Dendritic PARACEST contrast agents for magnetic resonance imaging

MRI contrast agents based on chemical exchange-dependent saturation transfer (CEST), such as Yb(III)DOTAM complexes, are highly suitable for pH mapping. In this paper, the synthesis of Yb(III)DOTAM-functionalized poly(propylene imine) dendrimers is described. The applicability of these dendritic PARACEST MRI agents for pH mapping has been evaluated on a 7 T NMR spectrometer and on a 3 T clinical MRI scanner. As expected, based on the different numbers of exchangeable amide protons, the lowest detectable concentration of the first and third generation dendritic PARACEST agents is by a respective factor of about 4 and 16 lower than that of a mononuclear reference complex. The pH dependence of the CEST effect observed for these compounds depends on the generation of the poly(propylene imine) dendrimer. Upon going to higher generations of the Yb(III)DOTAM-terminated dendrimer, a shift of the maximum CEST effect towards lower pH values was observed. This allows for a fine-tuning of the responsive pH region by varying the dendritic framework.

Diagnostic analysis of experimental artefacts in DOSY NMR data by covariance matrix of the residuals

Multivariate curve resolution (MCR) has been applied to separate pure spectra and pure decay profiles of DOSY NMR data. Given good initial guesses of the pure decay profiles, and combined with the nonlinear least square regression (NLR), MCR can result in good separation of the pure components. Nevertheless, due to the presence of artefacts in experimental data, validation of a MCR model is still necessary. In this paper, the covariance matrix of the residuals (CMR), obtained by postmultiplying the residual matrix with its transpose, is proposed to evaluate the quality of the results of an experimental data set. Plots of the rows of this matrix give a general impression of the covariance in the frequency domain of the residual matrix. Different patterns in the plot indicate possible causes of experimental imperfections. This new criterion can be used as diagnosis in order to improve experimental settings as well as suggest appropriate preprocessing of DOSY NMR data.

Characterization of late radiation effects in the rat thoracolumbar spinal cord by MR imaging using USPIO

The aim of this study was to detect late radiation effects in the rat spinal cord using MR imaging with ultra-small particles of iron oxide (USPIO) contrast agent to better understand the development of late radiation damage with emphasis on the period preceding neurological signs. Additionally, the role of an inflammatory reaction was assessed by measuring macrophages that internalized USPIO. T2-weighted spin echo MR measurements were performed at 7T in six rats before paresis was expected (130-150 days post-irradiation, early group), and in six paretic rats (150-190 days post-irradiation, late group). Measurements were performed before, directly after and, only in the early group, 40 h after USPIO administration and compared with histology. In the early group, MR images showed focal regions in grey matter (GM) and white matter (WM) with signal intensity reduction after USPIO injection. Larger lesions with contrast enhancement were located in and around edematous GM of three animals of the early group and five of the late group. Forty hours after injection, additional lesions in WM, GM and nerve roots appeared in animals with GM edema. In the late paretic group, MR imaging showed WM necrosis adjacent to areas with large contrast enhancement. In conclusion, detection of early focal lesions was improved by contrast administration. In the animals with extended radiation damage, large hypo-intense regions appeared due to USPIO, which might be attributed to blood spinal cord barrier breakdown, but the involvement of blood-derived iron-loaded macrophages could not be excluded.

Techniques for precision irradiation of the lateral half of the rat cervical spinal cord using 150 MeV protons [corrected]

Techniques for high precision irradiation experiments with protons, to investigate the volume dependence of the tolerance dose of the rat cervical spinal cord are described. In the present study, 50% of the lateral cross section of the spinal cord was irradiated. The diameter of the cross section of this part of the rat spinal cord is at maximum 3.5 mm. Therefore, a dedicated procedure was developed to comply with the needs for a very high positioning accuracy and high spatial resolution dosimetry. By using 150 MeV protons a steep dose gradient (20-80% = 1 mm) in the centre of the spinal cord was achieved. This yields a good dose contrast between the left and right halves of the cord. A home-made digital x-ray imager with a pixel resolution of 0.18 mm/pixel was used for position verification of the spinal cord. A positioning accuracy of 0.09 mm was obtained by using information of multiple pixels. The average position stability during the irradiation was found to be 0.08 mm (1 SD) without significant systematic deviations. Profiles of the dose distribution were measured with a 2D dosimetry system consisting of a scintillating screen and a CCD camera. Dose volume histograms of the whole spinal cord as well as separately of the white and grey matters were calculated using MRI imaging of the cross section of the rat cervical spinal cord. From the irradiation of 20 animals a dose-response curve has been established. MRI showed radiation-induced damage at the high dose side of the spinal cord. Analysis of the preliminary dose-response data shows a significant dose-volume effect. With the described procedure and equipment it is possible to perform high precision irradiations on selected parts of the spinal cord.

