BIO - TERMS - DNA Flashcards
A-DNA A right-handed DNA double helix that has 11 base pairs per turn
DNA exists in this form when partially dehydrated.
Acridine dyes
A class of positively charged polycyclic molecules that intercalate into DNA and induce frameshift mutations.
Actinomycin D
An inhibitor of transcription that binds to double-stranded DNA.
Adenine (A)
A purine base found in RNA and DNA.
Agrobacterium tumefaciens-mediated transformation
A naturally occurring process of DNA transfer from the bacterium A. tumefaciens to plants.
AIM2 (absent in melanoma 2)
A member of PYHIN subfamily of NLR (NOD-like receptor) family containing an N-terminal HIN domain. It activates caspase 1 in response to viral double-stranded DNA.
Amplification (recombinant DNA molecules)
The production of many copies of a newly constructed recombinant DNA molecule.
antisense DNA
DNA that is complementary to the DNA encoding a protein; the antisense RNA transcript will hybridize with the mRNA encoding the protein and inhibit synthesis of the protein.
AP endonuclease
An endonuclease that cleaves a phosphodiester bond formed by a baseless (“apurinic”) nucleotide in DNA.
apurinic/apyrimidinic endonuclease 1 (APE1)
A DNA repair endonuclease involved in class switch recombination.
ATM (ataxia telangiectasia mutated protein)
Protein kinase activated by double-strand DNA breaks. If breaks are not repaired, ATM initiates a signal cascade that culminates in cell cycle arrest. Related to ATR.
ATR (ataxia telangiectasia and Rad3 related protein)
Protein kinase activated by DNA damage. If damage remains unrepaired, ATR helps initiate a signal cascade that culminates in cell cycle arrest. Related to ATM.
Autoradiograph
A record or photograph prepared by labeling a substance such as DNA with a radioactive material such as tritiated thymidine and allowing the image produced by radioactive decay to develop on a film over a period of time.
B-DNA
Double-stranded DNA that exists as a right-handed helix with 10.4 base pairs per turn; the conformation of DNA when present in aqueous solutions containing low salt concentrations.
baculovirus
Any of a group of double-stranded DNA viruses that infect invertebrates, particularly insects, and are widely used for purposes of protein expression in biotechnology.
base-excision repair
Type of DNA repair that can lead to mutation and that is involved in somatic hypermutation and class switching in B cells.
branch migration
Movement of the branch point in a branched DNA formed from two DNA molecules with identical sequences. See also Holliday intermediate.
Bromouracil
An analog of thymine that causes mutations after being incorporated into DNA.
Cas9
The CRISPR associated endonuclease from Streptococcus pyogenes that is guided to a specific DNA sequence by an RNA complementary to that sequence.
Cdc6
Protein essential in the preparation of DNA for replication. With Cdt1 it binds to an origin recognition complex on chromosomal DNA and helps load the Mcm proteins onto the complex to form the prereplicative complex.
Cdt1
Protein essential in the preparation of DNA for replication. With Cdc6 it binds to origin recognition complexes on chromosomes and helps load the Mcm proteins on to the complex, forming the prereplicative complex.
cell memory
Retention by cells and their descendants of persistently altered patterns of gene expression, without any change in DNA sequence. See also epigenetic inheritance.
CG island
Region of DNA in vertebrate genomes with a greater than average density of CG sequences; these regions generally remain unmethylated.
Chimeric selectable marker gene
A gene constructed using DNA sequences from two or more sources that allows a cell or organism to survive under conditions where it would otherwise die.
Chromatin fiber
A basic organizational unit of eukaryotic chromosomes that consists of DNA and associated proteins assembled into a strand of average diameter 30 nm.
Chromatin remodeling
The alteration of the structure of DNA and its associated protein molecules, especially histones, by a protein complex; this remodeling often involves the chemical modification of the histones.
Chromosome jumping
A procedure that uses large DNA fragments to move discontinuously along a chromosome from one site to another site. (See also Positional cloning.)
