Search · four archives
Search · four archives
27 papers · ranked by Valyu relevance
Zi-Chun Mu, Ya-Lan Tan, Ben-Gong Zhang, Jie Liu + 1 more
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both…
Jan Zrimec
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like representations are algorithmically very useful, here we fused over 60 currently…
Deng Luo, Alexandre Kouyoumdjian, Ondřej Strnad, Haichao Miao + 2 more
'Ivan Barišić' 'Ivan Viola'] We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar and designing novel visuals, as well as…
Bohdan Schneider, Paulína Božíková, Petr Čech, Daniel Svozil + 3 more
'Jiří Černý' 'Linda Bloom' 'Jörg Bungert'] We analyzed the structural behavior of DNA complexed with regulatory proteins and the nucleosome core particle (NCP). The three-dimensional structures of almost 25 thousand dinucleotide steps from more than 500 sequentially non-redundant crystal structures were classified by…
Patrycja Obara, Paweł Wolski, Tomasz Pańczyk, Carla Bazzicalupi
This article provides a comprehensive examination of non-canonical DNA structures, particularly focusing on G-quadruplexes (G4s) and i-motifs. G-quadruplexes, four-stranded structures formed by guanine-rich sequences, are stabilized by Hoogsteen hydrogen bonds and monovalent cations like potassium. These structures…
Stephen Neidle
The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 68 years. Their structural diversity has…
Zhiyuan Peng, Yuanbo Tang, Yang Li
Recovery Authors: ['Zhiyuan Peng' 'Yuanbo Tang' 'Yang Li'] DNA sequences encode vital genetic and biological information, yet these unfixed-length sequences cannot serve as the input of common data mining algorithms. Hence, various representation schemes have been developed to transform DNA sequences into fixed-length…
Jinsen Li, Tsu-Pei Chiu, Remo Rohs
Understanding the mechanisms of protein-DNA binding is critical in comprehending gene regulation. Three-dimensional DNA shape plays a key role in these mechanisms. In this study, we present a deep learning-based method, Deep DNAshape, that fundamentally changes the current k-mer based high-throughput prediction of DNA…
Sabrina Harteis, Sabine Schneider
DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and…
Charlotte Polo, Ameeta Thandi, Olivia Chandler, Paula Lugert + 11 more
Deoxyribonucleic acid (DNA) stands as one of the most foundational concepts in life sciences, essential for students to master. However, when surveyed about the forces that stabilize the double-stranded DNA structure, many students exhibited a conceptual bias—favoring base pairing as the primary stabilizing force…
Jonathan P. K. Doye, Thomas E. Ouldridge, Ard A. Louis, Flavio Romano + 7 more
'Flavio Romano' 'Petr Šulc' 'Christian Matek' 'Benedict Snodin' 'Lorenzo Rovigatti' 'John S. Schreck' 'Ryan M. Harrison' 'William P. J. Smith'] To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such…
Cindy Ng, Anirban Samanta, Ole Aalund Mandrup, Emily Tsang + 3 more
The folding of double-stranded DNA around histones is a central mechanism in eukaryotic cells for compacting the genetic information into chromosomes. Very few artificial methods are available for controlling the shape of dsDNA at any level, whereas several artificial methods have been developed to efficiently organize…
Thomas E. Ouldridge
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key…
Subhash Kak
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher recursive levels. It was shown previously that an information-theoretic geometry of…
Alex Lee, Joshua Rackers, William Bricker
One of the fundamental limitations of accurately modeling biomolecules like DNA is the inability to perform quantum chemistry calculations on large molecular structures. We present a machine learning model based on an equivariant Euclidean Neural Network framework to obtain quantum-accurate electron densities for…
Taro Nishinaka
A triplex DNA model bound to a helical filament of homologous recombination protein, such as Escherichia coli RecA, is presented. This model suggests that a function of the nucleoprotein filament could be at least partly attributed to the lowering of transition energy of duplex DNA structure having the E-type sugar…
Min Duan, Bing Meng, Lei Zhou, Lijie Wu + 5 more
The CRISPR–Cas9 system locates genomic targets through gRNA pairing and recognition a protospacer-adjacent motif (PAM). While PAM specificity is typically sequence-determined, we previously found that DNA topology can regulate PAM specificity, relaxing PAMs of various Cas9 effectors and allowing near-PAMless cleavage…
Elvira Tarasova, Sonali Dhindwal, Matthew Popp, Sakeenah Hussain + 3 more
'Reza Khayat' 'Hong Zhou' 'Blossom Damania'] Title: ABSTRACT Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses infect members from all three domains of life (Archaea, Prokarya, and Eukarya). The replicase (Rep) from these viruses is responsible for initiating rolling circle replication (RCR) of their…
Authors not listed
While divalent ions are known to be involved in key biological processes such as RNA folding or DNA-histone interactions, these interactions are poorly captured in molecular dynamics simulations with empirical force fields, which suffer from strong overbinding artefacts. Hence, there is a high need for improved…
Authors not listed
By offering exquisite programmability, sequence-specific DNA self-assembly is the fundament of structural DNA nanotechnology but necessitates custom-designed DNA strands. Finding assembly principles orthogonal to base pairing is thus desirable not only to organize DNA in a sequence-independent manner but also to bring…
Tanay Debnath, G. Andres Cisneros
Incorporation of artificial 3rd base pairs (Unnatural base pairs, UBPs) has emerged as a fundamental technique in pursuit of expanding the genetic alphabet. 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN), a potential unnatural base pair (UBP) developed by Romesberg and…
Pengyu Liu, Jacob Lusk, Nataša Jonoska, Mariel Vázquez
R-loops are a class of non-canonical nucleic acid structures that typically form during transcription when the nascent RNA hybridizes the DNA template strand, leaving the DNA coding strand unpaired. Co-transcriptional R-loops are abundant in nature and biologically relevant. Recent research shows that DNA sequence and…
Tanay Debnath, G. Andrés Cisneros
DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Longbing Cao, Chengzhang Zhu
Enterprise data typically involves multiple heterogeneous data sources and external data that respectively record business activities, transactions, customer demographics, status, behaviors, interactions and communications with the enterprise, and the consumption and feedback of its products, services, production…
Nicholas Gao, Daniele Mazzoletti, Adele Peng, Paul Dominic B. Olinares + 13 more
The Vibrio cholerae (Vc) DnaB replicative helicase structure bound to single-stranded (ss) DNA is depicted in the ribbon (top left) and sphere-cylinder representation (top right). In the bottom center is a native mass spectrum showing Vc DnaB helicase loading onto single-stranded DNA (ssDNA). Replicative helicases are…
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…