Design and NMR study of an immobile DNA four-way junction containing 38 nucleotides

The DNA Holliday junction is a central intermediate in genetic recombination. We have designed and synthesized a DNA oligomer, J1a, as a model compound for the Holliday junction suitable to be studied by NMR spectroscopy and future molecular modelling. The design was based on a 46-base oligomer, J4, previously studied by Pikkemaat, J. A., van den Elst, H., van Boom, J. H. & Altona, C. [Biochemistry 33, 14896-14907 (1994)], including the propensity to undergo a self-folding process to give a four-way junction in which three of the four arms are capped with a hairpin loop. J1a, however, is considerably shortened by eight bases and thus contains only 38 residues which significantly facilitates the proton resonance assignments. The base sequence at the branch point is identical to that in J4. 1H-NMR data clearly point to the presence of three hairpin loops in J1a and show that the double-helical arms adopt the B-DNA form. Quasicontinuous pairwise stacking between helical arms to give a single preferred stacked X-conformation is evident. The extent of folding into this stacked conformation is strongly dependent upon the magnesium concentration. Full Watson-Crick base pairing at the branch point is completely preserved. The A/D-stacking preference of the small junction is the same as that exhibited by J4.

Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: comparison with distance geometry calculations

The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer present in a 10 basepair (bp) sense-antisense DNA duplex was studied with a genetic algorithm designed to interpret NOE distance restraints. Trial solutions were represented by torsion angles. This means that bond angles for the dimer trial structures are kept fixed during the genetic algorithm optimization. Bond angle values were extracted from a 10 bp sense-antisense duplex model that was subjected to energy minimization by means of a modified AMBER force field. A set of 63 proton-proton distance restraints defining the methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizes the difference between distances in the trial structures and distance restraints. A large conformational search space could be covered in the genetic algorithm optimization by allowing a wide range of torsion angles. The genetic algorithm optimization in all cases led to one family of structures. This family of the methylene-acetal-linked thymine dimer in the duplex differs from the family that was suggested from distance geometry calculations. It is demonstrated that the bond angle geometry around the methylene-acetal linkage plays an important role in the optimization.

Conformational aspects of an uncharged phosphate analogon built in at the branch-point of a DNA four-way junction

Electrostatic interactions appear to be important in the conformation and dynamics of DNA four-way junctions. Particularly, the Coulomb repulsion between two approaching phosphate groups at the site of strand exchange is commonly supposed to have a negative influence on the thermodynamic stability of the fully stacked conformation. We synthesized a unimolecular DNA four-way junction containing an uncharged methylene-acetal linkage, -O3'-CH2-O5'-, instead of a regular phosphodiester linkage, -O3'-PO2-O5'-, between two specific residues at the branch-point to examine the effect of charge removal. Complete sequential 1H-NMR assignments of the non-exchangeable base protons and H1'/H2'/H2" sugar protons were obtained with the aid of NOESY and TOCSY experiments. On the basis of the NMR data it is concluded that the stacking arrangement at the branch-point of the modified oligonucleotide is similar to that of the previously studied parent four-way junction. Surprisingly, this is not the stacking arrangement in which the close phosphate-phosphate contact at the site of strand exchange would be absent. Some implications of this novel information regarding the role of the phosphate-phosphate repulsion in four-way junctions are discussed.

Three-way and four-way junctions in DNA: a conformational viewpoint

DNA junctions are potential intermediates in various important genetic processes, including mutagenesis and recombination. The quantity of research carried out in this area is rapidly increasing. Examples of three-way and four-way junctions are now relatively well characterized and a few common properties have been recognized, of which the most important is the tendency of junctions to fold into one or more coaxially stacked helical conformations or cross-over structures.

NMR studies of DNA three-way junctions containing two unpaired thymidine bases: the influence of the sequence at the junction on the stability of the stacking conformers

DNA three-way junctions (TWJs) containing unpaired residues at the branch point can adopt a conformation in which one helix is stacked upon another, forming a coaxial, quasicontinuous double helix. As in four-way junctions (FWJs), two conformers with different stacking arrangements between the arms are possible. However, in both types of structures a markedly strong preference for one conformer has been observed. To investigate the basis for this preference, in particular the influence of the stacking proclivity of the base-pairs at the centre of the junction, two linear oligomers (36 nucleotides), TWJ1 and TWJ2, differing only in one base-pair (G.C versus C.G, respectively) at the branch point, were designed and chemically synthesized. Each one is expected to fold into a stable three-way junction, containing two unpaired thymidine bases at the junction region and two arms capped with a hairpin loop. The data obtained from 1H and 31P-NMR spectroscopy confirm that both oligomers are present as stable three-way junctions. In both TWJs two of the helical arms stack preferentially upon each other. However, the stacking arrangement is similar in both molecules. From this it is deduced that purine-purine stacking across the junction cannot be considered as a major factor that determines the preferred stacking arrangement.

