Molecular states in single-stranded adenylate chains by relaxation analysis

Short PolyA RNA Homopolymers Undergo Mg2+-Mediated Kinetically Arrested Condensation

RNA-RNA interactions have increasingly been recognized for their potential to shape the mesoscale properties of biomolecular condensates, influencing morphology, organization, and material state through networking interactions. While most studies have focused on networking via Watson-Crick base pairing interactions, previous work has suggested a potential for noncanonical RNA-RNA interactions to also give rise to condensation and alter overall material state. Here, we test the phase separation of short polyA RNA (polyrA) homopolymers. We discover and characterize the potential for short polyrA sequences to form RNA condensates at lower Mg²⁺ concentrations than previously observed, which appear as internally arrested droplets with slow polyrA diffusion despite continued fusion. Our work also reveals a negative cooperativity effect between the effects of Mg²⁺ and Na⁺ on polyrA condensation. Finally, we observe that polyrA sequences can act as promoters of phase separation in mixed sequences. These results demonstrate the potential for noncanonical interactions to act as networking stickers, leading to specific condensation properties inherent to polyrA composition and structure, with implications for the fundamental physical chemistry of the system and function of polyA RNA in biology.

Nuclear Magnetic Resonance Spectra and AMBER OL3 and ROC-RNA Simulations of UCUCGU Reveal Force Field Strengths and Weaknesses for Single-Stranded RNA

Single-stranded regions of RNA are important for folding of sequences into 3D structures and for design of therapeutics targeting RNA. Prediction of ensembles of 3D structures for single-stranded regions often involves classical mechanical approximations of interactions defined by quantum mechanical calculations on small model systems. Nuclear magnetic resonance (NMR) spectra and molecular dynamics (MD) simulations of short single strands provide tests for how well the approximations model many of the interactions. Here, the NMR spectra for UCUCGU at 2, 15, and 30 °C are compared to simulations with the AMBER force fields, OL3 and ROC-RNA. This is the first such comparison to an oligoribonucleotide containing an internal guanosine nucleotide (G). G is particularly interesting because of its many H-bonding groups, large dipole moment, and proclivity for both syn and anti conformations. Results reveal formation of a G amino to phosphate non-bridging oxygen H-bond. The results also demonstrate dramatic differences in details of the predicted structures. The variations emphasize the dependence of predictions on individual parameters and their balance with the rest of the force field. The NMR data can serve as a benchmark for future force fields.

Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer

Thermally driven conformational fluctuations (or "breathing") of DNA play important roles in the function and regulation of the "macromolecular machinery of genome expression." Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here, we use microsecond-resolved single-molecule Förster resonance energy transfer (smFRET) experiments to investigate the backbone fluctuations of short [oligo(dT)_n] templates within DNA constructs that also serve as models for ss-dsDNA junctions. Such junctions, together with the attached ssDNA sequences, are involved in interactions with the ssDNA binding (ssb) proteins that control and integrate the functions of DNA replication complexes. We analyze these data using a chemical network model based on multiorder time-correlation functions and probability distribution functions that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)_n tails of ss-dsDNA constructs interconvert, on submillisecond time scales, between three macrostates with distinctly different end-to-end distances. These are (i) a "compact" macrostate that represents the dominant species at equilibrium; (ii) a "partially extended" macrostate that exists as minority species; and (iii) a "highly extended" macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA-associating proteins.

Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer

Some DNA sequences in crystals and in complexes with proteins can exist in the forms intermediate between the B- and A-DNA. Based on this, it was implied that the B-to-A transition for any DNA molecule should go through these intermediate forms also in kinetics. More precisely, the helix parameter Slide has to change first, and the molecule should take the E-form. After that, the Roll parameter changes. In the present work, we simulated the kinetics of the B-A transition in the Drew-Dickerson dodecamer, a known B-philic DNA oligomer. We used the "sugar" coarse-grained model that reproduces ribose flexibility, preserves sequence specificity, employs implicit water and explicit ions, and offers the possibility to vary friction. As the control parameter of the transition, we chose the volume available for a counterion and considered the change from a large to a small volume. In the described system, the B-to-A conformational transformation proved to correspond to a first-order phase transition. The molecule behaves like a small cluster in the region of such a transition, jumping between the A- and B-forms in a wide range of available volumes. The viscosity of the solvent does not affect the midpoint of the transition but only the overall mobility of the system. All helix parameters change synchronously on average, we have not observed the sequence "Slide first, Roll later" in kinetics, and the E-DNA is not a necessary step for the transition between the B- and A-forms in the studied system. So, the existence of the intermediate DNA forms requires specific conditions, shifting the common balance of interactions: certain nucleotide sequence in specific solution or/and the interaction with some protein.

Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics

Molecular dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments. Analysis of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments. Combining MD simulations with HMSM analysis is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.

Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.

Physics-based all-atom modeling of RNA energetics and structure

The database of RNA sequences is exploding, but knowledge of energetics, structures, and dynamics lags behind. All-atom computational methods, such as molecular dynamics, hold promise for closing this gap. New algorithms and faster computers have accelerated progress in improving the reliability and accuracy of predictions. Currently, the methods can facilitate refinement of experimentally determined nuclear magnetic resonance and x-ray structures, but are 'unreliable' for predictions based only on sequence. Much remains to be discovered, however, about the many molecular interactions driving RNA folding and the best way to approximate them quantitatively. The large number of parameters required means that a wide variety of experimental results will be required to benchmark force fields and different approaches. As computational methods become more reliable and accessible, they will be used by an increasing number of biologists, much as x-ray crystallography has expanded. Thus, many fundamental physical principles underlying the computational methods are described. This review presents a summary of the current state of molecular dynamics as applied to RNA. It is designed to be helpful to students, postdoctoral fellows, and faculty who are considering or starting computational studies of RNA. WIREs RNA 2017, 8:e1422. doi: 10.1002/wrna.1422.

Kinetics of the B-A transition of DNA: analysis of potential contributions to a reaction barrier

Because of open problems in the relation between results obtained by relaxation experiments and molecular dynamics simulations on the B-A transition of DNA, relaxation measurements of the B-A dynamics have been extended to a wider range of conditions. Field-induced reaction effects are measured selectively by the magic angle technique using a novel cell construction preventing perturbations from cell window anisotropy. The kinetics was recorded for the case of poly[d(AT)] up to the salt concentration limit of 4.4 mM, where aggregation does not yet interfere. Now experimental data on the B-A dynamics are available for poly[d(AT)] at salt concentrations of 0.18, 0.73, 2.44 and 4.4 mM. In all cases, a spectrum of time constants is found, ranging from ~ 10 μs up to components approaching ~ 1 ms. The relatively small dependence of these data on the salt concentration indicates that electrostatic effects on the kinetics are not as strong as may be expected. The ethanol content at the transition center is a linear function of the logarithm of the salt concentration, and the slope is close to that expected from polyelectrolyte theory. The B-A transition dynamics was also measured in D₂O at a salt concentration of 2.4 mM: the center of the transition is found at 20.0 mol/l H₂O and at 20.1 mol/l D₂O with an estimated accuracy of ± 0.1 mol/l; the spectrum of time constants at the respective transition centers is very similar. The experimental results are discussed regarding the data obtained by molecular dynamics simulations.

On the origin of multiexponential fluorescence decays from 2-aminopurine-labeled dinucleotides

The fluorescent probe 2-aminopurine (2Ap) has been used for decades to study local conformational fluctuations in DNA. Steady-state and time-resolved measurements of 2Ap fluorescence have been used to predict specific conformational states through suitable modeling of the quenching of the fluorescence of a 2Ap residue incorporated site-specifically into a DNA strand. The success of this approach has been limited by a lack of understanding of the precise factors responsible for the complex, multiexponential decays observed experimentally. In this study, dinucleotides composed of 2Ap and adenine were studied by the time-correlated single-photon counting technique to investigate the causes of heterogeneous emission kinetics. Contrary to previous reports, we argue that emission from 2Ap that is stacked with a neighboring base contributes negligibly to the emission signals recorded more than 50 ps after excitation, which are instead dominated by emission from unstacked 2Ap. We find that the decay kinetics can be modeled using a continuous lifetime distribution, which arises from the inherent distance dependence of electron transfer rates without the need to postulate a small number of discrete states with decay times derived from multiexponential fits. These results offer a new perspective on the quenching of 2Ap fluorescence and expand the information that can be obtained from experiments.

