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DNA glossary & taxonomy
Related glossaries include Expression, Gene definitions, Maps, Proteins, protein structures, RNA, SNPs & other genetic variations, Sequences, DNA & beyond Not until the technologies for working with nucleic acids and proteins are better integrated will their researchers be better integrated than they are now.
catalytic DNA: Molecules of DNA that possess enzymatic activity. MeSH, 2001
chloroplast DNA: Eukaryotic cells that are capable of photosynthesis contain chloroplasts with chloroplast DNA. [Andy Vierestrate, DNA in a cell, Univ. of Ghent, Belgium,1999 http://allserv.rug.ac.be/~avierstr/principles/cell.html
chromosomal DNA: Is this different (and if so, how?) from nuclear DNA?
complementary cDNA: Gene definitions
corporate DNA [metaphorical]: Business of biopharmaceuticals glossary
DNA deoxyribonucleic acid: A high- molecular- mass linear polymer, composed of nucleotides containing 2-deoxyribose and linked between positions 3’ and 5’ by phosphodiester groups; DNA contains the genetic information of organisms. The double- stranded form consists of a double helix of two complementary chains that run in opposite directions and are held together by hydrogen bonds between pairs of the complementary nucleotides. [IUPAC Compendium]
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double- stranded state, yet several important biological processes transiently involve single- stranded regions. DNA, which consists of a polysugar- phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). MeSH
No state or federal law defines DNA. Genetics Task Force Working Glossary, Draft for subcommittees, Washington State Dept. of Health, May 2002 http://22.214.171.124/sboh/Goals/Past/Genetics/2002_04-12/docs/Tab08_GTFWorkingGlossary.pdf
Building on the DNA Revolution,
Science, April 11, 2003 http://www.sciencemag.org/feature/data/dna/
Narrower terms: cDNA, chromosomal DNA, double helix, exons, genes, introns, LINES, mitochondrial DNA, nuclear DNA, SINES; Pharmaceutical biology glossary recombinant DNA. Related terms: Sequences, DNA & beyond glossary; Microarrays glossary Southern blotting
DNA computing: Computers & computing glossary
DNA fingerprinting The term "DNA fingerprinting" was coined by British geneticist Alec Jeffreys only ten years ago. Since that time, DNA forensics has become an important tool in law enforcement. In some cases, the DNA tests have helped convict suspects, while in others the tests have exonerated suspects or overturned previous convictions. Recent high profile court cases have put the spotlight on DNA forensics and created the impression that there is a lack of agreement among the experts on the reliability of this evidence. Interview with DNA Forensics Authority Dr. Bruce Weir, Access Excellence, William Neal Reynolds, Interviewed by Sean Henahan, January 1995 http://www.accessexcellence.org/RC/AB/BA/Interview_Weir.html
Alec Jeffreys describes discovering DNA fingerprinting http://genome.wellcome.ac.uk/doc_wtd020877.html
DNA packaging: The folding of an organism's DNA molecule into a compact, orderly structure that fits within the limited space of a CELL or VIRUS PARTICLE. MeSH 2004
DNA probes: Gene amplification & PCR glossary
DNA repair: The reconstruction of a continuous two- stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post- replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post- replication repair are sometimes referred to as "dark repair" because they do not require light. MeSH, 1974
DNA synthesis: DNA replication, the process of making copies of strands of DNA. Existing DNA is used as a template for synthesizing the new strands. [PhRMA] Related terms protein synthesis, translation
DNA transposable elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. MeSH, 1999
double helix: The shape that two linear strands of DNA assume when bonded together. [DOE] And the title of James Watson’s first- hand account of his (and colleagues') Nobel Prize winning discovery.