Slow conformational exchange in DNA minihairpin loops: a conformational study of the circular dumbbell d<pCGC-TT-GCG-TT>

In recent years various examples of highly stable two-residue hairpin loops (miniloops) in DNA have been encountered. As the detailed structure and stability of miniloops appear to be determined not only by the nature and sequence of the two bases in the loop, but also by the closing base pair, it is desirable to carry out in-depth studies of especially designed small model DNA compounds. Therefore, a circular DNA dumbbell-like molecule is tailored to consist of a stem of three Watson-Crick base pairs, flanked on each side by a minihairpin loop. The resulting circular DNA decamer 5'-d<pCGC-TT-GCG-TT>-3' (I) is studied in solution by means of nmr spectroscopy. At a temperature of 269 K the molecule occurs in a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4). L2L2 contains three Watson-Crick C-G base pairs and two two-residue loops (H2-family type) in opposite parts of the molecule. On raising the temperature from 269 to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted closing G-C base pair in the 5'-GTTC-3' loop with only one remaining solvent-accessible hydrogen bond between NH alpha of the cytosine C(1) and O6 of the guanine G(8), whereas the opposite 5'-CTTG-3' loop remains stable. The disruption of the C(1)-G(8) base pair in the L2L4 form is correlated with the presence of a syn orientation for the C(1) base at the 5'-3' loop-stem junction in the 5'-GTTC-3' loop. The two conformers, L2L2 and L2L4, occur in slow equilibrium (2-20 s-1). Moderate line broadening of specific 1H, 13C, and 31P resonances of residues C(1), G(8), T(9), and T(10) at low temperatures, due to chemical exchange between L2L2 and L2L4, show that the interconversion from an anti to syn conformer in residue C(1) has a small local effect on the structure of the dumbbell. T1 relaxation measurements, chemical-shift considerations, and complete band-shape calculations of the exchange process of the G(8) imino proton reveal a possibility for the existence of multiconformational states in the anti-syn equilibrium.

Thermodynamics of melting of the circular dumbbell d<pCGC-TT-GCG-TT>

The conformational behavior of DNA minihairpin loops is sensitive to the directionality of the base pair that closes the loop. Especially tailored circular dumbbells, consisting of a stem of three Watson-Crick base pairs capped on each side with a minihairpin loop, serve as excellent model compounds by means of which deeper insight is gained into the relative stability and melting properties of hairpin loops that differ only in directionality of the closing pair: C-G vs G-C. For this reason the thermodynamic properties of the circular DNA decamers 5'-d<pCGC-TT-GCG-TT>-3' (I) and reference compounds 5'-d<pGGC-TT-GCC-TT>-3' (II) and 5'-d(GCG-TC-CGC)-3' (III) are studied by means of nmr spectroscopy. Molecules I and II adopt dumbbell structures closed on both sides by a two-membered hairpin loop. At low temperature I consists of a mixture of two slowly exchanging forms, denoted L2L2 and L2L4. The low-temperature L2L2 form is the fully intact minihairpin structure with three Watson-Crick C-G base pairs. The high-temperature form, L2L4, contains a partially disrupted closing G-C base pair in the 5'-GTTC-3' loop, with the cytosine base placed in a syn orientation. The opposite 5'-CTTG-3' loop remains stable. A study of the noncircular hairpin structure III shows similar conformational behavior for the 5'-GTTC-3' loop as found in I; a syn orientation for C(6) and two slowly exchanging imino proton signals for G(3). The melting point Tm of II was estimated to lie above 365 K. The Tm value of the duplex stem and the 5'-CTTG-3' loop of the L2L4 form of I is 352 +/- 2 K. The delta H0 is calculated as -89 +/- 10 kJ/mol. The Tm value determined for the individual residues of the 5'-GTTC-3' loop lies 4 degrees-11 degrees lower. The enthalpy delta H0 of melting the thymine residues in the 5'-GTTC-3' loop is calculated to be -61 +/- 7 kJ/mol. Thermodynamic data of the equilibrium between the slowly exchanging two- and four-membered loop conformers of I reveal an upper limit for delta H0 of +30 kJ/mol in going from a two-membered to a four-membered loop, in agreement with the enthalpy difference of +28 kJ/mol between the two loops at the Tm midpoint. For hairpin III the upper limit for delta H0 in going from a two-membered to a four-membered loop amounts to +/- 21 kJ/mol.(ABSTRACT TRUNCATED AT 400 WORDS)