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models

Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely, atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures. After properly removing structures that are artificially stabilized by known inaccuracies of the current RNA AMBER force field, the kinetic properties predicted are consistent with the time scales of previously reported relaxation experiments.

Optimization of an AMBER force field for the artificial nucleic acid, LNA, and benchmarking with NMR of L(CAAU)

Locked Nucleic Acids (LNAs) are RNA analogues with an O2'-C4' methylene bridge which locks the sugar into a C3'-endo conformation. This enhances hybridization to DNA and RNA, making LNAs useful in microarrays and potential therapeutics. Here, the LNA, L(CAAU), provides a simplified benchmark for testing the ability of molecular dynamics (MD) to approximate nucleic acid properties. LNA χ torsions and partial charges were parametrized to create AMBER parm99_LNA. The revisions were tested by comparing MD predictions with AMBER parm99 and parm99_LNA against a 200 ms NOESY NMR spectrum of L(CAAU). NMR indicates an A-Form equilibrium ensemble. In 3000 ns simulations starting with an A-form structure, parm99_LNA and parm99 provide 66% and 35% agreement, respectively, with NMR NOE volumes and (3)J-couplings. In simulations of L(CAAU) starting with all χ torsions in a syn conformation, only parm99_LNA is able to repair the structure. This implies methods for parametrizing force fields for nucleic acid mimics can reasonably approximate key interactions and that parm99_LNA will improve reliability of MD studies for systems with LNA. A method for approximating χ population distribution on the basis of base to sugar NOEs is also introduced.

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions

Accurately modeling unpaired regions of RNA is important for predicting structure, dynamics, and thermodynamics of folded RNA. Comparisons between NMR data and molecular dynamics simulations provide a test of force fields used for modeling. Here, NMR spectroscopy, including NOESY, (1)H-(31)P HETCOR, DQF-COSY, and TOCSY, was used to determine conformational preferences for single-stranded GACC RNA. The spectra are consistent with a conformational ensemble containing major and minor A-form-like structures. In a series of 50 ns molecular dynamics (MD) simulations with the AMBER99 force field in explicit solvent, initial A-form-like structures rapidly evolve to disordered conformations. A set of 50 ns simulations with revised χ torsions (AMBER99χ force field) gives two primary conformations, consistent with the NMR spectra. A single 1.9 μs MD simulation with the AMBER99χ force field showed that the major and minor conformations are retained for almost 68% of the time in the first 700 ns, with multiple transformations from A-form to non-A-form conformations. For the rest of the simulation, random-coil structures and a stable non-A-form conformation inconsistent with NMR spectra were seen. Evidently, the AMBER99χ force field improves structural predictions for single-stranded GACC RNA compared to the AMBER99 force field, but further force field improvements are needed.

Unique Physical Signature of DNA Curvature and Its Implications for Structure and Dynamics

A particularly sensitive birefringence technique is used to analyze a curved DNA fragment with 118 bp and a standard DNA with 119 bp. At salt concentrations from 0.5 to 10 mM, both fragments show the usual negative stationary birefringence and monotonic transients - differences are relatively small. At 100 mM salt the curved DNA shows a positive stationary birefringence and non-monotonic transients with processes having amplitudes of opposite sign, whereas signals of the standard DNA remain as usual. Transients induced by reversal of the field vector indicate the existence of a permanent dipole for the curved DNA. 2-MHz-ac pulses induce a negative stationary birefringence in both DNAs. These results are consistent with calculations on models for curved DNA predicting a quasi-permanent dipole and a positive dichroism/birefringence. The quasi-permanent dipole results from the loss of symmetry in the charge distribution of the curved polyelectrolyte. The appearance of the unique signature of curvature at high salt is mainly due to a strong decrease of the polarizability by about 2 orders of magnitude. The special mode of orientation resulting from the quasi-permanent dipole is expected to contribute to the gel migration anomaly. The time constants of birefringence decay for the curved fragment are shorter than those of the 119 bp fragment by a factor of approximately 1.10 at 0.6 mM salt, whereas this factor is approximately 1.20 at 100 mM Na+. If both fragments were normal DNA with 3.4 A rise per base pair, the factor would be approximately 1.02. At high salt and high electric field strengths the factor increases up to 1.37. The implications for the bending dynamics and the potential to distinguish static from dynamic persistence by field reversal experiments are discussed. The dependence of the curvature on the salt concentration indicated by the time constants is consistent with a clear decrease of the electrophoretic anomaly at decreasing salt concentration.