Double Helix: 50 years of DNA, Nature, 2003 http://www.nature.com/nature/dna50/
ds: Double-stranded (DNA or RNA)
of DNA Elements: The goal of this
project is to comprehensively identify functional elements in the human genome
sequence. The ENCODE project will begin as a pilot project that will test and
compare methods for the exhaustive identification and verification of functional
sequence elements in 30 Mb of human genomic DNA. NHGRI http://grants1.nih.gov/grants/guide/rfa-files/RFA-HG-03-003.html
environmental DNA: Many of the most powerful drugs used today have come from studying the natural products produced by soil bacteria. The continued screening of easily cultured soil microbes for the production of interesting biologically active small molecules has increasingly led to the rediscovery of known molecules. Many lines of evidence now suggest that only a tiny and unrepresentative minority of soil microbes is cultured using conventional approaches. Soil microbes that have not yet been cultured outnumber their cultured counterparts by two to three orders of magnitude, and this uncultured majority no doubt produces secondary metabolites that could serve as molecular probes of biological processes or future therapeutic agents. Jon Clardy Lab, Environmental DNA, Harvard University, Dept of Biological Chemistry and Molecular Pharmacology http://clardy.med.harvard.edu/research
EST Expressed Sequence Tag: Partial gene sequence data of a cDNA clone, which provide a sequence tag for a gene. In order to achieve a very high throughput, these sequences are usually only subjected to a single pass of sequencing so the error rate in these sequences can be high, perhaps approaching 5%. [NCBI]
Developed by Craig Venter and colleagues and further established by the Merck Gene Index. Clones from cDNA libraries are sequenced (single read) from the 3’ end. [R Strausberg et al "The Cancer Genome Anatomy Project" Trends in Genetics 16(3): 103-106 March 2000]
Sequence tags derived from cDNAs. Expressed sequence tags (ESTs) are partial DNA sequences from clones. MeSH, 1999
Often, but not necessarily represent genes, generated through rapid, but error- prone, sequencing methods. Related terms: ORESTES, ORFS, Gene definitions cDNA, transcript clusters; Maps genomic & genetic EST maps; Combinatorial libraries & synthesis gene library
exons: Gene definitions
genomic DNA gDNA: The entire length of DNA, including non coding regions. (Sometimes called gDNA.)
DNA which includes exons and introns, coding and noncoding regions. Compare with cDNA.
integrons: DNA elements capable of mobilizing individual gene cassettes into bacterial chromosomes by site- specific recombination. Integrons consist of a central variable region that often harbors antibiotic- resistance gene cassettes, flanked by 5' and 3' conserved sequences (CS) (2). Integrons have been categorized into four different classes on the basis of the distinctive integrase (int) genes they carry on their 5'-CS. Amita, Chowdhury SR, Thungapathra M, Ramamurthy T, Nair GB, Ghosh A. Class I integrons and SXT elements in El Tor strains isolated before and after 1992 Vibrio cholerae O139 outbreak, Calcutta, India. Emerg Infect Dis [serial online] 2003 Apr [date cited];8. http://www.cdc.gov/ncidod/EID/vol9no4/02-0317.htm
intergenic DNA: Any of the DNA in between gene- coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions. MeSH, 2001 See also under intragenic DNA
intragenic DNA: One cannot assume that there are no genes in a sequenced region, just because no genes were annotated. We introduce another approach to this problem, based on an analysis of the cDNA-to-genomic alignments, in all of the complete or nearly- complete genomes from the multicellular organisms. Our conclusion is that, in animals but not in plants, most of the "junk" is intron DNA. … We consider only the euchromatic portion of the genome. The heterochromatic portion (e.g., centromeres and telomeres) is highly repetitive and largely devoid of genes. It is extremely difficult to clone, extremely polymorphic, and unlikely to be sequenced correctly anytime soon. We define the exons and introns as "intragenic" and everything else as "intergenic." This is not to imply that intergenic DNA is nonfunctional, especially as we have incorporated the promoters into our definition. However, promoters are difficult to identify, whereas exons and introns are reliably identified by cDNA-to-genomic alignments. Gane Ka-Shu Wong, et al Is "Junk" DNA Mostly Intron DNA? Genome Research 10 (11): 1672- 1678, November 2000 http://www.genome.org/cgi/content/full/10/11/1672
intron: An intervening section of DNA which occurs almost exclusively within a eukaryotic gene, but which is not translated to amino acid sequences in the gene product. The introns are removed from the pre- mature mRNA through a process called splicing, which leaves the exons untouched, to form an active mRNA. [IUPAC Bioinorganic, IUPAC Compendium]
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes. MeSH, 1987
A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [DDBJ/ EMBL/ GenBank Feature Table] http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html Related terms: "junk DNA", non- coding, untranslated regions UTR. Gene definitions: exons
"junk DNA": A general term that encompasses many different types of DNA sequences. These sequences run the gamut from introns, the parts of genes that are edited out during protein synthesis; transposable elements, repeated DNA sequences that, like parasites, duplicate themselves, adding nothing to the genome except more redundant sequence; and pseudo genes, fossils of one- time genes…all of the regulatory elements – promoters and inhibitors - required for gene transcription are spelled out somewhere between the genes. The same is true of other elements deemed junk, such as introns and RNA genes, which clearly hold important clues to understanding alternative splicing … the term junk DNA is frequently used incorrectly. Numerous articles in the medical literature use junk and non- coding DNA interchangeably. B. Kuska "Bring in Da Noise, Bring in Da Junk" JNCI 90(15): 1125-1127 Aug. 5, 1998
Dr. Susumu Ohno, writing in the Brookhaven Symposium on Biology in 1972 in the article "So Much ‘Junk DNA" in our Genome’ is credited with originating the term. But his paper was focused "mainly on the fossilized genes, called pseudo genes, that are strewn like tombstones throughout our DNA. But as the term caught on in the 1980’s, its meaning was extended to all non- coding sequences, the vast stretches of DNA that are not genes and do not produce proteins" (about 95% of the genome) … some [scientists] have begun the scrap the notion that all non- coding DNA is junk … "I don't think people take the term very seriously anymore" says Eric Green [NHGRI] whose group is mapping chromosome 7. B. Kuska "Should Scientists Scrap the Notion of Junk DNA?" JNCI 90(14): 1032-1033 July 15 1998 Narrower terms intron, non- coding, repetitive sequences.
