Caesium fluoride-induced changes in the c.d. spectra of synthetic DNA fragments

Trypsin immobilization by direct adsorption on metal ion chelated macroporous chitosan-silica gel beads

Silica gel bead coated with macroporous chitosan layer (CTS-SiO(2)) was prepared, and the metal immobilized affinity chromatographic (IMAC) adsorbents could be obtained by chelating Cu(2+), Zn(2+), Ni(2+) ions, respectively on CTS-SiO(2), and trypsin could be adsorbed on the IMAC adsorbent through metal-protein interaction forces. Batch adsorption experiments show that adsorption capacity for trypsin on these IMAC adsorbent variated with change of pH. The maximal adsorption reached when the solution was in near neutral pH in all three IMAC adsorbents. Adsorption isothermal curve indicated that maximal adsorption capacity could be found in the Cu(2+)-CTS-SiO(2) with the value of 4980+/-125 IUg(-1) of the adsorbent, while the maximal adsorption capacity for trypsin on Zn(2+) and Ni(2+) loaded adsorbent was 3762+/-68 IUg(-1) and 2636+/-53 IUg(-1), respectively. Trypsin immobilized on the IMAC beads could not be desorbed by water, buffer and salt solution if the pH was kept in the range of 5-10, and could be easily desorbed from the IMAC beads by acidic solution and metal chelating species such as EDTA and imidazole. The effect of chelated metal ions species on CTS-SiO(2) beads on the activity and stability of immobilized trypsin was also evaluated and discussed. Trypsin adsorbed on Zn-IMAC beads retained highest amount of activity, about 78% of total activity could be retained. Although the Cu-IMAC showed highest affinity for trypsin, only 25.4% of the calculated activity was found on the beads, while the activity recovery found on Ni-IMAC beads was about 37.1%. A remarkable difference on stability of trypsin immobilized on three kinds of metal ion chelated beads during storage period was also found. Activity of trypsin on Cu-IMAC decreased to 24% of its initial activity after 1-week storage at 4 degrees C, while about 80% activity was retained on both Ni-IMAC and Zn-IMAC beads. Trypsin immobilized on Zn-CTS-SiO(2) could effectively digest BSA revealed by HPLC peptide mapping.

The unusual X-form DNA in oligodeoxynucleotides: dependence of stability on the base sequence and length

X-form is an unusual double helix of DNA adopted by poly(dA-dT) or (dT-dA)4 at high concentrations of CsF. On the other hand, poly(dA), poly(dT), (dA-dT)4 and most other DNAs do not adopt this conformer. Here we demonstrate that the X-form is strongly destabilized by GC pairs or even minute perturbations of the alternating pyrimidinepurine sequence. For example, the 30-mer d(TATAAT)5, containing five tandem repeats of the Pribnow box, fails to isomerize into the X-form. After (dT-dA)4, the 16-mer (dT-dA)8 is shown to be the second most predisposed oligodeoxynucleotide in the (dT-dA)n series to isomerize into the X-form while the duplex lengths corresponding to n = 3,5,6,7,9,12 and 20 make the X-form unstable even in the strictly alternating (dT-dA)n sequence. Consequently, the (dT-dA)n duplex length is also a crucial factor of the X-form stability on the oligodeoxynucleotide level. We discuss a possibility that the X-form is a solution counterpart of the D-form adopted in dehydrated poly(dA-dT) fibers because properties of these two conformers are remarkably similar in many respects.

Acyclic oligonucleotide analogues

Acyclic analogues of oligothymidylate and oligoadenylate and their alternating copolymers were synthesized to study their thermal melting, their stability against snake venom phosphodiesterase and their primer/template properties using the Klenow fragment of the Escherichia coli DNA polymerase I enzyme. Acyclic dodecaadenylate (GlyA)12 hybridized to dodecathymidylate p(dT)12, and the complex presented a sharp melting with a Tm at 24 degrees C. This association was confirmed by circular dichroism curves which were similar to those of the natural oligonucleotide duplexes in A-conformation. (GlyA)12 proved very stable against snake venom phosphodiesterase hydrolysis. The reaction rate was more than 10,000 times slower than that of p(dT)12. (GlyA)12 served as a primer for the Klenow DNA polymerase. When (GlyA)12 was complexed with the poly(dT) template, the enzyme polymerized dATP but the reaction was much slower than with the (GlyT)12 primer. Molecular modelling of atactic (GlyA)12.(dT)12 of the A-conformation indicates that this conformation is energetically possible.

Flow linear dichroism and Fourier transform IR spectra reveal geometry for X-form DNA

Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the bases incline are different. Hydrogen-bonded base pairs are consistent with the geometry for the standard B, C, D, and Z forms of natural DNA, but will not fit into the A form. Fourier transform ir spectra indicate that the X form has sugar pucker and phosphate geometry similar to B-form DNA, and supports the dinucleotide repeat with two kinds of phosphates seen in earlier work, in analogy to Z-form DNA. Clearly, X-form DNA has a unique geometry.