The nature of "unusual" electro-optical transients observed for DNA

Unusual electro-optical transients have been observed for many different polymers and colloidal systems. These effects provoked serious confusion, because a simple-minded interpretation can be completely misleading. The case of double helical DNA is of particular interest, because DNA has been studied in more detail than other systems and because of its biological function. DNA is subject to bending, which implies a loss of symmetry. Due to its high charge density, non-symmetric conformations must have a non-symmetric distribution of charges leading to a torque of considerable magnitude in the presence of external electric fields. The dipole moment describing this torque must be calculated in a coordinate system with its origin at the center of diffusion. The resulting dipole values are in the range of thousands of Debye units. Because the new dipole type is analogous to but not identical with permanent dipoles, the notation "quasi-permanent" dipole is suggested. Application of this concept, using commonly accepted parameters for DNA and established procedures for calculation of electro-optical transients, leads to "unusual" transients. Thus, these transients must be expected from well-known parameters of DNA double helices. The influence of the quasi-permanent dipole moment may be amplified considerably by hydrodynamic coupling. This effect has been demonstrated for the case of smoothly bent rods. Both model calculations and experiments illustrate the danger of getting data that may be completely misleading. For example, depending on pulse amplitudes and/or pulse lengths, electro-optical decays may be accelerated artificially due to superposition of decay components with opposite amplitudes. Experiments show that unusual transients and apparent acceleration effects disappear, when high frequency sine pulses are used for the electro-optical analysis of DNA. Electro-optical effects depend upon the internal dynamics of the object under investigation. In general, the dynamics of DNA bending was assumed to be fast compared to rotational diffusion. Because stacking rearrangements in single stranded nucleic acids are relatively slow and recently the dynamics of the B-A transition was observed in the time range >1 micros, it is likely that there are also relatively slow rearrangements between bending conformers. Bending transitions are expected to be relatively fast, when there are no activation barriers in the bending pathway, and may be slow, when activation barriers must be passed between bending conformers.

Mesoscopic modeling for nucleic acid chain dynamics

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin--a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop--studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.

Chain persistency in single-stranded DNA

We develop a theoretical approach to hairpin-loop formation of single-stranded (ss) DNA by treating the strand as a two-state system in which bases are either "stacked" or "unstacked." The looping kinetics of ssDNA is shown to be intrinsically different from that of a wormlike chain; it is mainly controlled by stacking-breakage probability, not by the mean curvature of loops, and highly sensitive to the composition of the loop as seen in recent experiments. Our estimate of a stacking energy for poly ( dA ), -3.9 kcal/mol, is consistent with known results.

The base sequence dependent flexibility of linear single-stranded oligoribonucleotides correlates with the reactivity of the phosphodiester bond

The effect of base sequence on the structure and flexibility of linear single-stranded RNA molecules and the influence of the base sequence on phosphodiester bond reactivity have been studied. Molecular dynamics simulations of 2.1 ns were carried out for nine chimeric oligonucleotides containing only one unsubstituted ribo unit, all the rest of sugars being 2'-O-methylated. The base sequence has recently been reported to make a big contribution to the reactivity of these compounds. A detailed examination of the interaction energies between the base moieties shows that base stacking is strongly context-dependent and cooperative. The strength of stacking at the site susceptible to chain cleavage by intramolecular transesterification was observed to be dependent on both the flanking bases of the cleavage site and those further apart in the molecule. The interaction energies between the bases in the vicinity of the scissile linkage were found to correlate well with the experimental phosphodiester bond cleavage rates: the stronger the bases close to the cleavage site are stacked, the slower the cleavage rate is.

