29 papers · ranked by Valyu relevance
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…
Norbert Schormann, Surajit Banerjee, Robert Ricciardi, Debasish Chattopadhyay
'Debasish Chattopadhyay'] Background Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a…
Xiakun Chu, Fei Liu, Brian A. Maxwell, Yong Wang + 5 more
'Haijun Wang' 'Wei Han' 'Jin Wang' 'Alexander Donald MacKerell'] Protein-DNA recognition is a central biological process that governs the life of cells. A protein will often undergo a conformational transition to form the functional complex with its target DNA. The protein conformational dynamics are expected to…
Thomas Carzaniga, Giuliano Zanchetta, Elisa Frezza, Luca Casiraghi + 8 more
'Luka Vanjur' 'Giovanni Nava' 'Giovanni Tagliabue' 'Giorgio Dieci' 'Marco Buscaglia' 'Tommaso Bellini' 'Paolo Vincenzo Pedone' 'Ilaria Baglivo'] Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is…
Sandip Mandal, Khadka B. Chhetri, Yun Hee Jang, Yves Lansac + 1 more
Protamine, an arginine-rich protein, compacts DNA more tightly than histones in somatic cells, yet its sequence-specific binding remains unclear. Using all-atom MD simulations with an arginine-rich short cationic peptide that mimics the protamine characteristics, we discovered distinct sequence preferences: the peptide…
Cynthia Wolberger
The past 4 decades have seen remarkable advances in our understanding of the structural basis of gene regulation. Technological advances in protein expression, nucleic acid synthesis, and structural biology made it possible to study the proteins that regulate transcription in the context of ever larger complexes…
Yufan Liu, Boxue Tian
Protein-DNA interaction is critical for life activities such as replication, transcription, and splicing. Identifying protein-DNA binding residues is essential for modeling their interaction and downstream studies. However, developing accurate and efficient computational methods for this task remains challenging.…
Amol Tagad, G. Naresh Patwari
The accessibility of genetic information and packaging of long chromosomal DNA into micron-sized nuclei is a great example of protein-DNA interaction. A large number of protein-DNA structures are available in the database and is continuously increasing. The analysis of such huge data to extract meaningful insights…
Priyanka Garg, Thejas Satheesh, Mahipal Ganji, Somnath Dutta
DNA-binding protein under starvation (Dps), is a miniature ferritin complex which plays a vital role in protecting bacterial DNA during starvation for maintaining the integrity of bacteria from hostile conditions. Mycobacterium smegmatis is one such bacteria that express MsDps2, which binds DNA to protect it under…
Ekaterina Morgunova, Yimeng Yin, Pratyush K. Das, Arttu Jolma + 4 more
Most transcription factors (TFs) can bind to a population of sequences closely related to a single optimal site. However, some TFs can bind to two distinct sequences that represent two local optima in the Gibbs free energy of binding (ΔG). To determine the molecular mechanism behind this effect, we solved the…
Jannette Carey, Jan Kormanec
Nearly all of biology depends on interactions between molecules: proteins with small molecules, proteins with other proteins, nucleic acids with small molecules, and nucleic acids with proteins that regulate gene expression, our concern in this Special Issue. All those kinds of interactions, and others, constitute the…
M. S. Rocha
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using…
Michael Liaofan Liu, Daniel W. Oo, Ryan B. McMillan, Ashley R. Carter
'Ashley R. Carter'] DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend in the DNA. Eventually, enough bending leads to the…
Mikhail Kuravsky, Gabriel Grey, Conor Kelly, Polenus Sarkar + 2 more
The operation of Eukaryotic transcription factors remains enigmatic. Cyclic AMP-responsive element-binding protein (CREB) is a member of the basic zipper family, a superfamily of transcription factors which operate exclusively in eukaryotes and bind DNA targets as homodimers or heterodimers. Modulation of…
Likai Du, Chengbu Liu
Transcription factor (TF) are proteins that regulates the transcription of genetic information from DNA to messenger RNA by binding to a specific DNA sequence. Nucleic acid-protein interactions are crucial in regulating transcription in biological systems. This work presents a quick and convenient method for…
Gabriel Rosenblum, Ivan Terterov, Sujeet Kumar Mishra, Nadav Elad + 4 more
Metabolism, gene expression, and signaling all require the adaptation of protein activity to the mixture of reactants and products in a cell. This trait to adapt, called allostery, is hardwired in the structure of proteins. Binding a ligand at one location in a protein can change distant locations, thus tuning protein…
Maria Barbi, Fabien Paillusson
Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in absence of any active process. It has been rapidly recognized that to achieve this task these…
Shane Scott, Zhi Ming Xu, Fedor Kouzine, Daniel J. Berard + 9 more
We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies on containing the DNA molecules within an enclosed array of glass…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
Krzysztof Fink, Jakub Cebula, Zdeněk Tošner, Mateusz Psurski + 2 more
Cobalt bis(dicarbollide) (COSAN) is a metallacarborane used as a versatile pharmacophore to prepare biologically active hybrid organic‒inorganic compounds or to improve the pharmacological properties of nucleosides, antisense oligonucleotides, and DNA intercalators. Despite these applications, COSAN interactions with…
Fadwa Mekkaoui, Robert A. Drewell, Jacqueline M. Dresch, Donald E. Spratt
'Donald E. Spratt'] Homeodomain transcription factors (TFs) bind to specific DNA sequences to regulate the expression of target genes. Structural work has provided insight into molecular identities and aided in unraveling structural features of these TFs. However, the detailed affinity and specificity by which these…
Authors not listed
Stretches of double-stranded DNA sharing the same sequence can recognise each other in cells. This phenomenon, known as homologous recognition, is essential for DNA recombination and repair. Yet, its mechanism remains debated, with purely physical duplex duplex interactions being proposed as a contributing factor.…
Artem K. Efremov, Jie Yan
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such proteins is frequently subject to force and torque constraints applied to the DNA.…
Derek J. Hart, Jiyoun Jeong, James C. Gumbart, Harold D. Kim
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we…
Authors not listed
The binding of the protein streptavidin (SAv) to biotin-modified DNA origami nanostructures (DONs) is widely employed in the single-molecule study of chemical reactions, the arrangement of functional proteins and nanomaterials with molecular precision, and numerous instances of DON-based cryptography, steganography…
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…
Alireza Mashaghi, Allard J. Katan
Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an interesting molecular tool for physicists to test and explore physical laws and…
Authors not listed
Nonenzymatic self-replication is considered as one of the most primordial functions of RNA, which likely preceded the emergence of more complex ribozymes. Among different possible scenarios, nucleotide activation with imidazole derivatives attracted substantial attention over the last years. However, despite the…
Authors not listed
We developed a method to evaluate the degree of influence of attraction and electrostatic repulsion forces in DNA during its chemical denaturation. Our approach shows that when a solution can split apart a target molecule, the forces inside the molecule can be deduced by analyzing the properties of the surrounding…