Tom Schneider's Left Handed DNA Hall of Fame http://users.fred.net/tds///leftdna/
metagenomic DNA: A Census of rRNA
Genes and Linked Genomic Sequences within a Soil Metagenomic Library, Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM, Appl Environ
Microbiol 2003 May; 69(5): 2684- 91
clarifies human evolution, Max Ingman, 2004 http://www.actionbioscience.org/evolution/ingman.html
naked DNA: For a genetic expression to work properly, genes have to enter a cell; in conventional practice, however, genes may only come as close as to be attached to the cell membrane, unable to penetrate it. A carrier, an agent to introduce the genetic expression to a cell, becomes necessary at this point. An improved virus vector (i.e., purified not to pose danger to the host cell) is usually used for these purposes, and the method features a genetic expression introduced to a cell by a ribosome. Projects Glossary, AnGesMG, Inc. http://www.anges-mg.com/en/project/word.htm Related? term: naked proteins, naked DNA vaccines
natural competence: Natural competence, the ability of many bacteria to take up DNA from their surroundings, raises a number of important questions: How are inflexible and highly charged DNA molecules transported across membranes? What environmental or physiological signals trigger this ability? Is the DNA used primarily as a genetic or a nutritional resource? Redfield Lab, University of British Columbia, Canada http://www.zoology.ubc.ca/~redfield/index.html
non-coding DNA: Introns, spliced out of the messenger RNA following transcription. [NHLBI]
(also known as selfish, ignorant, parasitic and incidental DNA) includes introns, transposable elements, pseudogenes, repeat elements, satellites, UTRs, hnRNAs, LINEs, SINEs, as well as unidentified junk and makes up approximately 97% of the human genome. Some scientists were so overwhelmed by the amount of non- coding DNA, that they referred to the genome as “a collection of non- coding regions interrupted by small coding regions.” Dov. S. Greenbaum "Junk?" Genomics & Bioinformatics MBB 452a, Yale Univ. http://bioinfo.mbb.yale.edu/mbb452a/projects/Dov-S-Greenbaum.html Related terms: "junk DNA", non-coding regions, repetitive sequences; pseudogenes Gene Definitions Narrower terms: LINEs, non- coding first exons, SINEs, UTRs, others?
non-coding first exons: Gene definitions
non-coding region(s): The part of a gene that does not specify the structure of a protein. Non- coding regions of DNA often contain elements that regulate when a protein will be made, and how much of that protein will be produced [SNP] Related term: non-coding DNA
non-specific DNA: A new discovery about how cells regulate protein synthesis helps explain the complex interactions between proteins and DNA and may have far reaching implications for future biotechnology research. In order to inhibit gene expression, proteins need to bind to specific DNA target sites, which are often located in stretches of non- specific DNA. The mechanism for recognition and discrimination between non- specific and specific sites has remained a mystery. Researchers at the Institute of Molecular Biology, University of Oregon, used a new imaging technique called scanning force microscopy (SFM) to visualize DNA and protein complexes in the process of binding.. SFM fills a need for quantitative analysis of DNA not possible with x-ray crystallography. SFM provides a topographic image of a molecular surface by scanning a surface underneath a tip modified with an electron beam. Deflections sensed by the tip can be amplified and recorded, providing a quantitative topographic map of the surface. Previous studies have shown that recognition of a specific target site is often accompanied by DNA "bending." However, the significance of this bending has not been understood. SFM studies revealed crucial differences in DNA bending induced by protein binding to non- specific and specific sites. Sean Henahan "DNA bends to bind", Access Excellence, Mar. 2001 http://www.accessexcellence.org/AB/BC/DNA_Bends_to_Bind.html
nuclear DNA nDNA: The nuclear genome is the DNA complement located in the cell nucleus. Nuclear DNA in eukaryotes (organisms with nucleated cells) is arranged into separate chromosomes and contains the bulk of the coding information. Diploid organisms have two copies of each chromosome Migratory Birds Conservation Tool Chest, Canadian Wildlife Service, Environment Canada http://www.cws-scf.ec.gc.ca/birds/gene/too_e.cfm
ORESTES open reading frame expressed sequence tags: Approach provides sequence information along the whole length of each transcript, rather than just the ends. The method involves low- stringency PCR to produce cDNA libraries, samples of which are then sequenced.