Single-strand stacking free energy from DNA beacon kinetics

DNA beacons are short single-stranded chains which can form closed hairpin shapes through complementary base pairing at their ends. Contrary to the common polymer theory assumption that only their loop length matters, experiments show that their closing kinetics depend on the loop composition. We have modeled the closing kinetics and in so doing have obtained stacking enthalpies and entropies for single-stranded nucleic acids. The resulting change of persistence length with temperature effects the dynamics. With a Monte Carlo study, we answer another polymer question of how the closing time scales with chain length, finding tau approximately N(2.44+/-0.02). There is a significant crossover for shorter chains, bringing the effective exponent into good agreement with experiment.

Luminescence excitation spectra reveal low-lying excited states in stacked adenine bases

Luminescence emission, polarization, and excitation spectra of polyadenylic acid (poly(A)) have been studied in room-temperature aqueous solution (pH 8). The temperature dependence of the luminescence of poly(A) at two different excitation wavelengths in the range 10-70 degrees C has also been studied and compared with that of adenosine 5'-monophosphate (AMP). It has been found that the luminescence excitation spectrum and the polarization curve of poly(A) solution reveal a low-intensity electronic transition at about 320 nm which is red-shifted by approximately 0.9 eV from the maximum of the absorption spectrum at 260 nm. A model of two luminescent stacked forms is suggested. The difference in the ground state levels of these two stacked forms obtained from the temperature dependencies of the emissions is insignificant ( approximately 1 kcal/mol). This means a lowering of the excited state of the stacked form with the 320 nm/420 nm absorption/emission bands by approximately 0.9 eV as compared to the main form with the 260 nm/400 nm absorption/emission bands. The low-lying excited states suggest the stronger electronic coupling of the bases in a certain stacked form. It is proposed that such clusters of the stacked bases could provide the wire-like conductivity in the short segments of DNA.

Dynamics of gapped DNA recognition by human polymerase beta

Kinetics of human polymerase beta binding to gapped DNA substrates having single stranded (ss) DNA gaps with five or two nucleotide residues in the ssDNA gap has been examined, using the fluorescence stopped-flow technique. The mechanism of the recognition does not depend on the length of the ssDNA gap. Formation of the enzyme complex with both DNA substrates occurs by a minimum three-step reaction, with the bimolecular step followed by two isomerization steps. The results indicate that the polymerase initiates the association with gapped DNA substrates through the DNA-binding subsite located on the 8-kDa domain of the enzyme. This first association step is independent of the length of the ssDNA gap and is characterized by similar rate constants for both examined DNA substrates. The subsequent, first-order transition occurs at the rate of approximately 600-1200 s(-1). This is the major docking step accompanied by favorable free energy changes in which the 31-kDa domain engages in interactions with the DNA. The 5'-terminal PO(4)(-) group downstream from the primer is not a specific recognition element of the gap. However, the phosphate group affects the enzyme orientation in the complex with the DNA, particularly, for the substrate with a longer gap.

Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-LTR by high resolution 2D-NMR

The understanding of early events in the expression of genes has vastly improved in recent years with the identification of a variety of gene- and sequence-specific DNA binding transcription factors. One such protein, Sp1, has been implicated in activating transcription of various cellular and viral genes including those of HIV, and SIV types of retroviruses. The basic recognition site for Sp1 has been identified as variants of a 10 base-pairs long GC-rich DNA, often containing a hexanucleotide segment 5'-GGGCGG (termed GC-box). However, variations in both the relative protein-DNA binding affinity and the nature of binding sequences have been noted. Two-dimensional 1H-NMR experiments (500 MHz) were employed for conformational studies of two decadeoxyribonucleotide duplexes, d(GAGGCGTGGC).d(GCCACGCCTC), termed Sp1-III, and d(GGGAGTGGCG).d(CGCCACTCCC), termed Sp1-I. These are two of the highest affinity Sp1 binding sites and consist of diverse positioning of the tri- and tetranucleotide segments GAG, GTG, GCG, GGCG, GTGG and GGAG, that occur frequently in other Sp1 binding sites as well, and may form specific contacts with the protein. Phase-sensitive nuclear Overhauser enhancement (2D-NOESY and MINSY) and correlation (COSY) spectra were obtained for the assignment of the exchangeable and nonexchangeable protons in a sequence-specific fashion. As a prelude to determination of the detailed solution structures of the selected sequences, numerous structural constraints were obtained from angle-dependent coupling constants and relative intensities of distance-dependent intra- and internucleotide NOEs. Overall, each duplex adopts a structure similar to B-DNA with predominantly C2'-endo/S-type sugar conformation and anti-glycosidic torsion angles. A selective disruption of sequential NOE connectivities at the GAG.CAC and GTG.CAC steps, irrespective of the flanking sequence, suggests that conformational changes at these sites may act as unique determinants of sequence specific recognition/binding of Sp1. Implications for a specific inhibition of Sp1-mediated transcription by minor groove binding class of drugs, designed to recognize GC-rich sequences, are also briefly discussed.

