4.5 Article

TripDesign: A DNA Triplex Design Approach Based on Interaction Forces

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Oncology

A feedforward circuit between KLF5 and lncRNA KPRT4 contributes to basal-like breast cancer

Guangshi Du et al.

Summary: This study identifies the promoting role of KPRT4 in BLBC cell proliferation and reveals the underlying mechanism of mutual regulation between KLF5 and KPRT4. Additionally, the study finds that targeting KPRT4 can attenuate tumor growth, suggesting KPRT4 as a major molecule for BLBC progression.

CANCER LETTERS (2022)

Article Multidisciplinary Sciences

The RNA-bound proteome of MRSA reveals post-transcriptional roles for helix-turn-helix DNA-binding and Rossmann-fold proteins

Liang-Cui Chu et al.

Summary: RNA-binding proteins play a crucial role in controlling gene expression. This study identifies hundreds of RNA-binding proteins in methicillin-resistant Staphylococcus aureus (MRSA) and demonstrates that a major transcription factor binds RNAs near intrinsic transcription terminators using its helix-turn-helix domain.

NATURE COMMUNICATIONS (2022)

Review Chemistry, Multidisciplinary

DNA Walkers for Biosensing Development

Lu Song et al.

Summary: DNA nanomaterials, with the ability to design arbitrary shapes and controllable motions, have been widely used to construct diverse nanomachines. Among them, DNA walkers are popular nanodevices with ingenious design and flexible function, showing great potential in biosensing applications.

ADVANCED SCIENCE (2022)

Article Biochemistry & Molecular Biology

Multi-TransDTI: Transformer for Drug-Target Interaction Prediction Based on Simple Universal Dictionaries with Multi-View Strategy

Gan Wang et al.

Summary: A novel end-to-end learning model was proposed to encode drugs and proteins and was evaluated on the BindingDB dataset, outperforming other models.

BIOMOLECULES (2022)

Article Mathematics

Bio-Constrained Codes with Neural Network for Density-Based DNA Data Storage

Abdur Rasool et al.

Summary: This paper presents a computational model that combines neural networks with combinatorial biological constraints to design large DNA libraries. The model enables storing large amounts of data in shorter nucleotide sequences and avoids non-specific hybridization errors by satisfying biological constraints. It achieves significant improvement in the DNA library.

MATHEMATICS (2022)

Article Biotechnology & Applied Microbiology

SDNN-PPI: self-attention with deep neural network effect on protein-protein interaction prediction

Xue Li et al.

Summary: In this paper, a PPI prediction method SDNN-PPI based on self-attention and deep learning is proposed. Satisfactory results are obtained on various datasets, and the method not only explores the mechanism of protein-protein interaction but also provides new ideas for drug design and disease prevention.

BMC GENOMICS (2022)

Article Biochemical Research Methods

DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions

Tao Song et al.

Summary: In this study, DeepFusion, a deep learning based multi-scale feature fusion method, is proposed for predicting drug-target interactions. Experimental results show that DeepFusion achieves good prediction performance on different sub-datasets.

METHODS (2022)

Article Mathematical & Computational Biology

Adaptive coding for DNA storage with high storage density and low coverage

Ben Cao et al.

Summary: This paper proposes an adaptive coding DNA storage system to address the low space utilization, high read coverage, and poor coding coupling in DNA storage. The system achieves high storage density and low read coverage, promoting the development of carbon-based storage.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2022)

Review Computer Science, Interdisciplinary Applications

A Comprehensive Analysis of Nature-Inspired Meta-Heuristic Techniques for Feature Selection Problem

Manik Sharma et al.

Summary: Meta-heuristics are problem-independent optimization techniques that provide optimal solutions through iterative exploration and exploitation of the entire search space. This study aims to comprehensively analyze the application of nature-inspired meta-heuristics in feature selection through a systematic review of 176 articles.

ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING (2021)

Article Engineering, Multidisciplinary

An adaptive variational mode decomposition based on sailfish optimization algorithm and Gini index for fault identification in rolling bearings

M. G. A. Nassef et al.

Summary: This paper presents a framework using the SFO algorithm and GI criterion to adaptively select the optimum VMD parameters for fault identification from vibration signals of rolling bearings. Experimental results indicate the high efficiency of the proposed method in extracting fault features and excluding noise.

MEASUREMENT (2021)

Article Chemistry, Analytical

Label-free triplex DNA-based biosensing of transcription factor using fluorescence resonance energy transfer between N-doped carbon dot and gold nanoparticle

Mohamad Mahani et al.

Summary: A new turn-on fluorescent assay based on triplex DNA labeled with N-doped carbon dots and gold nanoparticles was established for sensitive and selective detection of transcription factor NF-kB p50.

ANALYTICA CHIMICA ACTA (2021)

Review Pharmacology & Pharmacy

Nucleic acids therapeutics using PolyPurine Reverse Hoogsteen hairpins

Veronique Noe et al.

Summary: PPRHs are DNA hairpins formed by intramolecular reverse Hoogsteen bonds that can bind to polypyrimidine stretches in dsDNA, leading to gene silencing, gene expression inhibition, point mutation correction, and applications as biosensor probes. They have high stability and lack immunogenicity, hepatotoxicity, or nephrotoxicity in vitro, making them a promising biotechnological tool with diverse biomedical applications.

BIOCHEMICAL PHARMACOLOGY (2021)

Article Chemistry, Multidisciplinary

Probing the Conformational States of a pH-Sensitive DNA Origami Zipper via Label-Free Electrochemical Methods

Paul Williamson et al.

