laboratories gives -151 +/- 16 (SD, 7 sources) deg.cm2.mmol-1. In our laboratory, nonpolymerizable rabbit alpha-tropomyosin and two alpha-tropomyosin subsequences yield -135 +/- 10 (SD, 190 values) deg.cm2.mmol-1. Thus, given [theta lambda i] for a peptide of known concentration, it is possible to estimate the concentration of any other peptide provided that it has an isodichroic point at which the ellipticity is accurately measurable. It is then possible to calculate [theta lambda] at any other wavelength for which theta is known. It is advisable to determine [theta lambda i] for the best known peptide in one's own laboratory, since it depends on absolute instrument and cell calibrations and an absolute concentration determination.

Alpha-helix to random coil transitions: interpretation of the CD in the region of linear temperature dependence.

Alpha-helix to random coil transitions: interpretation of the CD in the region of linear temperature dependence.

Conformation transitions in aqueous solutions of poly(L-glutamic acid): a radiowave dielectric study

The dielectric properties of poly(L-glutamic acid) aqueous solutions during the entire conformational helix to random coil transition induced by pH have been measured in the frequency range from 1 kHz to 10 MHz. The dielectric spectra have been decomposed into two separate dielectric relaxations attributed to counterion fluctuation in the neighborhood of the polyion. The characteristic parameters underlying the counterion polarization dielectric models have been estimated

Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water.

The enthalpy change (delta H) accompanying the alpha-helix to random coil transition in water has been determined calorimetrically for a 50-residue peptide of defined sequence that contains primarily alanine. The enthalpy of helix formation is one of the basic parameters needed to predict thermal unfolding curves for peptide helices and it provides a starting point for analysis of the peptide hydrogen bond. The experimental uncertainty in delta H reflects the fact that the transition curve is too broad to measure in its entirety, which precludes fitting the baselines directly. A lower limit for delta H of unfolding, 0.9 kcal/mol per residue, is given by assuming that the change in heat capacity (delta Cp) is zero, and allowing the baseline to intersect the transition curve at the lowest measured Cp value. Use of the van't Hoff equation plus least-squares fitting to determine a more probable baseline gives delta H = 1.3 kcal/mol per residue. Earlier studies of poly(L-lysine) and poly(L-glutamate) have given 1.1 kcal/mol per residue. Those investigations, along with our present result, suggest that the side chain has little effect on delta H. The possibility that the peptide hydrogen bond shows a correspondingly large delta H, and the implications for protein stability, are discussed.

α‐Helix to random coil transitions of two‐chain coiled coils: Experiments on the thermal denaturation of ββ tropomyosin cross‐linked selectively at C36

Current ideas on unfolding equilibria in two-chain, coiled-coil proteins are examined by studies of a species of beta beta tropomyosin that is sulfhydryl blocked at C190 and disulfide cross-linked at C36 (.beta-beta.). The desired species is produced by a seven-step process: (1) Rabbit skeletal muscle, comprising predominantly alpha alpha and alpha beta species, is oxidized with ferricyanide, cross-linking both species at C190. (2) The product is carbamylated at C36 of beta chains, using cyanate in denaturing medium at pH 6. (3) All C190 cross-links are reduced with dithiothreitol (DTT). (4) All C190 sulfhydryls are permanently blocked by carboxyamidomethylation. (5) Chromatography on carboxymethylcellulose in denaturing medium is used to separate C190-blocked alpha chains from C190-blocked, C36-carbamylated beta chains. (6) The latter are decarbamylated in denaturing medium by raising the pH to 8.0. (7) The C190-blocked beta chains are renatured and cross-linked at C36 by ferricyanide. The procedure and the quality of the final product are judged by NaDodSO4/polyacrylamide gel electrophoresis, titration of free sulfhydryls, and electrophoretic analysis of trypsin digestion products. Thermal unfolding curves are reported for the resulting pure .beta-beta. species and for its DTT-reduction product. The latter (.beta beta.) show equilibrium thermal unfolding curves that are very similar to those of the parent beta beta noncross-linked species. The .beta-beta. cross-linked species unfolds in a single-phase, cooperative transition with a melting temperature intermediate between the pretransition and posttransition shown by its cross-linked counterpart, the C190 cross-linked, C36-blocked species (.beta-beta.), which was studied earlier. These transitions are compared with one another and with that of the doubly cross-linked species, beta-(-)beta, in the light of two extant physical models for such transitions. The all-or-none segments model successfully rationalizes the data qualitatively for the .beta-beta. and .beta-beta. species if the usual postulates of greater inherent stability of the amino vs the carboxyl end of the molecule and of strain at each cross-link are accepted. However, the same model then requires that the beta-(-)beta species be the least stable of the three, whereas experiment shows the opposite, thus falsifying the all-or-none segments model. The continuum-of-states model is also qualitatively in accord with data on the .beta-beta. and .beta-beta. species.(ABSTRACT TRUNCATED AT 400 WORDS)

α‐Helix to random coil transitions of two‐chain coiled coils: Experiments on the thermal denaturation of isolated segments of αα‐tropomyosin

