Related papers: Irreducibility in RNA structures
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the unfolded states is Gaussian, which follows from central…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
An RNA secondary structure is designable if there is an RNA sequence which can attain its maximum number of base pairs only by adopting that structure. The combinatorial RNA design problem, introduced by Hale\v{s} et al. in 2016, is to…
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases,…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
We consider the Combinatorial RNA Design problem, a minimal instance of RNA design where one must produce an RNA sequence that adopts a given secondary structure as its minimal free-energy structure. We consider two free-energy models where…