Chromosome painting
The study of the organization and evolution of chromosomes by in situ hybridization using DNA probes labeled with fluorescent dyes that emit light at different wavelengths.
cis-regulatory sequences
DNA sequences to which transcription regulators bind to control the rate of gene transcription. In nearly all cases, these sequences must be on the same chromosome (that is, in cis) to the genes they control.
clamp loader
Protein complex that utilizes ATP hydrolysis to load the sliding clamp on to a primer–template junction in the process of DNA replication.
cloning
The production of large numbers of identical DNA molecules, cells, or organisms from a single ancestral DNA molecule, cell, or organism.
Cloning (gene)
The production of many copies of a gene or specific DNA sequence.
Cloning vector
A small, self-replicating DNA molecule—usually a plasmid or viral chromosome—into which foreign DNAs are inserted in the process of cloning genes or other DNA sequences of interest.
Coactivator
A protein that stimulates transcription by RNA polymerase II without binding to a specific DNA sequence; generally interacts with sequence-specific transcriptional activators. (Chapter 8)
coding joint
DNA join formed by the imprecise joining of a V gene segment to a (D)J gene segment during recombination of the immunoglobulin or T-cell receptor genes. It is the joint retained in the rearranged gene. Cf. signal joint.
colony hybridization
The identification of a colony containing a desired gene by using a DNA probe that is complementary to that gene.
Comparative genomic hybridization
A method for the detection of copy number variations (deletions, duplications) in DNA.
Complementarity
The relationship between the two strands of a double helix of DNA. Thymine in one strand pairs with adenine in the other strand, and cytosine in one strand pairs with guanine in the other strand.
Composite transposon
A transposable element formed when two identical or nearly identical transposons insert on either side of a nontransposable segment of DNA—for example, the bacterial transposon Tn5.
Concatemer
A DNA molecule comprising multiple, tandem copies of a viral genome (or other DNA sequence) joined end to end. (Chapter 9)
conservative site-specifc recombination
A type of DNA recombination that takes place between short, specific sequences of DNA and occurs without the gain or loss of nucleotides. It does not require extensive homology between the recombining DNA molecules.
Continuous replication
The synthesis of a nascent strand of DNA by the sequential addition of nucleotides to the 3′-OH terminus of the strand. Characteristic of the synthesis of the leading strand—the strand being extended in the overall 5′ 3′ direction.
Copy choice
A mechanism of recombination in which an RNA or DNA polymerase first copies the 3’ end of one parental strand and then exchanges one template for another at the corresponding position on a second parental strand. (Chapters 6 and 7)
copy number variations (CNVs)
A difference between two individuals in the same population in the number of copies of a particular block of DNA sequence. This variation arises from occasional duplications and deletions of these sequences.
Core promoter
The minimal set of DNA sequences required for accurate initiation of transcription by RNA polymerase II. (Chapter 8)
Covariance
A measure of the statistical association between variables. cpDNA. The DNA of plant plastids, including chloroplasts.
Cre recombinase
An integrase from a bacteriophage, used for highly selective splicing reactions in recombinant DNA technology.
cruciform
Secondary structure in doublestranded RNA or DNA in which the double helix is denatured at palindromic repeat sequences in each strand, and each separated strand is paired internally to form opposing hairpin structures. See also hairpin.
cryptochrome
Plant flavoprotein sensitive to blue light. Structurally related to blue-light-sensitive enzymes called photolyases (involved in the repair of ultraviolet-induced DNA damage) but do not have a role in DNA repair. Also found in animals, where they have an important role in circadian clocks.
cyclic AMP response element binding protein (CREB)
A protein that binds to specific regions of DNA (cyclic AMP response elements) and functions to regulate gene transcription; a key regulator of protein synthesis–dependent memory consolidation.
Cytosine (C)
A pyrimidine base found in RNA and DNA.
DDX41 (DEAD box polypeptide 41)
A candidate DNA sensor of the RLR family that appears to signal through the STING pathway.
detergent
Small amphiphilic molecule, more soluble in water than lipids, that disrupts hydrophobic associations and destroys the lipid bilayer thereby solubilizing membrane proteins. D gene segment A short DNA sequence that encodes a part of the variable region of an immunoglobulin heavy chain or the β chain of a T cell receptor (TCR).
