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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 sequencing
DNA sequencing, also known as base sequence analysis, determines the exact order of the four bases that make up DNA, revealing genes, regulatory instructions, and disease-causing changes.
DNA shuffling
DNA shuffling is an in vitro recombination method that randomly fragments homologous genes and reassembles them by primerless PCR, producing chimeric genes for directed evolution.
DNA strand displacement circuits
DNA strand displacement circuits are enzyme-free molecular computing systems in which input DNA strands displace output strands, cascading into logic gates, integrated circuits, and neural networks.
DNA topoisomerase I (human TOP1)
Human DNA topoisomerase I (TOP1, chromosome 20) is a type IB enzyme that nicks and rejoins one DNA strand via Tyr723 to relax supercoils; it is the target of camptothecin drugs irinotecan and topotecan and of ADC payloads like DXd.
DNA Topoisomerase II
DNA topoisomerase II (Top2, EC 5.99.1.3) is an ATP-dependent enzyme that passes one DNA duplex through a transient double-strand break in another, untangling and unlinking DNA. Type IIA and IIB families; eukaryotic isoforms Top2α and Top2β; target of etoposide and doxorubicin.
DNA topoisomerase III
DNA topoisomerase III (Topo III, TOP3A/TOP3B, E. coli topB) is a type IA topoisomerase that decatenates DNA and RNA, removes precatenanes at the replication fork with Topo IV, and partners with RecQ/BLM helicases; no inhibitors are known.
DNA transfection
DNA transfection is a laboratory method that introduces foreign DNA into cultured cells, typically with chemical reagents or electric pulses, to express proteins or study gene function.
DNA vaccination
DNA vaccination delivers plasmid DNA encoding an antigen into a recipient's cells, so the host produces the antigen and develops antibody and T-cell immunity against infectious disease or cancer.
DNA virus
DNA virus: a virus with a DNA genome (single or double stranded, linear or circular), including poxviruses, herpesviruses, adenoviruses, and phages; low mutation rates, nuclear or phage-nucleus replication, and wide use as gene therapy and oncolytic vectors.
DNA virus genome strategies
DNA virus genome strategies are the design choices viruses make for their DNA genomes, from single- or double-stranded and circular or linear forms to genome size.
DNA walker
A DNA walker is an artificial molecular machine made of DNA that steps along a pre-designed track of binding sites, first demonstrated autonomously in 2004 by Yin.
DNA-binding domain
DNA-binding domain (DBD): protein domain recognizing specific DNA sequences, used by transcription factors. Key families: helix-turn-helix/homeodomain, Cys2His2 zinc finger (3% of human genes), winged helix; ~60 amino acids average.
DNA-binding protein Fis, N-terminal domain
Fis N-terminal domain: the residues 11-26 beta-hairpin arm of Fis (factor for inversion stimulation), a 98-aa homodimeric E. coli nucleoid protein; the arm stimulates Hin and Gin DNA inversion, while the C-terminal helix-turn-helix binds DNA.
DNA-binding protein, curved-DNA
Curved-DNA-binding proteins, chiefly E. coli CbpA and CbpB (Rob), are nucleoid-associated proteins preferring intrinsically curved AT-rich DNA; CbpA is also a DnaJ co-chaperone induced in stationary phase.
DNA-directed RNA polymerase III subunit RPC1
RPC1 (POLR3A, O14802), largest subunit of human RNA polymerase III; forms the catalytic core with RPC2; mutations cause POLR3-related leukodystrophy, Wiedemann-Rautenstrauch syndrome, and VZV susceptibility.
DNA-encoded chemical library
A DNA-encoded chemical library, often shortened to DEL, is a collection of small molecules each coupled to a DNA barcode, screened in mixture against drug targets.
DNA-PAINT
DNA-PAINT (DNA-based point accumulation for imaging in nanoscale topography) is a super-resolution microscopy method, introduced in 2010, that reaches sub-5-nanometer resolution by transiently binding fluorescent DNA imager strands to targets.
DNA–DNA hybridization
DNA–DNA hybridization is a technique in which DNA from two organisms reassociates, measuring genome-wide similarity; it was the bacterial species standard until whole-genome methods like ANI replaced it.
DnaG Primase
DnaG primase, the bacterial DNA primase encoded by dnaG, is a 65-kDa single-subunit toprim-fold RNA polymerase that makes 10–12-nt RNA primers for DNA polymerase III; structurally unrelated to archaeo-eukaryotic primases and a proposed, still-unexploited antibiotic target.
DnaJ domain
DnaJ domain (J-domain): ~70-residue, four-helix module defining Hsp40/J-domain proteins, named for E. coli DnaJ; its HPD motif stimulates Hsp70 ATP hydrolysis at the NBD-SBD interface.
DNAJB1
DNAJB1 (Hdj1, Hsp40, Sis1) is a human class B Hsp40/J-domain co-chaperone on chromosome 19p13.12 that stimulates Hsp70 ATPase, is autoinhibited by its GF region, drives amyloid disaggregation, and forms the DNAJB1-PRKACA fusion defining fibrolamellar carcinoma.
DNAJB6
DNAJB6 (MRJ, Hsj2), gene at 7q36.3, encodes a human Hsp40/J-domain co-chaperone of HSP70 that suppresses polyglutamine aggregation; dominant G/F-domain mutations cause limb-girdle muscular dystrophy D1 (LGMDD1).
DNAJB6-related limb-girdle muscular dystrophy D1
DNAJB6-related limb-girdle muscular dystrophy D1, also called LGMD1D, is a rare autosomal dominant muscular dystrophy caused by DNAJB6 gene mutations, typically causing adult-onset pelvic girdle weakness.
DNase-Seq
DNase-Seq is a sequencing method that maps DNase I hypersensitive sites, the nucleosome-depleted open chromatin regions where regulatory DNA is accessible, across a genome, combining DNase I footprinting with next-generation sequencing.
DNASE1
DNASE1 (DNL1, DRNI), gene ID 1773 at 16p13.3, encodes the secreted endonuclease DNase I, which cleaves DNA to 5'-phosphate fragments, clears apoptotic DNA, and as recombinant dornase alfa (Pulmozyme) treats cystic fibrosis lung disease.