Mathematical Models on RNA Evolution, Simulations In Silico , and Concepts for In Vitro Selection

Abstract

Sol Spiegelman and his group carried out the first successful evolution experiments in vitro in the 1960s (for a review see, for example, Spiegelman, 1971). These experiments were based on replication of single-strand RNA through catalysis by a bacteriophage-specific enzyme, mostly Qb replicase. A sample of RNA molecules carrying the recognition site for the replicase is introduced into a buffer solution that contains the four nucleotide triphosphates (ATP, CTP, GTP, and UTP) as well as the replicase. Consumed materials are replenished through transfer of small samples into fresh stock solution. After a sufficient number of repeated transfers RNA molecules are isolated that are adapted to the stock solution, in the sense that they replicate most efficiently. Although the molecular details of the replication process and the nature of the optimization process were largely unknown in the early days, the interpretation of the serial transfer experiments as Darwinian evolution in the test was essentially correct. The Qb RNA evolution experiments were repeated and put on a firm molecular basis later on, and finally, they were applied to the design of RNA molecules with predefined properties (for a collection of reviews see Watts and Schwarz, 1997).The mechanism of RNA replication by virus-specific enzymes like Qb replicase consists of two multistep RNA polymerization cycles, each synthesizing the complementary strand of an RNA template molecule, plus-I or minus-I, respectively (Biebricher and Eigen, 1988): plus-I + activated monomers p minus-I + plus-I minus-I + activated monomers p plus-I + minus-I

Heuristic algorithms in evolutionary computation and modular organization of biological macromolecules: Applications to in vitro evolution

“…Not only the methodology, but also the character of the selected RNA devices (their modularity) bring this experimental area closer to EC. Modularity is the basis for the design of RNA devices and it dictates approaches to their development: plug and play strategy [Spirov, Holloway, 2012, Schuster, 2006, Chappell et al, 2015.…”

“…In addition to tuning, similar approaches are used for experimental evolutionary search of devices with new functions, based on existing devices [Schuster, 2006, Chappell et al, 2015, De Jong, 2006]. This technique is called a modification of the device.…”

“…A number of key problems of the directed evolution of modern synthetic biology certainly belong to the field at the intersection of biology and computer science. At the same time, the area of directed evolution of biomolecules (RNA, DNA and proteins) suffers from a lack of effective mathematical and computer approaches required to reduce the cost of experimental molecular evolution and improve its efficiency [Schuster, 2006]. This makes the purposeful transfer of algorithms and approaches from EC to this biological field extremely promising.…”

Seleção de aptâmeros que se ligam ao receptor humano para o gosto doce

“…A estrutura secundária é constituída de subestruturas, cujas energias livres são somadas. O cálculo dessas energias livres se baseia em tabelas que contêm parâmetros derivados de investigações cinéticas e termodinâmicas de compostos modelos (Schuster, 2006). Espera-se, normalmente, que os motivos conservados estejam em grampos ou alças, em regiões que interajam com o receptor.…”