Dicot
A plant with two cotyledons, or seed leaves. 2′,3′-Dideoxyribonucleoside triphosphates (ddNTPs). Chainterminating DNA precursors (nucleoside triphosphates) with a hydrogen (H) linked to the 3′ carbon in place of the hydroxyl (OH) group in normal DNA precursors (2′-deoxyribonucleotide triphosphates); ddNTPs are used in DNA sequencing reactions.
dideoxy sequencing
The standard enzymatic method of DNA sequencing.
Dideoxyribonucleotides
Nucleotide analogs that are used for chain termination in DNA sequencing.
Discontinuous replication
The synthesis of a nascent strand of DNA by the formation of short segments of DNA (Okazaki fragments) that are subsequently joined by DNA ligase. Characteristic of the synthesis of the lagging strand—the strand being extended in the overall 3′ → 5′ direction.
diversity gene segment (DH)
Short DNA sequences that form a join between the V and J gene segments in rearranged immunoglobulin heavy-chain genes and in T-cell receptor β- and δ-chain genes. See gene segments.
DNA chimera
DNA containing genetic information derived from two different species.
DNA looping
The interaction of proteins bound at distant sites on a DNA molecule so that the intervening DNA forms a loop.
DNA probe
A short, labeled, single strand of DNA or RNA used to locate its complementary strand in a quantity of DNA.
DNA profile (DNA print)
A recorded pattern of DNA polymorphisms.
DNA profiling (DNA fingerprinting)
The use of DNA sequence data—especially highly polymorphic short tandem repeats (STRs) and variable number tandem repeats (VNTRs)—in personal identity cases.
DNA repair
A set of processes for repairing the many accidental lesions that occur continually in DNA.
DNA replication
Process by which a copy of a DNA molecule is made.
DNA transposons
Genetic elements encoding their own transposase that can insert themselves into and excise themselves from the DNA genomes of a host.
DNA tumor virus
General term for a variety of different DNA viruses that can cause tumors.
DNA-dependent protein kinase (DNA-PK)
Protein kinase in the DNA repair pathway involved in the rearrangement of immunoglobulin and T-cell receptor genes.
DNA-only transposon
Transposable element that exists as DNA throughout its life cycle. Many move by cut-and-paste transposition. See also transposon.
Dot blotting
A rapid screening method for mutations and DNA polymorphisms.
double-strand break repair (DSBR)
A nonhomologous end joining pathway of DNA repair used in the completion of isotype switching. double-stranded RNA (dsRNA) A chemical structure that is a replicative intermediate of many viruses that is recognized by TLR-3.
Downstream sequence
A sequence in a unit of transcription that follows (is located 3′ to) the transcription start site. The nucleotide pair in DNA corresponding to the nucleotide at the 5′ end of the transcript (RNA) is designated +1. The following nucleotide pair is designated +2. All of the following (+) nucleotide sequences are downstream sequences (cf. Upstream sequence).
epigenetic inheritance
Inheritance of phenotypic changes in a cell or organism that do not result from changes in the nucleotide sequence of DNA. Can be due to positive feedback loops of transcription regulators or to heritable modifications in chromatin such as DNA methylation or histone modifications.
error-prone ‘translesion’ DNA polymerases
A DNA polymerase operates during DNA repair, such as Polη which can repair a basic lesion by incorporating untemplated nucleotides into the newly formed DNA strand.
Eukaryotic cells
The cells of organisms classified as eukaryotes. These cells are characterized by having a membrane-bound nucleus that contains the chromosomal DNA.
Excinuclease
The endonuclease-containing protein complex that excises a segment of damaged DNA during excision repair.
Excision repair
DNA repair processes that involve the removal of the damaged segment of DNA and its replacement by the synthesis of a new strand using the complementary strand of DNA as template.
Extrachromosomal
Structures that are not part of the chromosomes; DNA units in the cytoplasm that control cytoplasmic inheritance.
extrachromosomal DNA
DNA not contained within chromosomes, such as the circular DNA produced by V(D)J recombination occurring between RSSs in the same chromosomal orientation and is eventually lost from the cell.
Folded genome
The condensed intracellular state of the DNA in the nucleoid of a bacterium. The DNA is segregated into domains, and each domain is independently negatively supercoiled.
footprinting
A technique for identifying the nucleic acid sequence bound by a DNA- or RNA-binding protein.
