All articles starting with D

DNA origami mechanical devices

DNA origami mechanical devices are nanoscale machines made by folding long DNA strands into shapes that move, sense forces, and deliver payloads, introduced by Paul Rothemund in 2006.

DNA origami nanopores

A DNA origami nanopore is a nanometer-scale pore made by folding DNA into a preprogrammed 3D shape, used in hybrid solid-state pores and as self-standing lipid membrane channels.

DNA origami nanorobot

A DNA origami nanorobot is a nanoscale DNA structure designed to respond to molecular stimuli by changing configuration or delivering a payload, exemplified by a 2012 hexagonal barrel.

DNA origami plasmonic nanostructures

DNA origami plasmonic nanostructures are metal nanoparticle assemblies positioned with nanometer-scale precision by folded DNA origami templates, used in LSPR and surface-enhanced Raman scattering biosensors, chiral sensing, and metasurfaces.

DNA origami plasmonics

DNA origami plasmonics is the use of scaffolded DNA origami structures as nanoscale templates to arrange metallic nanoparticles into precise configurations, enabling engineered optical responses.

DNA origami rotary motor

A DNA origami rotary motor is a nanoscale rotating machine self-assembled from DNA strands that imitates biological motors like ATP synthase, driven by electric fields, ion gradients, or strand displacement.

DNA origami rotary nanomachine

A DNA origami rotary nanomachine is a nanoscale device built from self-assembled DNA nanostructures in which components rotate about a defined axis, driven by electric fields or Brownian motion.

DNA origami vaccines

DNA origami vaccines are experimental vaccines built on folded DNA nanostructures that co-display viral antigens and adjuvants at precisely controlled nanoscale spacings to boost immune responses.

DNA origami-templated nanoparticle assembly

DNA origami-templated nanoparticle assembly is a bottom-up nanofabrication method in which nanoparticles, quantum dots, and dyes are placed with sub-nanometer precision on folded DNA origami scaffolds, chiefly for plasmonics and biosensing.

DNA photolyase class 2

DNA photolyase class 2 (CPD class II photolyase) is a blue-light, FADH−-dependent enzyme repairing cyclobutane pyrimidine dimers in plants, archaea, marsupials, and viruses, absent from placental mammals, with 8-HDF antenna in most lineages.

Sep 29, 2026

DNA ploidy analysis

DNA ploidy analysis is a cytometric method measuring the DNA content of individual cells by flow or image cytometry to detect aneuploidy in cancers and estimate the S-phase fraction.

DNA polymerase

DNA polymerase, the enzyme family (A, B, C, D, X, Y, RT) that synthesizes DNA 5'-to-3' with two-metal-ion catalysis and 3'-to-5' proofreading; includes Taq, Pfu, and KOD used in PCR and sequencing.

DNA polymerase epsilon catalytic subunit

POLE, the DNA polymerase epsilon catalytic subunit (Gene ID 5426, chromosome 12), is the 2,286-amino-acid leading strand replicase and proofreading exonuclease of four-subunit Pol epsilon; exonuclease-domain mutations cause ultramutated endometrial and colorectal cancers responsive to immunotherapy.

DNA polymerase I

DNA polymerase I (Pol I), first DNA polymerase, isolated from E. coli by Arthur Kornberg in 1956; not the main replicative enzyme; fills Okazaki gaps, repairs DNA, and yields the Klenow fragment.

DNA polymerase III holoenzyme

DNA polymerase III holoenzyme (Pol III HE) is the E. coli chromosomal replicase, a 10-subunit machine with two αεθ cores, a β sliding clamp, and a γ complex clamp loader; τ dimerizes the cores for leading and lagging strand synthesis.

DNA polymerase III, beta sliding clamp

Beta sliding clamp (β clamp, dnaN gene product) of bacterial DNA polymerase III: a head-to-tail homodimeric ring that encircles DNA, boosting Pol III processivity beyond 50 kb, loaded by the DnaX ATPase clamp loader.

