![]() ![]() Lecture Notes in Computer Science (eds Doty, D. In DNA Computing and Molecular Programming. A reaction network scheme which implements the EM algorithm. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Experimental measurement of binding energy, selectivity and allostery using fluctuation theorems. Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase. Molecular-level similarity search brings computing to DNA data storage. Predicting DNA hybridization kinetics from sequence. ![]() RNA sequence analysis defines Dicer’s role in mouse embryonic stem cells. Absolute quantification of microRNAs by using a universal reference. Thermodynamic analysis of interacting nucleic acid strands. NUPACK: analysis and design of nucleic acid systems. DNA computing circuits using libraries of DNAzyme subunits. A deoxyribozyme-based molecular automaton. Scaling up digital circuit computation with DNA strand displacement cascades. Molecular computation of solutions to combinatorial problems. Propelling DNA computing with materials’ power: recent advancements in innovative DNA logic computing systems and smart bio-applications. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R. Enzyme-based logic systems for information processing. Biocomputing based on particle disassembly. ![]() Molecular logic gates: the past, present and future. A molecular photoionic and gate based on fluorescent signalling. Enhancement of the blood-circulation time and performance of nanomedicines via the forced clearance of erythrocytes. Advanced smart nanomaterials with integrated logic-gating and biocomputing: dawn of theranostic nanorobots. Biomolecular computing systems: principles, progress and potential. Molecular digital data storage using DNA. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. This Article uncovers the information-processing power of the low-affinity interactions that may underlie major processes in an organism-from short-term memory to cancer, ageing and evolution. Most importantly, I show potential pathways of gene regulation with strands of maximum non-complementarity to the gene sequence that may be key to the reduction of off-target therapeutic effects. I demonstrate this mechanism by constructing a memory circuit, a 5-min square-root circuit for 4-bit inputs comprising only nine processing ssDNAs, simulating a 572-input AND gate (surpassing the bitness of current electronic computers), and elementary algebra systems with continuously changing variables. ![]() Here I reveal the ‘strand commutation’ phenomenon-a fundamentally different mechanism of information storage and processing by DNA/RNA based on the reversible low-affinity interactions of essentially non-complementary nucleic acids. The discovery of the DNA double helix has revolutionized our understanding of data processing in living systems, with the complementarity of the two DNA strands providing a reliable mechanism for the storage of hereditary information. ![]()
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