G-quadruplex
A structure formed from G-rich regions of DNA in which four guanine bases form a planar hydrogen-bonded network, or guanine tetrad, that can further stack on other guanine tetrads. G-quadruplexes processed from intronic switch region RNA may target AID back to the switch regions during isotype switching.
G2/M transition
Point in the eukaryotic cell cycle at which the cell checks for completion of DNA replication before triggering the early mitotic events that lead to chromosome alignment on the spindle.
Gap phases (G 1 and G 2)
Phases in the cell cycle between the mitosis (M) and DNA synthesis (S) phases. (Chapter 6)
gel electrophoresis
The separation of substances (such as serum proteins or DNA) by their rate of movement through an electrical field.
GenBank
The DNA sequence databank maintained by the National Center for Biotechnology Information at the National Institutes of Health in the United States. Similar databanks are maintained in Europe (the European Molecular Biology Laboratory Data Library) and Japan (the DNA DataBank of Japan).
Gene amplification
A phenomenon whereby the DNA of a specific gene or set of genes is replicated independently of the rest of the genome to increase the number of gene copies.
Gene cloning
The incorporation of a gene of interest into a selfreplicating DNA molecule and the amplification of the resulting recombinant DNA molecule in an appropriate host cell.
gene control region
The set of linked DNA sequences regulating expression of a particular gene. Includes promoter and cis-regulatory sequences required to initiate transcription of the gene and control the rate of transcription.
genetic recombination
The process of joining pieces of DNA from different sources.
Genomic DNA library
A collection of clones containing the genomic DNA sequences of an organism.
genotoxin
A chemical that damages DNA or RNA.
Guanine (G)
A purine base found in DNA and RNA.
hairpin
Secondary structure in single-stranded RNA or DNA, in which complementary parts of a palindromic repeat fold back and are paired to form an antiparallel duplex helix that is closed at one end.
haplotype block
Combination of alleles and DNA markers that has been inherited in a large, linked block on one chromosome of a homologous pair—undisturbed by genetic recombination—across many generations.
Helix
Any structure with a spiral shape. The Watson and Crick model of DNA is in the form of a double helix.
heptamer
The conserved seven-nucleotide DNA sequence in the recombination signal sequences (RSSs) flanking gene segments in the immunoglobulin and T-cell receptor loci.
Heteroplasmy
Presence of both normal and pathogenic mitochondrial DNA.
histone H1
“Linker” (as opposed to “core”) histone protein that binds to DNA where it exits from a nucleosome and helps package nucleosomes into the 30-nm chromatin fiber.
Holliday intermediate
An intermediate in genetic recombination in which two doublestranded DNA molecules are joined by a reciprocal crossover involving one strand of each molecule.
Holliday junction (cross-strand exchange)
X-shaped structure observed in DNA undergoing recombination, in which the two DNA molecules are held together at the site of crossing-over, also called a cross-strand exchange.
homologous genetic recombination
Recombination between two DNA molecules of similar sequence, occurring in all cells; occurs during meiosis and mitosis in eukaryotes.
Hox proteins
Transcription regulator proteins encoded by Hox genes; possess a highly conserved, 60-amino-acid-long DNA-binding homeodomain.
hyperchromic effect
The large increase in light absorption at 260 nm occurring as a double-helical DNA unwinds (melts).
IFI16 (IFN-γ-inducible protein 16)
A member of the PYHIN subfamily of NLR (NOD-like receptor) family containing an N-terminal HIN domain. It activates the STING pathway in response to double-stranded DNA.
Induced mutation
A mutation that results from the exposure of an organism to a chemical or physical agent that causes changes in the structure of DNA or RNA (cf. Spontaneous mutation).
Infectious DNA clone
A double-stranded DNA copy of the viral genome carried on a bacterial plasmid or other vector. (Chapter 3)
Insertional mutation
A mutation caused by the insertion of foreign DNA such as a transposable element or the T-DNA of the Ti plasmid of Agrobacterium tumefaciens.
Intercalating agent
A chemical capable of inserting between adjacent base pairs in a DNA molecule.
Interspersed elements
Repetitive, mobile DNA sequences in eukaryotic genomes.
Inverted repeat
A sequence present twice in a DNA molecule but in reverse orientation.
Inverted terminal repetitions
Sequences that are present in the opposite orientation at the ends of certain linear viral DNA genomes. (Chapter 9)
irradiation-sensitive SCID (IR-SCID)
A type of severe combined immunodeficiency due to mutations in DNA repair proteins, such as Artemis, that causes abnormal sensitivity to ionizing radiation and defects in V(D)J recombination.
IS element (insertion sequence)
A short (800–1400 nucleotide pairs) DNA sequence found in bacteria that is capable of transposing to a new genomic location; other DNA sequences that are bounded by IS elements may also be transposed.
J gene segment
Short DNA sequences that encodes part of the variable region of light and heavy immunoglobulin chains and of α and β chains of T cell receptors.
joining gene segment, J gene segment
Short DNA sequences that encode the J regions of immunoglobulin and T-cell receptor variable domains. In a rearranged light-chain, TCRα, or TCRγ genes, the J gene segment is joined to a V gene segment. In a rearranged heavy-chain, TCRβ, or TCRδ locus, a J gene segment is joined to a D gene segment.
Junk DNA
Noncoding DNA of unknown function.
kinetic proofreading
A principle for increasing the specificity of catalysis. In the synthesis of DNA, RNA, and proteins, it refers to a time delay that begins with an irreversible step (such as ATP or GTP hydrolysis) and during which incorrect base pairs are more likely to dissociate than correct pairs.
Ku A
DNA repair protein required for immunoglobulin and T-cell receptor gene rearrangement.
LDL-receptor-related protein (LRP)
Co-receptor bound by Wnt proteins in the regulation of β-catenin proteolysis. leading strand One of the two newly synthesized strands of DNA found at a replication fork. The leading strand is made by continuous synthesis in the 5′-to-3′ direction.
Leber hereditary optic neuropathy
Adult-onset blindness caused by mutations in mitochondrial DNA.
Leptonema (adj, leptotene)
Stage in meiosis immediately preceding synapsis in which the chromosomes appear as single, fine, threadlike structures (but they are really double because DNA replication has already taken place).
Ligation
The joining of two or more DNA molecules by covalent bonds.
Linker (DNA)
The unprotected DNA double helix that connects adjacent nucleosomes.
linking number
The number of times one closed circular DNA strand is wound about another; the number of topological links holding the circles together.
Long terminal repeat
A direct repeat of genetic information that is present in the proviral DNA of retroviruses; it is formed by reverse transcription of the RNA template and includes cis -acting elements required for viral DNA integration and its subsequent transcription. (Chapter 7)
loss of heterozygosity
The result of errant homologous recombination that uses the homolog from the other parent instead of the sister chromatid as the template, converting the sequence of the repaired DNA to that of the other homolog.
lysogenic cycle
Stages in viral development that result in the incorporation of viral DNA into host DNA.
Lysogenic pathway
A reproductive strategy of some bacteriophages that involves the integration of the viral DNA into the host cell chromosome.
Megaloblastic anemia
A type of anemia characterized by oversized red blood cells; caused by impaired DNA synthesis.
metagenomics
The study of the genomes of uncultured organisms by the collection and sequencing of DNA from environmental samples.
Metallomics
An investigation of interactions and functional connections between metal ions and DNA, RNA, proteins and metabolites.
Microprojectile bombardment
A procedure for transforming plant cells by shooting DNA-coated tungsten or gold particles into the cells.
mobile genetic elements
Segments of DNA (e.g., plasmids) that can move between chromosomes or between cells.
molecular biology
The science dealing with DNA and protein synthesis of living organisms.
MRE11A (meitotic recombination 11 homolog a)
A protein involved in DNA damage and repair mechanisms that also recognizes cytoplasmic dsDNA and can activate the STING pathway.
mRNA (messenger RNA)
A single-stranded copy of DNA synthesized in the nucleus of a cell; enters the cytoplasm to direct the correct assembly of amino acids composing a protein.
mtDNA
The DNA of mitochondria.
mycophenolate mofetil
Pro-drug used in cancer treatment that is metabolized to mycophenolate, and inhibitor of inosine monophosphate dehydrogenase, thereby impairing guanosine monophosphate, and thus DNA, synthesis.