Circular dichroism (CD) experiments in the backbone (200-240 nm) region are reported for four isolated, excised two-chain, coiled-coil segments whose chains comprise, respectively, residues 11-127, 142-281, 1-189, and 190-284 of the rabbit alpha alpha-tropomyosin (Tm) sequence. The uv and CD spectra for the noncross-linked segments are very similar to those for parent Tm. At 3 degrees C, all have a helix content of 90% or more; moreover, all thermal denaturation curves depend on concentration, as required by mass action, and are completely reversible. At comparable concentrations, solutions show values of T1/2 (the temperature at which the helix content is 50%) following the order of 11Tm127 approximately 1Tm189 greater than 142Tm281 greater than 190Tm284. The thermal unfolding data for 11Tm127, 190Tm284, and 142Tm281 fall on apparently monophasic curves (single inflection point). However, curves for 1Tm189 show a heretofore unknown low temperature transition in which the helix content drops from approximately 90% at 2 degrees C to approximately 73% at 20 degrees C, indicating that this segment has one or more weak sections totaling approximately 50 residues per chain. Since thermal denaturation curves for noncross-linked 11Tm127, 142Tm281, and Tm have no such low temperature transition, i.e., the helix content is not additive, the weak region probably comprises the bulk of the residues between 127 and 189 in 1Tm189, but is somehow stabilized in 142Tm281 and in parent Tm.(ABSTRACT TRUNCATED AT 250 WORDS)

Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: three-state and four-state thermodynamic models.

Chemical shifts of base and H1' protons of the single-stranded hexamers d(ATTACC) and d(GGTAAT), of the 1:1 mixtures of these complementary hexamers, and of the self-complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation. Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B-DNA duplex or a hairpin-loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin-loop formation. In the analysis of the duplex formation of the hexamers, a two-state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three-state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two-state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual delta Hd degrees and delta Sd degrees values. Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an average Tmd value of 341 K (1M DNA) and delta Hd degrees of - 121 kJ.mol-1 for the dimer/random-coil transition of the hexamer duplex d(ATTACC).d(GGTAAT). For the duplex in equilibrium random-coil transition of the 12-mer d(ATTACCGGTAAT) an average Tmd value of 336 K (1M DNA) and delta Hd degrees of -372 kJ.mol-1 are found. The hairpin/random-coil transition of d(ATTACCGGTAAT) is characterized by a rather large delta Hh degrees value, -130 kJ.mol-1, and an average Tmh value of 304 K.

Influence of uracil on the conformational behaviour of RNA oligonucleotides in solution

NMR studies were carried out on some alternating pyrimidine-purine sequences: the single-stranded tetramers CACA and UGUG and the self-complementary octamer CACAUGUG. Assignments, based upon COSY, homonuclear Hartmann-Hahn, and NOESY experiments, are given for the resonances of all base protons and of several sugar protons. Chemical shift vs temperature profiles were used to obtain thermodynamic parameters for the single-stranded stack in equilibrium with random coil and the duplex in equilibrium with random coil equilibria. The populations of N-type conformer of the ribose rings were estimated from the observed J1'2'. Comparisons with another alternating pyrimidine-purine sequence Um2(6)AUm2(6)A and with the deoxyribose counterparts d(CACA), d(TGTG) and d(CACATGTG) are given. Previous 1H-NMR investigations of Um2(6)AUm2(6)A revealed that the population of bulge-out structure diminishes compared to m2(6)AUm2(6)A due to the U(1)-m2(6)A(2) stacking interaction. In CACA a strong stacking proclivity (Tm = 310 K) together with a clear preference for N-type ribose is observed. However, the stacking interactions in UGUG are relatively less stable (Tm = 288 K) and a bias towards S-type sugar is present. Besides a small amount of stack, a significant contribution of bulge out structure is proposed for UGUG. We conclude that the nature of the pyrimidine base mainly determines the formation of bulge-out structures. The poor stacking properties of uracil now appear to be mainly responsible for this phenomenon. Comparison with the deoxyribose counterparts shows a reasonable agreement between the Tm values of CACA and d(CACA), whereas the Tm of UGUG (288 K) is much lower than the Tm of d(TGTG) (315 K). It is suggested that the absence of bulge-out structures in DNA purine-pyrimidine-purine sequences is related to the relatively strong stacking proclivity of dT residues compared to that of U residues. The Tm values (average 341 K) for the duplex in equilibrium with random coil transition obtained for each residue of CACAUGUG appear very similar. All ribose rings, except the G(8), adopt a pure N conformer in the duplex. This is taken to mean that the differences in conformational behaviour of the constituent tetramers disappear upon duplex formation.

Energetics of order/order transitions in nucleic acids

Besides the temperature induced canonical helix to random coil transition, which serves as a prototype of an order/disorder transition, there is a second group of conformational changes in helical polynucleotides, which will be termed order/order transitions. Depending on the environmental conditions and the sequence of the polynucleotides involved, there are four alternative reaction schemes: (i) The inversion of the helical handedness from a right-handed to a left-handed conformation, (ii) the disproportionation of a double helix into a single strand and a triple helix, (iii) the addition of a single strand to a double helix, and (iv) the single/double strand displacement reactions, that is, the displacement of one of the two strands of the helix by a matching single-stranded polynucleotide or the mutual exchange of one strand each between two helical structures. The first three reactions are considered reversible while the last reaction is irreversible; that is, one cannot regain the initial state by inversing the course of the change, here the change in temperature. Both ribo and deoxyribo polynucleotides can undergo these reactions. In the following paper at least one example is given for each of these reactions.