The activating transcription factor region within the E2A promoter exists in a novel conformation

The ATF (activating transcription factor) binding site within the E2A promoter region of adenovirus is shown to exist in a novel conformation in vitro via nuclear magnetic resonance methods. This novel conformation may be important to the protein DNA recognition process. This conformation has characteristics of both A- and B-form DNA. From circular dichroism and through-space-based NMR experiments, it is clear that the overall helical structure is B-like. However, the 1H-1H coupling constant information indicates that most of the sugar puckers of the individual nucleotides are in the C3'-endo/C4'-exo range which is more characteristic of A-form DNA. The sugar conformation can also be described as a mixture of two states, C3'-endo and C2'-endo, where many of the sugars exist mainly in the C3'-endo state. These data show that the conformation of the sugar puckers does not determine the nature of the overall base stacking on the DNA. Helical parameters were calculated from NOE build-up curves for half of the dinucleotide pairs. Severe spectral overlap on the nuclear Overhauser based spectra prevented determination of the helical parameters for all of the dinucleotide base-pairs. Energy minimization and molecular dynamic simulation methods using the sugar pucker and glycosidic torsion angles determined from the NMR data as constraints were carried out in order to demonstrate that such a conformation was energetically favorable.

Agreement between single crystal X-ray and molecular mechanical sugar ring conformations

We have calculated the deoxyribose sugar energy for a wide range of puckering parameters, (q, W), using different force fields. The intra-ring bond lengths, bond angles, and dihedral angles are calculated for every energy minimized structure and compared with 224 sugar ring structures available from DNA single crystal x-ray data. A modified Weiner's force field yields an excellent agreement with x-ray data. The calculated energy surface shows a variable amplitude repuckering path, with an average distortion of 0.42 A. Most of the experimental values of (q, W) fall within 1.0 Kcal/mol from the calculated minimum.

Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method

A graphical method is presented for the conformational analysis of the sugar ring in DNA fragments by means of proton-proton couplings. The coupling data required for this analysis consist of sums of couplings, which are referred to as sigma 1' (= J1'2' + J1'2''), sigma 2' (= J1'2' + J2'3' + J2'2''), sigma 2'' (= J1'2'' + J2''3' + J2'2'') and sigma 3' (= J2'3' + J2''3' + J3'4'). These sums of couplings correspond to the distance between the outer peaks of the H1', H2', H2'' and H3' [31P] resonances, respectively, (except for sigma 2' and sigma 2'' in the case of a small chemical shift difference between the H2' and H2'' resonances) and can often be obtained from 1H-NMR spectra via first-order measurement, obviating the necessity of a computer-assisted simulation of the fine structure of these resonances. Two different types of graphs for the interpretation of the coupling data are discussed: the first type of graph serves to probe as to whether or not the sugar ring occurs as a single conformer, and if so to analyze the coupling data in terms of the geometry of this sugar ring. In cases where the sugar ring does not occur as a single conformer, but as a blend of N- and S-type sugar puckers, the second type of graph is used to analyze the coupling data in terms of the geometry and population of the most abundant form. It is shown that the latter type of analysis can be carried out on the basis of experimental values for merely sigma 1',sigma 2' and sigma 2'', without any assumptions or restrictions concerning a relation between the geometry of the N- and S-type conformer. In addition, the question is discussed as to how insight can be gained into the conformational purity of the sugar ring from the observed fine structure of the H1' resonance. Finally, a comparison is made between experimental coupling data reported for single-stranded and duplex DNA fragments and covalent RNA-DNA hybrids on the one hand and the predicted couplings and sums of couplings presented in this paper on the other hand.

