Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a variety of RNAs and are used to characterize conformational changes in riboswitches. However, the structural determinants that lead to differential reactivities in unpaired nucleotides have not been investigated yet. In this work we used a combination of theoretical approaches, i.e., classical molecular dynamics simulations, multiscale quantum mechanical/molecular mechanical calculations, and enhanced sampling techniques in order to compute and interpret the differential reactivity of individual residues in several RNA motifs including members of the most important GNRA and UNCG tetraloop families. Simulations on the multi ns timescale are required to converge the related free-energy landscapes. The results for uGAAAg and cUUCGg tetraloops and double helices are compared with available data from in-line probing experiments and show that the introduced technique is able to distinguish between nucleotides of the uGAAAg tetraloop based on their structural predispositions towards phosphodiester backbone cleavage. For the cUUCGg tetraloop, more advanced ab initio calculations would be required. This study is the first attempt to computationally classify chemical probing experiments and paves the way for an identification of tertiary structures based on the measured reactivity of non-reactive nucleotides.
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc- and stack-length restrictions. Our main result reads as follows: in the simplex of the nucleotide ratios there exists a convex region in which, in the limit of long sequences, a random structure a.a.s.~has compatible sequence with these ratios and outside of which a.a.s.~a random structure has no such compatible sequence. We localize this region for RNA sec…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules, and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D st…
It is acknowledged that co-evolutionary nucleotide-nucleotide interactions are essential for RNA structures and functions. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence alignment across different species. DCA and similar approaches that use sequence information alone usually yield a low accuracy, especially when the available homologous sequences are limited. Here we present a new method that incorporates a Restricted Boltzmann Machine (RBM) to augment the information on sequence co-variations with structural patterns in contact…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA secondary structure formation, including pseudoknots, that takes into account the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleoti…
Stanford University（斯坦福大学）；NVIDIA Corporation（英伟达公司）；Kaggle；Eterna Massive Open Laboratory（Eterna大规模开放实验室）；State University of New York at Buffalo（纽约州立大学布法罗分校）；High-flyer AI；DeNA；Yanfu Investments；Ghent University（根特大学）；University of Dundee（邓迪大学）；Universal Knowledge Inc.（Universal Knowledge公司）；Keyence Corporation（基恩士公司）；Texas A&M University（得克萨斯农工大学）；Rist Inc（Rist公司）；Kakao Brain；H2O；Clover Health；Afiniti；Nile University（尼罗河大学）；National Research Centre（国家研究中心）
Messenger RNA-based medicines hold immense potential, as evidenced by their rapid deployment as COVID-19 vaccines. However, worldwide distribution of mRNA molecules has been limited by their thermostability, which is fundamentally limited by the intrinsic instability of RNA molecules to a chemical degradation reaction called in-line hydrolysis. Predicting the degradation of an RNA molecule is a key task in designing more stable RNA-based therapeutics. Here, we describe a crowdsourced machine learning competition ("Stanford OpenVaccine") on Kaggle, involving single-nucleotide resolution measure…
Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40--100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, our universe, created by a single inflation event, likely includes more than $10^{100}$ Sun-like stars. If life can emerge at least once in such a large volume, it is not in contradiction with our observations of life on Earth, even if …
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 Haleš et al. in 2016, is to determine whether or not a given RNA secondary structure is designable. Haleš et al. identified certain classes of designable and non-designable secondary structures by reference to their corresponding rooted trees. We introduce an infinite class of rooted trees containing unpaired nucleotides at the greatest depth, and prove constructively that their corresponding …
RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design
Yale University（耶鲁大学）；University of Cambridge (UK)（剑桥大学）；Lawrence Berkeley National Laboratory（伯克利国家实验室）；Prescient Design, Genentech, Roche（Prescient Design、基因泰克、罗氏）；University of Oxford (UK)（牛津大学）；National University of Singapore（新加坡国立大学）
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the algorithms are largely successful in identifying a distribution's constituent structures, it remains challenging to recover their relative weightings. In this paper, we quantify this issue using a total variation distance. Then, we prove under a Nussinov-Jacobson model that a large proportion of RNA structure pairs cannot be jointly reconstructed with low total …
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the ESCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-base model. This results in a representa…
Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach
非编码RNA的三维构象支持其生化功能，但在很大程度上回避了实验表征。在这里，我们报告说，将经典的突变/拯救策略与高通量化学作图相结合，可以快速推断RNA结构，并具有非常强的验证能力。我们重新审视了一个典型的16 S rRNA结构域，其中SHAPE（选择性2`-羟基酰化与引物延伸）表明了载脂蛋白和全核糖体构象之间的构象变化。计算支持的估计，来自替代化学探针的数据，以及突变和映射（M2）实验暴露了先前方法的局限性，而是给出了接近晶体学的二级结构。通过高通量突变/拯救方法对单个碱基对进行系统性询问，然后允许对基于M2的二级结构进行彻底验证和细化，并进一步揭示功能构象作为通过单核苷酸寄存器移位可访问的激发态（25+/-5%群体）。这些结果纠正了错误的形状推断的核糖体构象变化，并提出了一个通用的突变地图救援方法解剖RNA动态结构景观。
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using base-pairing probabilities. Two examples of the latter group are the popular maximum expected accuracy (MEA) method and the ProbKnot method. ProbKnot is a fast heuristic that pairs nucleotides that are reciprocally most probable pairing partners, and unlike MEA, can also predict structures with pseudoknots. However, ProbKnot's full potential has been largely ove…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides, which can be described by random matrix model. We obtain the generating function of the structures using Hermitian matrix model with Chebyshev polynomial of the second kind and analyze the statistics with respect to the number of stems. To match the experimental findings of the statistical behavior, we consider the structures in a grand canonical ensemble an…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) …
Sequence-Informed Geometric Evaluation of RNA 3D Structures
Aalborg University（奥尔堡大学）；Imperial College London（帝国理工学院）；Bioinformatics Institute (BII), A*STAR（新加坡科技研究局生物信息学研究所）；Genome Institute of Singapore (GIS), A*STAR（新加坡科技研究局新加坡基因组研究所）；Statens Serum Institut（丹麦国家血清研究所）；University of Copenhagen（哥本哈根大学）
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We found that the 3 and 5 prime ends are the most structured elements in the viral genome and the 5 prime end has the strongest propensity to associate with human proteins. The domain encompassing nucleotides 23000-24000 is highly conserved both at the sequence and structural level, while the region upstream varies significantly. Th…
Missouri Western State University（密苏里西部州立大学）；Meta-Analytics, Inc.（Meta-Analytics公司）
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in silico) are available for predicting 2-dimensional (secondary) structures however 3-dimensional (tertiary) structure prediction is much more difficult mainly due to the far greater number of feasible solutions and fewer experimental data on the thermodynamic energies of 3D structures. It is also challenging to verify the most likely three dimensional structure…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and this slowness limits their use in genome-wide applications. Results: We present a novel alternative $O(n^3)$-time dynamic programming algorithm for RNA folding that is amenable to heuristics that make it run in $O(n)$ time and $O(n)$ space, while producing a high-quality approximation to the optimal solution. Inspired by incremental parsing for context-free gra…