Camargo et al ["The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome" PNAS 2001, 98:12103-12108] generated almost 700,000 ORESTES from 24 types of normal or malignant tissue using 3,540 mini- libraries. They predict that their ORESTES dataset may represent as many as 60% of all human genes (including abundant and rare transcripts). The ORESTES approach generates a larger coverage and a greater number of contigs per gene than to standard EST methods, offering the possibility to complete the closure of most sequences using RT-PCR. http://www.biomedcentral.com/news/20011011/01 Related terms: EST, ORF
ORF Open Reading Frame: Sequences, DNA & beyond glossary
plasmid DNA pDNA: Gene therapy and gene vaccines are moving out of the research laboratory and into the clinic. These techniques promise to revolutionize the treatment of a wide variety of diseases. In order to meet the growing need for pharmaceutical grade plasmid DNA (pDNA), Boehringer Ingelheim Austria GmbH, in collaboration with BIA Separations d.o.o., Slovenia, have co-developed a production process for pDNA utilizing state-of-the-art technology. This process employs high cell density fermentation, followed by a powerful downstream process utilizing Convection Interaction Media® (CIM®) Technology to produce pDNA of greater than 99 per cent purity with very low levels of endotoxin and genomic DNA. Boehringer Ingelheim, Biopharmaceuticals, pDNA production, 1999-2005 http://www.boehringer-ingelheim.com/biopharm/technology/pdna.htm
promiscuous DNA: The occurrence of identical base sequences in more than one cellular compartment. Evidence for gene flow between organelles, or organelles and the nucleus. [PJ Bottino Biology 222 Univ. Maryland Fall 1996] http://www.life.umd.edu/classroom/biol222/lect33-37.html
protein-DNA interactions: Proteomics glossary
Radio Free Genome Experimental music unearthing the music hidden in DNA sequences http://www.epotential.com/radiofreegenome Related terms: data visualization
recombinant DNA: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected. MeSH, 1977
regulatory sequence: A DNA base sequence that controls gene expression. [DOE]
repetitive sequences: Make up at least 50% of the genome. Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. They hold important clues about evolutionary events, help chart mutation rates, and by seeding DNA rearrangements, they can modify genes and create new ones. They also serve as tools for genetic studies.
The vast majority of repeated sequences in the human genome are derived
from transposable elements - sequences like those that form viral genomes
- that propagate by inserting fresh copies of themselves in random places
in the genome. A full 45% of the human genome derives from such transposons.
A major surprise of this new global analysis of the human genome is that
many components in this diverse array of repeated sequences, traditionally
considered to be "junk," appear to have played a beneficial role over the
course of human evolution. NHGRI "Summary of the Initial Sequencing and
Analysis of the Human Genome" press release, Feb. 11, 2001 http://web.archive.org/web/20010721173830/http:/www.wi.mit.edu/news/genome/seqsum.html
ribosomal DNA rDNA: DNA sequences encoding ribosomal RNA (RNA, RIBOSOMAL) and the segments of DNA separating the individual ribosomal RNA genes, referred to as ribosomal spacer DNA (DNA, RIBOSOMAL SPACER). MeSH 1985
selfish DNA: See "junk DNA", non- coding DNA.
specific DNA: See under non- specific DNA
sticky ends: The staggered ends of complementary sequences of DNA which result from cleavage by restriction enzymes. [IUPAC Biotech]
thymine (T): A nitrogenous base, one member of the base pair AT (adenine/ thymine) [DOE].
yeast one hybrid: Proteomics glossary
IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.
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