Negative [(-)] strand
The strand of DNA or RNA that is complementary in sequence to the (+) (coding) strand. (Chapter 1)
Negative supercoiling
The formation of coiled tertiary structures in double-stranded DNA molecules with fixed (not free to rotate) ends when the molecules are underwound.
non-depleting antibodies
Immunosuppressive antibodies that block the function of target proteins on cells without causing the cells to be destroyed. nonhomologous end joining (NHEJ) DNA repair pathway that directly ligates double-stranded DNA breaks without use of a homologous template.
nonamer
Conserved nine-nucleotide DNA sequence in the recombination signal sequences (RSSs) flanking gene segments in the immunoglobulin and T-cell receptor loci.
Noncoding strand
An alternative name for the antisense strand of DNA.
nonretroviral retrotransposons
Type of transposable element that moves by being first transcribed into an RNA copy that is converted to DNA by reverse transcriptase then inserted elsewhere in the genome. The mechanism of insertion differs from that of the retroviral-like transposons.
Nontemplate strand
In transcription, the nontranscribed strand of DNA. It will have the same sequence as the RNA transcript, except that T is present at positions where U is present in the RNA transcript.
Nontransducing oncogenic retrovirus
Retroviruses that do not encode cell-derived oncogene sequences but can cause cancer (at low efficiency) when their DNA becomes integrated in the vicinity of a cellular oncogene, thereby perturbing its expression. (Chapter 6)
Nonviral retroposons
DNA sequences produced by the reverse transcription of a cellular RNA.
nucleic acid hybridization
The process of combining single complementary strands of DNA.
nucleic acid vaccine
A vaccine made up of DNA, usually in the form of a plasmid.
origin recognition complex (ORC)
Large protein complex that is bound to the DNA at origins of replication in eukaryotic chromosomes throughout the cell cycle.
Paleogenomics
The study of DNA sequences in the genomes of extinct organisms.
Photoreactivation
A DNA repair process that is light-dependent.
Physical map
A diagram of a chromosome or DNA molecule with distances given in base pairs, kilobases, or megabases.
plasmid vector
Small, circular molecules of double-stranded DNA derived from plasmids that occur naturally in bacterial cells; widely used for gene cloning.
polylinker
A short, often synthetic, fragment of DNA containing recognition sequences for several restriction endonucleases.
Polη
An error-prone, ‘translesion’, DNA polymerase involved in repairing DNA damage caused by UV radiation and in somatic hypermutation.
Positional cloning
The isolation of a clone of a gene or other DNA sequence based on its map position in the genome.
Positive [(+)] strand
The strand of DNA or RNA that corresponds in sequence to that of the messenger RNA. Also known as the sense strand. (Chapter 1)
Postreplication repair
A recombination-dependent mechanism for repairing damaged DNA.
Pregenomic mRNA
The hepadnaviral mRNA that is reverse transcribed to produce the DNA genome. (Chapter 7)
prereplicative complex (preRC)
Multiprotein complex that is assembled at origins of replication during late mitosis and early G1 phases of the cell cycle; a prerequisite to license the assembly of a preinitiation complex, and the subsequent initiation of DNA replication.
Probe
A labeled oligonucleotide or polynucleotide that is used to identify a specific base sequence in DNA.
Promoter sequence
A short sequence on DNA located upstream of the transcription start site and recognized by RNA polymerase.
Prophase
The stage of mitosis between interphase and metaphase. During this phase, the centriole divides and the two daughter centrioles move apart. Each sister DNA strand from interphase replication becomes coiled, and the chromosome is longitudinally double except in the region of the centromere. Each partially separated chromosome is called a chromatid. The two chromatids of a chromosome are sister chromatids.
Proviral DNA
(Provirus) Retroviral DNA that is integrated into its host cell genome and is the template for formation of retroviral mRNAs and genomic RNA. Also called proviral DNA. (Chapter 7)
Pseudodiploid
Having two RNA genomes per virus particle that give rise to only one DNA copy, as is the case for retroviruses. (Chapter 7)
Rad51
Eukaryotic protein that catalyzes synapsis of DNA strands during genetic recombination. Called RecA in E. coli.
radiation-sensitive SCID (RS-SCID)
Severe combined immunodeficiency due to a defect in DNA repair pathways, which renders cells unable to perform V(D)J recombination and unable to repair radiation-induced doublestrand breaks.
