Dataset Information

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

ABSTRACT: Our previous efforts have used in vitro selection to identify numerous Zn(2+)-dependent deoxyribozymes that ligate two RNA substrates with reaction at a 2',3'-cyclic phosphate. Each deoxyribozyme creates one of several different RNA linkages, including native 3'-5' and non-native 2'-5' phosphodiester bonds as well as many unnatural linkages. In this report, we describe experiments to reveal design aspects of the selection strategy that favor site-selective and regioselective synthesis of native 3'-5' RNA linkages. The results also reveal that an explicit selection pressure for RNA substrate sequence generality must be developed if the deoxyribozymes are to have practical generality.

SUBMITTER: Kost DM

PROVIDER: S-EPMC2790812 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

Kost Diana M DM Gerdt Joseph P JP Pradeepkumar P I PI Silverman Scott K SK

Organic & biomolecular chemistry 20081027 23

Our previous efforts have used in vitro selection to identify numerous Zn(2+)-dependent deoxyribozymes that ligate two RNA substrates with reaction at a 2',3'-cyclic phosphate. Each deoxyribozyme creates one of several different RNA linkages, including native 3'-5' and non-native 2'-5' phosphodiester bonds as well as many unnatural linkages. In this report, we describe experiments to reveal design aspects of the selection strategy that favor site-selective and regioselective synthesis of native ...[more]

PMID: 19005599

Similar Datasets

Project description:The discrimination of the direction of movement of sensory images is critical to the control of many animal behaviors. We propose a parsimonious model of motion processing that generates direction selective responses using short-term synaptic depression and can reproduce salient features of direction selectivity found in a population of neurons in the midbrain of the weakly electric fish Eigenmannia virescens. The model achieves direction selectivity with an elementary Reichardt motion detector: information from spatially separated receptive fields converges onto a neuron via dynamically different pathways. In the model, these differences arise from convergence of information through distinct synapses that either exhibit or do not exhibit short-term synaptic depression--short-term depression produces phase-advances relative to nondepressing synapses. Short-term depression is modeled using two state-variables, a fast process with a time constant on the order of tens to hundreds of milliseconds, and a slow process with a time constant on the order of seconds to tens of seconds. These processes correspond to naturally occurring time constants observed at synapses that exhibit short-term depression. Inclusion of the fast process is sufficient for the generation of temporal disparities that are necessary for direction selectivity in the elementary Reichardt circuit. The addition of the slow process can enhance direction selectivity over time for stimuli that are sustained for periods of seconds or more. Transient (i.e., short-duration) stimuli do not evoke the slow process and therefore do not elicit enhanced direction selectivity. The addition of a sustained global, synchronous oscillation in the gamma frequency range can, however, drive the slow process and enhance direction selectivity to transient stimuli. This enhancement effect does not, however, occur for all combinations of model parameters. The ratio of depressing and nondepressing synapses determines the effects of the addition of the global synchronous oscillation on direction selectivity. These ingredients, short-term depression, spatial convergence, and gamma-band oscillations, are ubiquitous in sensory systems and may be used in Reichardt-style circuits for the generation and enhancement of a variety of biologically relevant spatiotemporal computations.

Dataset Information

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

Publications

Controlling the direction of site-selectivity and regioselectivity in RNA ligation by Zn2+-dependent deoxyribozymes that use 2',3'-cyclic phosphate RNA substrates.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets