Nucleic Acid Foldamers: Design, Engineering and Selection of Programmable Biomaterials with Recognition, Catalytic and Self‐assembly Properties

Chworoś, Arkadiusz; Jaeger, Luc

doi:10.1002/9783527611478.ch10

Cited by 9 publications

(14 citation statements)

References 214 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The functional RNA does not have to be of natural origin as it can eventually result from in vitro experiments (e.g. Jaeger 1997; Chworos et al 2004;Chworos & Jaeger 2007). In this case, while the function could be the same (this is our prediction), any level of organization below that one would be different, allowing demonstration of top-down causation by information control without ambiguity.…”

Section: Experiments On Top-down Causationmentioning

confidence: 80%

Top-down causation by information control: from a philosophical problem to a scientific research programme

Auletta

Ellis

Jaeger

2008

J. R. Soc. Interface.

132

View full text Add to dashboard Cite

It has been claimed that different types of causes must be considered in biological systems, including top-down as well as same-level and bottom-up causation, thus enabling the top levels to be causally efficacious in their own right. To clarify this issue, the important distinctions between information and signs are introduced here and the concepts of information control and functional equivalence classes in those systems are rigorously defined and used to characterize when top-down causation by feedback control happens, in a way that is testable. The causally significant elements we consider are equivalence classes of lower level processes, realized in biological systems through different operations having the same outcome within the context of information control and networks.

show abstract

Section: Experiments On Top-down Causationmentioning

confidence: 80%

Top-down causation by information control: from a philosophical problem to a scientific research programme

Auletta

Ellis

Jaeger

2008

J. R. Soc. Interface.

132

View full text Add to dashboard Cite

show abstract

“…Additionally, this strategy offers great potential in nanobiology and nanomedicine10, 26, 27. Structural RNA NPs can be used to combine multiple functionalities in one delivery particle for various therapeutic purposes27.…”

Section: Resultsmentioning

confidence: 99%

Square-Shaped RNA Particles from Different RNA Folds

et al. 2009

Self Cite

View full text Add to dashboard Cite

The structural information encoding specific conformations of natural RNAs can be implemented within artificial RNA sequences to control both three-dimensional (3D) shape and self-assembling interfaces for nanotechnology and synthetic biology applications. We have identified three natural RNA motifs known to direct helical topology into approximately 90° bends: a five-way tRNA junction, a three-way junction and a two-helix bend. These three motifs, embedded within rationally designed RNAs (tectoRNA), were chosen for generating square-shaped tetrameric RNA nanoparticles (NPs). The ability of each motif to direct the formation of supramolecular assemblies was compared by both native gel assays and atomic force microscopy (AFM). While there are multiple structural solutions for building square-shaped RNA particles, differences in the thermodynamics and molecular dynamics of the 90°-motif can lead to different biophysical behaviors for the resulting supramolecular complexes. We demonstrate via structural assembly programming how the different 90°-motifs can preferentially direct the formation of either 2D or 3D assemblies.

show abstract

“…The ‘sequence network’ that results from the sequence and structural relationships existing between most tertiary motifs identified to date highlights the syntax of emerging folding and assembly principles and rules that direct the stacking, orientation and positioning of RNA helices with respect to one another. As such, this network can be seen as an emerging RNA 3D structure proto-language that can facilitate the prediction of the tertiary structure of natural RNA molecules and the rational design of novel RNA architectures ( 7 , 24 , 25 ). We present the refined prediction of the architecture for the aptamer core of two riboswitches as examples.…”

Section: Introductionmentioning

confidence: 99%

The UA_handle: a versatile submotif in stable RNA architectures†

Jaeger

Verzemnieks

Geary

2008

Nucleic Acids Research

Self Cite

121

View full text Add to dashboard Cite

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/ANnX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.

show abstract

Nucleic Acid Foldamers: Design, Engineering and Selection of Programmable Biomaterials with Recognition, Catalytic and Self‐assembly Properties

Cited by 9 publications

References 214 publications

Top-down causation by information control: from a philosophical problem to a scientific research programme

Top-down causation by information control: from a philosophical problem to a scientific research programme

Square-Shaped RNA Particles from Different RNA Folds

The UA_handle: a versatile submotif in stable RNA architectures†

Contact Info

Product

Resources

About