Summary: This study designed a DNA origami zipper structure with nine pH-responsive DNA locks, successfully immobilized on gold surfaces, and characterized using electrochemical methods. The findings suggest potential for developing DNA origami-based pH monitoring, sensing, and release strategies on functionalized gold surfaces.

LANGMUIR (2021)

Article Biochemistry & Molecular Biology

Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH

David A. Rusling

Summary: The introduction of the nucleobase 6-amino-5-nitropyridin-2-one (Z) enables stable and selective triplex formation of synthetic TFOs at neutral pH and above, overcoming the limitation of cytosine protonation at low pH. Furthermore, a universal strategy for enzymatic assembly of Z-containing TFOs using commercially available deoxyribonucleotide triphosphate has been demonstrated, aiming to improve the recognition properties of TFOs and reduce the cost and expertise associated with their chemical syntheses.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro

Beate Kaufmann et al.

Summary: Triplex-seq is a deep-sequencing method that systematically maps the interaction space between oligo library of ssDNA triplex-forming oligos and a particular dsDNA triplex target site. Through deep-sequencing platforms, our understanding of triplex binding rules can be expanded significantly.

ACS SYNTHETIC BIOLOGY (2021)

Article Biochemistry & Molecular Biology

A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions

Gyuri Park et al.

Summary: This study utilized advanced ab initio calculations to investigate nucleobase model structures and their interactions, comparing the interactions of DNA duplexes, triplexes, and quadruplexes under unified computational conditions. By considering factors such as water molecules and ion preferences, new structure factors were devised to effectively compare computationally-predicted and experimentally-determined structures, validating the potential of ab initio study in guiding the programming of complex DNA constructs.

NUCLEIC ACIDS RESEARCH (2021)

Article Automation & Control Systems

An Evolutionary Neuro-Fuzzy C-means Clustering Technique

Priyanka D. Pantula et al.

ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE (2020)

Article Chemistry, Multidisciplinary

DNA Structural Changes Induced by Intermolecular Triple Helix Formation

Ibrahim Sayoh et al.

ACS OMEGA (2020)

Article Chemistry, Multidisciplinary

Dynamic Programming of a DNA Walker Controlled by Protons

Dongbao Yao et al.

ACS NANO (2020)

Article Computer Science, Artificial Intelligence

Marine Predators Algorithm: A nature-inspired metaheuristic

Afshin Faramarzi et al.

EXPERT SYSTEMS WITH APPLICATIONS (2020)

Article Automation & Control Systems

The Sailfish Optimizer: A novel nature-inspired metaheuristic algorithm for solving constrained engineering optimization problems

S. Shadravan et al.

ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE (2019)

Article Biochemistry & Molecular Biology

A tunable assay for modulators of genome-destabilizing DNA structures

Imee M. A. del Mundo et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

Rational Design of pH-Responsive DNA Motifs with General Sequence Compatibility

Wenhao Fu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Article Biochemistry & Molecular Biology

Triplex-forming oligonucleotides: a third strand for DNA nanotechnology

Arun Richard Chandrasekaran et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism

Anna Reymer et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Chemistry, Multidisciplinary

Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above

Sarah Walsh et al.

CHEMICAL SCIENCE (2018)

Article Multidisciplinary Sciences

Selective control of reconfigurable chiral plasmonic metamolecules

Anton Kuzyk et al.

SCIENCE ADVANCES (2017)

Review Chemistry, Multidisciplinary

Triplex DNA Nanostructures: From Basic Properties to Applications

Yuwei Hu et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Article Biochemistry & Molecular Biology

The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

Piroon Jenjaroenpun et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci

Fabian A. Buske et al.

BIOINFORMATICS (2013)

Review Chemistry, Multidisciplinary

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

Osman Doluca et al.

CHEMICAL REVIEWS (2013)

Article Biochemistry & Molecular Biology

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

Fabian A. Buske et al.

GENOME RESEARCH (2012)

Article Biochemistry & Molecular Biology

Formation of stable DNA triplexes

Keith R. Fox et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2011)

Article Chemistry, Multidisciplinary

NUPACK: Analysis and Design of Nucleic Acid Systems

Joseph N. Zadeh et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Review Biochemistry & Molecular Biology

DNA triple helices: Biological consequences and therapeutic potential

Aklank Jain et al.

BIOCHIMIE (2008)

Article Biochemistry & Molecular Biology

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences

Oleg Kikin et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Chemistry, Organic

Synthesis and G-quadruplex binding studies of new 4-N-methylpyridinium porphyrins

Diana P. N. Goncalves et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2006)

Article Biochemistry & Molecular Biology

A web-based search engine for triplex-forming oligonucleotide target sequences

Sara S. Gaddis et al.

OLIGONUCLEOTIDES (2006)

Article Biochemistry & Molecular Biology

Triplex-forming oligonucleotide target sequences in the human genome

JR Goni et al.

NUCLEIC ACIDS RESEARCH (2004)

Review Biochemistry & Molecular Biology

Recent improvements in antigene technology

S Buchini et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2003)

Article Biochemistry & Molecular Biology

A directional nucleation-zipping mechanism for triple helix formation

P Alberti et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Chemistry, Multidisciplinary

BNAs: novel nucleic acid analogs with a bridged sugar moiety

T Imanishi et al.

CHEMICAL COMMUNICATIONS (2002)