The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regu...

Models of nucleic acid thermal stability are calibrated to a wide range of experimental observations, and typically predict equilibrium probabilities of nucleic acid secondary structures with reasonable accuracy. By comparison, a similar calibration and evaluation of nucleic acid kinetic models to a broad range of measurements has not been attempted so far. We introduce an Arrhenius model of in...

Target DNA fragments at 10 fM concentration (approximately 6 × 10(5) molecules) were detected against a DNA background simulating the noncomplementary genomic DNA present in real samples using a simple, PCR-free, optics-free approach based on electromechanical signal transduction. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is highly desired for a r...

Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation bet...

Deoxyribonucleic acid-deoxyribonucleic acid reassociation and deoxyribonucleic acid-ribosomal ribonucleic acid cistron similarity studies showed that the anaerobic, gram-positive cocci comprise a rather heterogeneous group of bacteria. The deoxyribonucleic acid-ribosomal ribonucleic acid hybridization studies distinguished seven groups. Groups 1 and 2 consisted of Peptostreptococcus magnus and ...

Sequence-specific protein-nucleic acid recognition is determined, in part, by hydrogen bonding interactions between amino acid side-chains and nucleotide bases. To examine the repertoire of possible interactions, we have calculated geometrically plausible arrangements in which amino acids hydrogen bond to unpaired bases, such as those found in RNA bulges and loops, or to the 53 possible RNA bas...

UNIVERSITY OF TURKU Depaartment of Chemistry/Faculty of Mathematics and Natural Sciences Golubev, Oleg: Recognition of nucleic acids by metal ion complexes Doctoral thesis, 144 p. Laboratory of Organic Chemistry and Chemical Biology March 2016 Metal-ion-mediated base-pairing of nucleic acids has attracted considerable attention during the past decade, since it offers means to expand the genetic...