27 papers · ranked by Valyu relevance
James M. Heather, Benjamin Chain
Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA…
Cheng-Yuan Liou, Shen-Han Tseng, Wei-Chen Cheng, Huai-Ying Tsai
In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical…
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma + 2 more
'Jian Ma' 'Huimin Zhao' 'Olgica Milenković'] Abstract—We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage…
Xingqin Qi, Edgar Fuller, Qin Wu, Cun-Quan Zhang
Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented…
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…
Xue Li, Ziqi Wei, Bin Wang, Tao Song
DNA computing is a new method based on molecular biotechnology to solve complex problems. The design of DNA sequences is a multi-objective optimization problem in DNA computing, whose objective is to obtain optimized sequences that satisfy multiple constraints to improve the quality of the sequences. However, the…
Akanksha Manghrani, Atul Kaushik Rangadurai, Or Szekely, Bei Liu + 2 more
The propensities to form lowly-populated short-lived conformations of DNA could vary with sequence, providing an important source of sequence-specificity in biochemical reactions. However, comprehensively measuring how these dynamics vary with sequence is challenging. Using ^1^H CEST and ^13^C R_1ρ_ NMR, we measured…
O.G. Akintunde, Trichina Tucker, Valerie J. Carabetta
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to elucidate the exact composition and sequence of DNA molecules. Discoveries and the…
Manas Mondal, Lijiang Yang, Zhicheng Cai, Piya Patra + 1 more
As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related…
Yao Yao, Xun Zhang, Xin Liu, Yuan Liu + 2 more
—DNA is not only the genetic material of life, but also a favorable material for a new computing model. Various research works based on DNA computing have been carried out in recent years. DNA sequence design is the foundation of such research. The sequence quality directly affects the universality, robustness, and…
Seongjun Seo, Thi Hong Nhung Vu, Anshula Tandon, Suyoun Park + 3 more
DNA is emerging as a promising medium for ultra-dense, long-term digital data storage, yet sequence design remains hindered by homopolymer formation and compositional bias, which compromise synthesis, sequencing, and decoding accuracy. Here, the study introduces a quantitative framework to evaluate and optimize…
Rebecca Andrews, Horst Steuer, Afaf H. El-Sagheer, Abhishek Mazumder + 4 more
Protein interactions with nucleic acids are central to all genetic processes and many biotechnological applications. While many sequence-dependent protein-DNA interactions have been studied in detail using single-molecule methods, there is no standard high-throughput way to link the complex single-molecule kinetics of…
Yotam Nahum, Eyar Ben-Tolila, Leon Anavy
As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential solution for the future of data storage. Several studies introduced DNA based…
Tsuneyuki Tatsuke
Although we represent the genetic code using four letters, namely A, T, G, and C, it is a chemical entity with sequence-dependent physical properties and a spatial extent. In other words, it can be said that genetic information is compressed and recorded in the genomic DNA as a storage medium with a spatial spread.…
Yixin Wang, Md Noor-A-Rahim, Erry Gunawan, Yong Liang Guan + 1 more
Using DNA as the medium to store information has recently been recognized as a promising solution for long-term data storage. While several system prototypes have been demonstrated, the error characteristics in DNA data storage are discussed with limited content. Due to the data and process variations from experiment…
Simeon D. Castle, Adrian Woolfson, Gregory Linshiz, Blake T. Riley + 5 more
DNA polymerases are complex molecular machines able to replicate genetic material using a template-driven process. While the copying function of these enzymes is well established, their ability to perform untemplated DNA synthesis is less well characterized. Here, we explore the ability of DNA polymerases to synthesize…
Alex El-Shaikh, Marius Welzel, Dominik Heider, Bernhard Seeger
Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA…
Reinhard Heckel, Gediminas Mikutis, Robert N. Grass
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by…
Yipeng Yin, Reed Arneson, Yinan Yuan, Shiyue Fang
The longest oligos that can be chemically synthesized using known methods are typically considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein (GFP) gene and a 1,728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled the breakthrough…
G. Nallappa Bhavithran, R. Selvakumar
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs should not be present in the code. These challenges are overcome by a proper choice…
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…
Hao-Che Peng, Shrijaa Mohan, Muhammad T. Huq, Julie A. Bull + 7 more
Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2=O stretching vibration when it is within the DNA duplex via iso-topic…
Noam Mamet, Gil Harari, Adva Zamir, Ido Bachelet
The Monty Hall problem is a decision problem with an answer that is surprisingly counter-intuitive yet provably correct. Here we simulate and prove this decision in a high-throughput DNA sequencing machine, using a simple encoding. All possible scenarios are represented by DNA oligonucleotides, and gameplay decisions…
Azat Akhmetov, Andrew D. Ellington, Edward M. Marcotte
Encoding arbitrary digital information in DNA has attracted attention as a potential avenue for large scale and long term data storage. However, in order to enable DNA data storage technologies there needs to be improvements in data storage fidelity (tolerance to mutation), the facility of writing and reading the data…
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…
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…
Authors not listed
Sequence is the critical determinant of macromolecular function, yet current polymer design approaches often optimize monomer composition and ratios while ignoring sequence. This creates poorly defined design spaces for active learning that miss the vast combinatorial landscape of sequence possibilities. We introduce…