New dynamical scaling universality for quantum networks across adiabatic quantum phase transitions.

We reveal universal dynamical scaling behavior across adiabatic quantum phase transitions in networks ranging from traditional spatial systems (Ising model) to fully connected ones (Dicke and Lipkin-Meshkov-Glick models). Our findings, which lie beyond traditional critical exponent analysis and adiabatic perturbation approximations, are applicable even where excitations have not yet stabilized and, hence, provide a time-resolved understanding of quantum phase transitions encompassing a wide range of adiabatic regimes. We show explicitly that even though two systems may traditionally belong to the same universality class, they can have very different adiabatic evolutions. This implies that more stringent conditions need to be imposed than at present, both for quantum simulations where one system is used to simulate the other and for adiabatic quantum computing schemes.

Biophysical and antisense properties of oligodeoxynucleotides containing 7-propynyl-, 7-iodo- and 7-cyano-7-deaza-2-amino-2'-deoxyadenosines.

The synthesis of 7-propynyl-, 7-iodo- and 7-cyano-7-deaza-2-amino-2'-deoxyadenosines is described. The nucleosides were synthesized, functionalized into the phosphoramidites and incorporated into oligodeoxynucleotides. Spectroscopic melting experiments against complementary RNA showed increases of 3-4 degreesC per modification for single substitutions and smaller increases per incorporation for multiple substitutions relative to unmodified control sequences. The 7-propyne and 7-iodo nucleosides were incorporated into antisense sequences targeting the 3'-UTR of murine C- raf mRNA. Both nucleosides demonstrated substitution-dependent potency. The sequences with three and four substitutions of the 7-propyne-7-deaza-2-amino-2'-deoxyadenosine exhibited a 2-3-fold increase in potency over unmodifed controls.

Inhibition of adenosine deaminase by azapurine ribonucleosides.

We have synthesized several 8-azapurine nucleosides as inhibitors of adenosine deaminase. The presence of a nitrogen on the imidazole ring decreased the Ki value for nebularine by 100-fold but did not lower the Ki value for coformycin. Evaluation of these compounds in a MOLT-4 growth assay revealed that 2-azacoformycin was as effective as 2'-deoxycoformycin in potentiating growth inhibition by 2'-deoxyadenosine. The azapurine nucleosides merit further study as antitumor agents.

The coherence of synthetic telomeres.

The chromosomal telomeres of Oxytricha were synthesized and their ability to cohere examined on non-denaturing acrylamide gels containing the stabilizing cation K+. At least 5 different mobility species were observed, in addition to that of the monomeric telomere. By cohering synthetic telomeres containing different lengths of subtelomeric DNA, we showed that each of the different mobility species was a dimer of two telomeres. Since the different mobility species did not differ in numbers or sequences of nucleotides, they must correspond to different molecular shapes probably caused by different degrees of bending of the dimer. Paradoxically, telomeres with longer subtelomeric stems cohered more efficiently. In the presence of K+, solutions had to be heated to over 90 degrees before the telomeres separated. Various synthetic constructs, restriction endonuclease and dimethyl sulfate protection experiments showed that the only nucleotides involved in the cohered structures were the 16 base 'tails' of sequence 3'G4T4G4T4. Extension of this motif was actually inimical to coherence. Oligomers containing 2 G4T4 motifs protected their GN7 positions by forming dimers, those with 5 G4T4 could do so by internal folding, but the 3' terminal group of G4 was left unprotected. This suggests that only four groups of G4 are necessary for the cohered structure. Single-chain specific nuclease, S1, as well as osmium tetroxide, which oxidizes the thymine residues of single chains, reacted less efficiently with the cohered structures. Synthetic telomeres containing inosine replacing guanosine were not observed to cohere, indicating that the C2-NH2 is strongly stabilizing. The cohered structures appear to be unusually compact and sturdy units in which four G4 blocks form quadruplexes stabilized by K+. A new model for the cohered structure is presented.

Non-enzymatic transcription of an oligodeoxynucleotide 14 residues long.

The 14-mer oligodeoxynucleotide d(C3GC3GC3GC2) acts as a template to facilitate the cooligomerization of guanosine 5'-phospho-2-methylimidazolide and cytidine 5'-phospho-2-methylimidazolide. The predominant products are a series of 3'-5'-linked oligonucleotides, complementary to the template, ranging in length from GGC to GGCGGGCGGGCGGG. Thus simple, non-enzymatic template-directed reactions can result in the accurate transfer of substantial amounts of information from template to products. The 15-mer oligodeoxynucleotide d(C3GC3GC3GC3) is also an efficient template, but directs the synthesis of the same family of products that are formed on the 14-mer template. This unexpected finding is explained by the preferential conversion of the dimer GG to GGC rather than to GGG. These results are interesting in the context of molecular evolution. They suggest that the detailed kinetics of template-directed synthesis could form the basis for the selection of one replicating oligonucleotide from a family of closely related oligonucleotides.

Template-directed oligonucleotide ligation on hydroxylapatite.

Bernal, and subsequently other authors, have suggested that the prebiotic synthesis of the precursors of biopolymers could have occurred on a solid surface such as that provided by clay or some other mineral. The separation of products from the other components of the reaction mixture in such a system is reminiscent of modern solid-phase synthesis of polypeptides and polynucleotides. One such scheme envisages that growing polymers were localized by adsorption to a mineral surface where an activating agent or activated monomers were supplied continuously or cyclically. We have been trying to test this scheme using reactions which we believe may be related to those that occurred during prebiotic evolution. We have already reported that oligonucleotides adsorbed onto hydroxylapatite provide suitable templates for the oligomerization of (guanosine 5'-phosphor)-2-methylimidazolide (2-MeImpG). However, this is not a suitable test reaction, as 2-MeImpG oligomerization proceeds almost to completion in a single step. Here we report that a sequence of reactions in which initially formed oligo(G)s are reactivated by conversion to phosphorimidazolides in the presence of poly(C) and then allowed to ligate is ideal, in that repeated cycles can be carried out on the surface of hydroxylapatite, whereas in the liquid phase the cycle could be achieved only with considerable difficulty.