AIMC Topic: DNA

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Electronic and Nuclear Quantum Effects on Proton Transfer Reactions of Guanine-Thymine (G-T) Mispairs Using Combined Quantum Mechanical/Molecular Mechanical and Machine Learning Potentials.

Molecules (Basel, Switzerland)
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine...

Precision Basecalling of Single DNA Nucleotide from Overlapped Transmission Readouts with Machine Learning Aided Solid-State Nanogap.

ACS applied materials & interfaces
DNA sequencing with the quantum tunneling technique heralds a paradigm shift in genetic analysis, promising rapid and accurate identification for diverging applications ranging from personalized medicine to security issues. However, the widespread di...

Autonomous assembly and disassembly of gliding molecular robots regulated by a DNA-based molecular controller.

Science advances
In recent years, there has been a growing interest in engineering dynamic and autonomous systems with robotic functionalities using biomolecules. Specifically, the ability of molecular motors to convert chemical energy to mechanical forces and the pr...

Prediction of Protein-DNA Interface Hot Spots Based on Empirical Mode Decomposition and Machine Learning.

Genes
Protein-DNA complex interactivity plays a crucial role in biological activities such as gene expression, modification, replication and transcription. Understanding the physiological significance of protein-DNA binding interfacial hot spots, as well a...

Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths.

Journal of chemical information and modeling
Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function of DNA sequence based o...

Prediction of Transcription Factor Binding Sites on Cell-Free DNA Based on Deep Learning.

Journal of chemical information and modeling
Transcription factors (TFs) are important regulatory elements for vital cellular activities, and the identification of transcription factor binding sites (TFBS) can help to explore gene regulatory mechanisms. Research studies have proved that cfDNA (...

Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA.

ACS sensors
Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, ...

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Science (New York, N.Y.)
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases w...

DNA shape features improve prediction of CRISPR/Cas9 activity.

Methods (San Diego, Calif.)
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine ...

A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems.

Physical chemistry chemical physics : PCCP
With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due...