RecA (RecA protein)
Prototype for a class of DNA-binding proteins that catalyze synapsis of DNA strands during genetic recombination.
recombination signal sequences (RSSs)
DNA sequences at one or both ends of V, D, and J gene segments that are recognized by the RAG-1:RAG-2 recombinase. They consist of a conserved heptamer and nonamer element separated by 12 or 23 base pairs.
regulatory sequence
A DNA sequence involved in regulating the expression of a gene; for example, a promoter or operator.
relaxed DNA
Any DNA that exists in its most stable and unstrained structure, typically the B form under most cellular conditions.
Repetitive DNA
DNA sequences that are present in a genome in multiple copies—sometimes a million times or more.
Replication bubble
The localized region of complementary strand separation that occurs at the origin of replication during the initiation of DNA replication.
Replication center
Specialized nuclear structures in which viral DNA genomes are replicated. Also called replication compartments. (Chapter 9)
Replication intermediate
An incompletely replicated DNA molecule containing newly synthesized DNA. (Chapter 9)
Replication licensing
Mechanisms that ensure that replication of cellular DNA is initiated at each origin once, and only once, per cell cycle. (Chapter 9)
replication origin
Location on a DNA molecule at which duplication of the DNA begins.
restriction nuclease
One of a large number of nucleases that can cleave a DNA molecule at any site where a specific short sequence of nucleotides occurs. Extensively used in recombinant DNA technology.
Restriction site polymorphism
DNA sequence variation that changes the cleavage site of a restriction endonuclease.
Retroposon
A transposable element that creates new copies via reverse transcription of RNA into DNA but that lacks the long terminal repeat sequences.
Reverse transcription
The synthesis of DNA from an RNA template.
Rolling-circle replication
A mechanism of replication of circular DNA molecules in which one parental strand of DNA is cleaved at the origin of replication while the other strand remains intact. The 5′ terminus of the cleaved strand is unwound and replicated discontinuously while continuous replication of the other strand occurs at the 3′ terminus with the intact circular strand as template.
S-cyclin
Member of a class of cyclins that accumulate during late G1 phase and bind Cdks soon after progression through Start; they help stimulate DNA replication and chromosome duplication. Levels remain high until late mitosis, after which these cyclins are destroyed.
SCF
Family of ubiquitin ligases formed as a complex of several different proteins. One is involved in regulating the eukaryotic cell cycle, directing the destruction of inhibitors of S-Cdks in late G1 and thus promoting the activation of S-Cdks and DNA replication.
Segmental duplications
DNA duplications that have become a normal feature of the human genome.
Self-priming
A mechanism by which some viral DNA genomes serves as primers, as well as templates, for DNA synthesis. (Chapter 9)
Sense strand
The coding strand of double-helical DNA that contains the gene.
Shelterin
A protein complex that binds to telomeres and protects the DNA in them from degradation.
signal joint
The noncoding joint formed in DNA by the recombination of RSSs during V(D)J recombination. Cf. coding joint.
Silent polymorphism
A variant in DNA that does not alter the amino acid sequence of a protein.
Simple tandem repeat
A tandemly repeated unit in DNA of only one to six nucleotides in length.
sliding clamp
Protein complex that holds the DNA polymerase on DNA during DNA replication.
somatic DNA recombination
DNA recombination that takes place in somatic cells (to distinguish it from the recombination that takes place during meiosis and gamete formation).
sticky ends
Two DNA ends in the same DNA molecule, or in different molecules, with short overhanging single-stranded segments that are complementary to one another, facilitating ligation of the ends; also known as cohesive ends.
STR loci
Short tandem repeat sequences of noncoding DNA that are unique to every individual and allow DNA ingerprinting.
strand exchange
Reaction in which one of the single-strand 3′ ends from one duplex DNA molecule penetrates another duplex and searches it for homologous sequences through base-pairing. Also called strand invasion.
strand-directed mismatch repair
A proofreading system that removes DNA replication errors missed by the DNA polymerase proofreading exonuclease. Detects the potential for DNA helix distortion from noncomplementary base pairs then recognizes and excises the mismatch in the newly synthesized strand and resynthesizes the excised segment using the old strand as a template.
