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DNA glossary & taxonomy Evolving Terminology for Emerging Technologies
Comments? Questions?
Revisions? Mary Chitty
MSLS mchitty@healthtech.com
Last revised
July 09, 2019
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
ATCG: Sequences,
DNA & beyond
adenine: Sequences,
DNA & beyond
antisense DNA: Pharmaceutical
biology
base, base pair: Sequences,
DNA & beyond
cDNA: Gene definitions
catalytic DNA:
Molecules of DNA that possess enzymatic activity. MeSH, 2001
chromosomal DNA:
Is this different (and if so,
how?) from nuclear DNA?
complementary cDNA: Gene
definitions
corporate DNA
[metaphorical]: Business
of biopharmaceuticals
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://198.187.3.177/sboh/Goals/Past/Genetics/2002_04-12/docs/Tab08_GTFWorkingGlossary.pdf
Narrower terms: cDNA, chromosomal DNA, double helix,
exons, genes, introns, LINES,
mitochondrial DNA, nuclear DNA, SINES; Pharmaceutical
biology recombinant DNA. Related terms: Sequences,
DNA & beyond; Microarrays Southern blotting
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
https://www2.le.ac.uk/departments/genetics/jeffreys
DNA forensics:
A primary forensic technology is Gene
amplification & PCR. Related terms: mitochondrial DNA analysis; Genetic
variations glossary DNA fingerprinting, markers, microsatellites,
VNTR.
DNA origami:
In
a triumph for cell biology, researchers have assembled the first
high-resolution, 3-D maps of entire folded genomes and found a structural basis
for gene regulation — a kind of “genomic origami” that allows the same
genome to produce different types of cells. http://news.rice.edu/2014/12/11/3-d-maps-reveal-the-genomes-origami-code/#sthash.Fk5xIKZU.dpuf
Cell article 2014
http://www.cell.com/cell/abstract/S0092-8674(14)01497-4
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 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/insights/6921.html
ds:
Double-stranded (DNA or RNA)
ENCODE Encyclopedia
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
ENCODE
project http://www.genome.gov/Pages/Research/ENCODE/
Related
term: Sequences, DNA and beyond genomic
sequence
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
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.
left-handed DNA:
Tom Schneider's Left Handed DNA Hall of Fame http://users.fred.net/tds///leftdna/
See also right handed DNA Hall of Fame http://users.fred.net/tds///leftdna/RightHanded.DNA.html
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
mitochondrial DNA mtDNA: The genetic material of the mitochondria,
the organelles that generate energy for the cell. [NHGRI] Related terms Gene Definitions
mitochondrial
genes; Cell biology mitochondria, organelles
Mitochondrial DNA
clarifies human evolution, Max Ingman, 2004 http://www.actionbioscience.org/evolution/ingman.html
Mary Claire King
and mitochondrial DNA
https://en.wikipedia.org/wiki/Mary-Claire_King#Human_rights_work
naked DNA:
DNA that has been modified to remove the proteins that normally surround it. It is used for genetic transfers and vaccine manufacture. Medical
Dictionary, © 2009 Farlex and Partners
https://medical-dictionary.thefreedictionary.com/naked+DNA
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
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
nuclear DNA nDNA:
the DNA contained
within the nucleus of
a eukaryotic
organism.[1] Nuclear
DNA encodes for the majority of the genome in
eukaryotes, with mitochondrial
DNA and plastid
DNA coding
for the rest. Nuclear DNA adheres to Mendelian
inheritance,
with information coming from two parents, one male and one female, rather than matrilineally,
as in mitochondrial DNA.[2]
Wikipedia
https://en.wikipedia.org/wiki/Nuclear_DNA accessed 2018 Feb 5
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
promiscuous DNA:
Any DNA sequence that occurs in more than one of the genetic systems (i.e.
nuclear, mitochondrial, or plastid) of eukaryotic cells. Many such DNA segments
have been found in yeast, fungi, plants, and animals.
Oxford Reference
http://www.oxfordreference.com/view/10.1093/oi/authority.20110803100349296
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
Related terms "junk
DNA", non- coding DNA, LINES, SINES Gene
definitions pseudogenes, transposons; SNPs
& other Genetic
variations tandem repeats
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].
DNA resources
NCBI, DNA and RNA databases
https://www.ncbi.nlm.nih.gov/guide/dna-rna/
How
to look for other unfamiliar terms
IUPAC definitions are reprinted with the permission of
the International Union of Pure and Applied Chemistry. |