DNA polymerase III, delta prime subunit

DNA polymerase III delta prime subunit (δ′, HolB, holB gene) of E. coli: non-ATP-binding AAA+ clamp-loader subunit, 334 aa, C-shaped three-domain structure (PDB 1A5T), regulates δ opening of the β sliding clamp.

DNA profiling

DNA profiling (DNA fingerprinting, DNA typing) identifies individuals from variable DNA regions, invented by Alec Jeffreys in 1984; modern STR-based profiling underpins CODIS, INTERPOL databases, paternity testing, and rapid DNA instruments.

DNA recombination/repair protein RecN

RecN (radB) is a bacterial SMC-like DNA repair protein, first identified in E. coli, that recognizes and coordinates double-strand breaks, bridges DNA molecules in a cohesin-like way, and stimulates RecA-mediated recombinational repair.

DNA repair

DNA repair: enzymatic pathways (base excision, nucleotide excision, mismatch repair, NHEJ, homologous recombination) that correct DNA damage; 2015 Nobel Prize to Lindahl, Modrich, Sancar; PARP inhibitors exploit repair defects in cancer therapy.

DNA repair protein RAD51 homologue 2

RAD51B (DNA repair protein RAD51 homolog 2, RAD51L1), human 384-aa protein on chromosome 14q23-q24.2; RAD51 paralog in the BCDX2 complex promoting RAD51 filament assembly in homologous recombination repair; linked to cancer and Fanconi anemia-like disorder.

DNA repair protein Rad59

Rad59 (RAD59) is a Saccharomyces cerevisiae DNA repair protein, a Rad52 paralog in the RAD52 epistasis group, that anneals single-stranded DNA in Rad51-independent recombination and short-repeat single-strand annealing.

DNA repair protein, Swi5

DNA repair protein Swi5 (InterPro IPR010760, Pfam PF07061) is a small conserved recombination mediator that forms the Swi5-Sfr1 complex stimulating Rad51/Rhp51 and Dmc1 strand exchange in double-strand break repair; distinct from budding yeast SWI5 transcription factor.

DNA replication

DNA replication: semiconservative copying of DNA at replication forks by helicase, primase, polymerases, and ligase; one origin in bacteria, thousands in eukaryotes; licensed once per cell cycle; ~1000 nt/s bacterial forks, ~20x slower in eukaryotes.

DNA replication checkpoint mediator, MRC1 domain

MRC1 domain (Pfam PF09444, IPR018564), a conserved domain in Mrc1/Claspin checkpoint mediators; residues 701-837 of S. pombe Mrc1 and 1045-1203 of human Claspin; required for ATR-mediated Chk1 phosphorylation and fork stalling; unrelated to the human MRC1 mannose receptor gene.

DNA replication initiation

DNA replication initiation: the process by which initiator proteins such as ORC (eukaryotes) and DnaA (bacteria) select replication origins, load MCM2-7 or DnaB helicases, and activate CMG to begin genome duplication exactly once per cell cycle.

DNA replication regulator Sld2

Sld2 (SLD2, Synthetic Lethal with Dpb11 2) is an essential budding yeast DNA replication initiation protein, 453 aa, whose CDK phosphorylation at Thr84 enables Dpb11 binding, origin firing, and CMG helicase assembly; vertebrate counterpart is RECQL4.

DNA replication regulator Sld3

Sld3 (Treslin/TICRR in metazoans) is an essential budding yeast DNA replication initiation protein that binds Cdc45, reads DDK phosphorylation of Mcm4/6, is phosphorylated by CDK at T600/S622 to bind Dpb11, and is inhibited by Rad53 to block late origin firing.

DNA robotics

DNA robotics is a field of molecular robotics in which synthetic DNA molecules self-assemble into nanoscale devices that sense their environment, compute, and act, including walkers, tweezers, and drug-delivering nanorobots.