Conformation of the circular dumbbell d<pCGC-TT-GCG-TT>: structure determination and molecular dynamics

The circular DNA decamer 5'-d<pCGC-TT-GCG-TT>-3' was studied in solution by means of NMR spectroscopy and molecular dynamics in H2O. At a temperature of 269 K, a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4) is present. The L2L2 form contains three Watson-Crick C-G base pairs and two two-residue loops is opposite parts of the molecule. On raising the temperature from 269 K to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted G(anti)-C(syn) closing base pair in the 5'-GTTC-3' loop with only one remaining (solvent-accessible) hydrogen bond between NH alpha of the cytosine dC(1) and O6 of the guanine dG(8). The opposite 5'-CTTG-3' loop remains stable. The two conformers occur in slow equilibrium (rate constant 2-20 s-1). Structure determination of the L2L2 and L2L4 forms was performed with the aid of a full relaxation matrix approach (IRMA) in combination with restrained MD. Torsional information was obtained from coupling constants. Coupling constant analysis (3JHH, 3JHP, 3JCP) gave detailed information about the local geometry around backbone torsion angles beta, gamma, delta, and epsilon, revealing a relatively high flexibility of the 5'-GTTC-3' loop. The values of the coupling constants are virtually temperature-independent. 'Weakly constrained' molecular dynamics in solvent was used to sample the conformational space of the dumbbell. The relaxation matrices from the MD simulation were averaged over <r-3> to predict dynamic NOE volumes. In order to account for the 1:1 conformational mixture of L2L2 and L2L4 present at 271 K, we also included S2 factors and <r-6> averaging of the <r-3>-averaged relaxation matrices. On matrix averaging, the agreement of NOE volumes with experiment improved significantly for protons located in the thermodynamically less stable 5'-GTTC-3' loop. The difference in stability of the 5'-CTTG-3' and 5'-GTTC-3' loops is mainly caused by differences in the number of potential hydrogen bonds in the minor groove and differences in stacking overlap of the base pairs closing the minihairpin loops. The syn conformation for dC(1), favored at high temperature, is stabilized by solvation in the major groove. However, the conformational properties of the dC(1) base, as deduced from R-factor analysis and MD simulations, include a large flexibility about torsion angle chi.

NMR studies and conformational analysis of a DNA four-way junction formed in a linear synthetic oligonucleotide

A linear DNA oligomer (M(r) 14,000, 46 nucleotides) was especially designed, chemically synthesized, and studied by means of 1H NMR spectroscopy. The design of the oligomer was guided by the idea that incorporation of three short palindromic sequences, each interspersed by 5'-CTTG-3' motifs at predetermined positions in the oligomer, would give rise to the formation of three stable minihairpin loops [Ippel, J. H., et al. (1992) J. Biomol. Struct. Dyn. 9, 1-16], which in turn were expected to encourage further folding of the strand into a stable four-way junction containing three "hairpin" arms and an open-ended duplex stem as the fourth arm. Linear DNA four-way junctions constructed according to this concept can be more compact and are therefore expected to be more suitable as model compounds for conformational studies compared to junctions that are built from two or more separate strands. A stable cruciform conformation was substantiated for the 46-mer in aqueous solution in the presence of Mg2+. Complete sequential 1H NMR assignments of the nonexchangeable protons (except H4', H5', and H5") were obtained with the aid of NOESY and HOHAHA experiments. The NMR data gave evidence for the expected existence of minihairpin-loop structures at the three 5'-CTTG-3' motifs in the sequence. The complementary stem domains adopt a regular B-DNA form. Watson-Crick type base pairing is preserved for all residues in the stem domains, including the residues at the center of the junction. A systematic investigation of the interresidual NOEs observed between the protons of the eight central residues revealed the complete stacking pattern of the residues at the branch point.

An NMR study of the conformation and thermodynamics of the circular dumbbell d [formula: see text] Slow exchange between two- and four-membered hairpin loops

The circular DNA decamer 5'-d [formula: see text] 3' is studied in solution by means of NMR spectroscopy. At low temperature the molecule adopts a dumbbell structure with three Watson-Crick C-G base pairs and two two-residue loops in opposite parts of the molecule. On raising the temperature another conformer appears, in which the closing C-G base pair in the 5'-GTTC-3' loop is disrupted, whereas the opposite 5'-CTTG-3' loop remains stable. The two conformers are in slow equilibrium over a limited temperature range.