The conformation of single stranded oligonucleotides and of oligonucleotide-oligopeptide complexes from their rotation relaxation in the nanosecond time range

The conformation of single stranded oligonucleotides is analysed by measurements of their rotation time constants. The oligomers are aligned to some degree by short electric field pulses; after pulse termination the transition to a random orientation is followed by measurements of the linear dichroism. An efficient deconvolution procedure is developed for evaluation of the experimental data obtained in the ns-time range. The increase of rotation time constants observed for chain lengths in the range from 14 to 22 residues are interpreted according to a weakly bending rod model providing a persistence length and a Stokes' diameter. The Stokes' diameters obtained for ribo- and deoxyriboadenylates are about 13A, in approximate agreement with the expectation for a single stranded helix. The persistence length L = 53A corresponding to approximately 16 nucleotide residues found for riboadenylates at 2 degrees C appears to reflect relatively strong stacking interactions at this temperature. However, a comparison with the average length of stacked residues evaluated from available thermodynamic parameters of base stacking indicate that unstacked residues are not completely flexible. Apparently the ribose-phosphate chain provides an essential contribution to the stiffness of oligomers and polymers, even when the bases are unstacked. Addition of 100 microM Mg2+ leads to an increase of the persistence length to 88A. Corresponding measurements with deoxyriboadenylates show a slightly lower value of the persistence length than that found for riboadenylates. Addition of LysTrpLys and LysTyrLys to A(pA)19 leads to an increase of the rotation time constant, which corresponds approximately to a length increment by one residue per bound peptide. Since controls performed with LysLeuLys do not show any similar effect, the increase of the time constants induced by LysTrpLys and LysTyrLys is attributed to intercalation of the aromatic amino acids.

Fluorescence decay studies of poly(riboadenylic acid) containing 1-N6-ethenoadenosine

The fluorescence properties of the 1-N6-etheno derivatives of poly(riboadenylic acid) (poly(rA, epsilon rA)) have been examined. The fluorescence quantum yield of poly(rA, epsilon rA) decreases with an increase in the degree of the epsilon A substitution and is much smaller than that for epsilon AMP even for low degrees of epsilon A substitution. The nearest-neighbor interactions such as epsilon-adenine-adenine and epsilon-adenine-epsilon-adenine may be responsible for this behavior. It is found that the fluorescence decay kinetics obeys a three-exponential decay law for poly(rA, epsilon rA), suggesting that there exist at least three different stacked conformational states.

Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid)

The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix formation is rotationally diffusion controlled. The rate of coil formation in poly(C) has an activation energy of approximately 11 kcal/mol, presumably reflecting the electronic stacking interactions which stabilize the helix. Viscous cosolvents, glycerol or sucrose, slow down the rate of coil formation; acetonitrile and formamide at 5 mol % increase the rate relative to that in water. The polar cosolvents may specifically attack a cytosine stack. The absorbance vs. temperature profiles for poly(C) are analyzed with the one-dimensional Ising model. When only optical data are used, the cooperativity parameter, sigma, and the enthalpy, delta H, cannot be uniquely determined. A method is proposed that allows determination of sigma by combining spectroscopic and calorimetric data. The values of sigma derived for poly(C) are between 0.8 and 1.0, and delta H is about -9 kcal/mol of stack. An alternative method using integration of the excess heat capacity curve and extrapolation to fully stacked and random coil species yields a delta H of -7 kcal/mol of stack.

Laser temperature jump study of solvent effects of poly(adenylic acid) stacking

The dynamics of the single-stranded, helix--coil transition of poly(adenylic acid) have been investigated by using the Raman laser temperature jump technique. The driving forces of this conformational transition have been probed by varying the cosolvent in mixed aqueous solutions. The rate of helix formation correlates well with the inverse of the solution viscosity. This correlation and the low activation barrier of approximately 4 kcal/mol for this process indicate a rotational diffusion controlled reaction. The rate of coil formation has a much higher activation barrier, presumably due to the strength of base stacking in the helix. This unstacking rate is virtually unaffected by alcohol cosolvents. A significant increase in this rate occurs when polar cosolvents such as urea, formamide, or acetonitrile are added. Absorbance changes with temperature suggest that urea specifically solvates the adenine base. The polar cosolvents appear to break up the stacked, helical conformation by interacting with the bases.