No abstract

No abstract

A conformational study of the double‐stranded decanucleotide d(GCCG*G*ATCGC) · d(GCGATCCGGC), with the G* guanines chelating a cis‐Pt(NH3)2 moiety, has been accomplished using 1H and 31P NMR, and molecular mechanics. Correlation of the NMR data with molecular models has disclosed an equilibrium between several kinked conformations and has ruled out an unkinked structure. The deformation is localized at the CG*G*· CCG trinucleotide where the helix is kinked by approximately 60° towards the major groove and unwound by 12–19°. The models revealed an unexpected mobility of the cytosine complementary to the 5′‐G*. This cytosine can stack on either branch of the kinked complementary strand. The energy barrier between the two positions has been calculated to be ≤ 12 kJ/mol. The NMR data are in support of rapid flip‐flopping of this cytosine. An explanation for the strong downfield shift observed in the 31P resonance of the G*pG* phosphate is given.

No abstract

The double-helical conformations of d(m5-C-G-C-G-m5-C-G) in aqueous solution were studied by circular dichroism and 1H NMR spectroscopy. In 0.1 M NaCl, only the B form is detected whereas the Z form is strongly predominant in 3 M NaCl. In the presence of 2 M NaCl, two resonance signals corresponding to the B and Z duplexes were observed for each proton below 50 degrees C, indicating a slow exchange between B and Z. However, the B-Z exchange becomes intermediate or fast in the 55-80 degrees C temperature interval. By contrast the exchange between B helix and single-stranded (or coil) forms is much faster for the same temperature conditions. The Z form is only detectable when the coil form is practically absent. With decreasing temperature the B form decreases in favor of the Z form. From proton line-width measurements under various experimental conditions, it was also shown that Z exchanges only with B, while the latter also exchanges with the single-stranded form (S): Z in equilibrium B in equilibrium S. The enthalpy value is about 8 +/- 1 kcal/mol for the B-Z transition and about 40 +/- 2 kcal/mol for the B-S dissociation (2 M NaCl solution). The activation energy is about 47 +/- 2 kcal/mol for the Z----B and 39 +/- 2 kcal/mol for the B----Z reaction. Very good agreement between the experimental results and computed data (based on the above kinetic reaction model) was found for the B, Z, and coil proportions. The B-Z transition of methylated d(C-G)n oligomers is only possible when the Watson-Crick hydrogen bonds between the CG base pairs are firmly maintained; otherwise, the transformation from B to Z would not occur, and B-S dissociation would take place instead.

CUUG loop is one of the most frequently occurring tetraloops in bacterial 16S rRNA. This tetraloop has a high thermodynamic stability as proved by previous UV absorption and NMR experiments. Here, we present our results concerning the thermodynamic and structural features of the 10mer 5'-r(GCG-CUUG-CGC)-3', forming a highly stable CUUG tetraloop hairpin in aqueous solution, by means of several optical techniques (UV and FT-IR absorption, Raman scattering). UV melting profile of this decamer provides a high melting temperature (60.7 degrees C). A set of Raman spectra recorded at different temperatures allowed us to analyze the order-to-disorder (hairpin-to-random coil) transition. Assignment of vibrational markers led us to confirm the particular nucleoside conformation, and to get information on the base stacking and base pairing in the hairpin structure. Moreover, comparison of the data obtained from two highly stable CUUG and UUCG tetraloops containing the same nucleotides but in a different order permitted an overall discussion of their structural features on the basis of Raman marker evidences.

To further examine to what extent a dodecyl-phosphocholine (DPC) micelle mimics a phosphatidylcholine bilayer environment, we performed 13C, 2H, and 31P NMR relaxation measurements. Our data show that the dynamic behavior of DPC phosphocholine groups at low temperature (12 degrees C) corresponds to that of a phosphatidylcholine interface at high temperature (51 degrees C). In the presence of helical peptides, a PMP1 fragment, or an annexin fragment, the DPC local dynamics are not affected whereas the DPC aggregation number is increased to match an appropriate area/volume ratio for accommodating the bound peptides. We also show that quantitative measurements of paramagnetic relaxation enhancements induced by small amounts of spin-labeled phospholipids on peptide proton signals provide a meaningful insight on the location of both PMP1 and annexin fragments in DPC micelles. The paramagnetic contributions to the relaxation were extracted from intra-residue cross-peaks of NOESY spectra for both peptides. The location of each peptide in the micelles was found consistent with the corresponding relaxation data. As illustrated by the study of the PMP1 fragment, paramagnetic relaxation data also allow us to supply the missing medium-range NOEs and therefore to complete a standard conformational analysis of peptides in micelles.

A detailed picture of hydration and counterion location in the B-DNA duplex d(GCGAATTCG) is presented. Detailed data have been obtained by single crystal x-ray diffraction at atomic resolution (0.89 Å) in the presence of Mg 2؉ . The latter is the highest resolution ever obtained for a B-DNA oligonucleotide. Minor groove hydration is compared with that found in the Na ؉ and Ca 2؉ crystal forms of the related dodecamer d(CGCGAAT-TCGCG). High resolution data (1.45 Å) of the Ca 2؉ form obtained in our laboratory are used for that purpose. The central GAATTC has a very stable hydration spine identical in all cases, independent of duplex length and crystallization conditions (counterions, space group). However, the organization of the water molecules (tertiary and quaternary layers) associated with the central spine vary in each case.When the first dodecamer structure in the B-form was established, a "spine of hydration" was found in the minor groove (1). Recent high resolution data on the same dodecamer (2-5) have shown that a series of water hexagons may build up on the spine of hydration. However, some of the water-water distances are too long to be considered hydrogen bonds, and they correspond rather to Van der Waals contacts. An additional result of the studies mentioned above is that either K ϩ (3) or Rb ϩ (5) may partially occupy the water sites. It has also been suggested (2) that Na ϩ may also occupy the water sites, but this suggestion has been challenged (4, 6).The use of flash cooling and synchrotron radiation allows a much higher resolution in the x-ray diffraction data of oligonucleotides than was possible a few years ago. As a result, a much greater detail on water and ion distribution can be obtained.The detailed study of water and ions around DNA is interesting in itself, but it is also relevant to understand protein-DNA interactions. It has been suggested (7, 8) that water-mediated polar contacts may contribute to the specificity of protein-DNA recognition. A better understanding of water structure around DNA is essential to ascertain the eventual role of ions and hydration waters in DNA interactions. The data obtained from high resolution oligonucleotide structures will be of great value in this sense.Here we report the arrangement of water and divalent cations in the related structures of d(GCGAATTCG) in the presence of Mg 2ϩ (resolution ϭ 0.89 Å) and the calcium form of d(CGCGAATTCGCG) (resolution ϭ 1.45 Å). The high resolution achieved with these structures allows us to position with certainty many of the water and ions in the crystal. Thus, the influence of either monovalent (Na ϩ ) or divalent (Mg 2ϩ , Ca 2ϩ ) cations can be ascertained. The structure of the water spine is very clear and allows us to determine which water molecules occupy fixed positions. Hydrogen bonds and Van der Waals contacts can be clearly distinguished.The nonamer was crystallized, using a batch method, in sitting drops containing 0.5 mM DNA duplex, 1 mM acridine (Arg 4 ) drug-peptide adduct, 20 mM sodium cacodylate buff...