STSs (sequence-tagged sites)
Short, unique DNA sequences (usually 200 to 500 bp) that are amplified by PCR and used to link physical maps and genetic maps.
Subunit
A single folded protein of a multimeric protein. (Chapter 4) Supercoiling The winding of one duplex DNA strand around another. (Chapter 9)
superhelical density ()
In a helical molecule such as DNA, the number of supercoils (superhelical turns) relative to the number of coils (turns) in the relaxed molecule.
Supertwisting
Overwinding or underwinding of double-helical DNA.
systemic lupus erythematosus (SLE)
An autoimmune disease in which autoantibodies against DNA, RNA, and proteins associated with nucleic acids form immune complexes that damage small blood vessels, especially in the kidney.
T-cell receptor excision circles (TRECs)
Circular DNA fragments excised from the chromosome during V(D)J recombination in developing thymoctytes that are transiently retained in T cells that have recently left the thymus.
T-DNA
The segment of DNA in the Ti plasmid of Agrobacterium tumefaciens that is transferred to plant cells and inserted into the chromosomes of the plant.
t-loop
A loop of DNA formed by telomere repeat sequences at the end of a linear chromosome when a single strand at the 3′ terminus invades an upstream repeat unit and pairs with the complementary strand, while displacing the equivalent strand.
Target site duplication
A sequence of DNA that is duplicated when a transposable element inserts; usually found at each end of the insertion.
TATAAT sequence (-10 sequence)
An AT-rich sequence in prokaryotic promoters that facilitates the localized unwinding of DNA and the initiation of RNA synthesis.
Terminal inverted repeat
Identical or nearly identical DNA sequences at opposite ends of a cut-and-paste transposon. One sequence is the inverted mirror image of the other.
Termini
Sites at which DNA replication stops. (Chapter 9)
Thymine (T)
A pyrimidine base found in DNA. The other three organic bases—adenine, cytosine, and guanine—are found in both RNA and DNA, but in RNA, thymine is replaced by uracil.
TLR-9
Endosomal Toll-like receptor that recognizes DNA containing unmethylated CpG.
topoisomers
Different forms of a covalently closed, circular DNA molecule that differ only in their linking number.
Transactivating RNA (tracrRNA)
The RNA that binds to a targeting endonuclease such as Cas9 and activates it for targeting to a specific genomic DNA sequence.
Transcription bubble
A locally unwound segment of DNA in which an RNA transcript is being synthesized.
transcription regulators
General name for any protein that binds to a specific DNA sequence (known as a cis-regulatory sequence) to influence the transcription of a gene.
Transcription unit
A segment of DNA that contains transcription initiation and termination signals and is transcribed into one RNA molecule.
Transcriptional control region
Local and distant DNA sequences necessary for initiation and regulation of transcription. (Chapter 8)
Transforming infection
A class of persistent infection in which cells infected by certain DNA viruses or retroviruses may exhibit altered growth properties and proliferate faster than uninfected cells. (Chapter 5)
Transition
A mutation caused by the substitution of one purine by another purine or one pyrimidine by another pyrimidine in DNA or RNA.
Transposon tagging
The insertion of a transposable element into or near a gene, thereby marking that gene with a known DNA sequence.
Transversion
A mutation caused by the substitution of a purine for a pyrimidine or a pyrimidine for a purine in DNA or RNA.
Unequal crossing over
Crossing over between repeated DNA sequences that have paired out of register, creating duplicated and deficient products.
Upstream sequence
A sequence in a unit of transcription that precedes (is located 5′ to) the transcription start site. The nucleotide pair in DNA corresponding to the nucleotide at the 5′ end of the transcript (RNA) is designated +1. The preceding nucleotide pair is designated −1. All preceding (−) nucleotide sequences are upstream sequences (cf. Downstream sequence).
Uracil (U)
A pyrimidine base found in RNA but not in DNA. In DNA, uracil is replaced by thymine.
V(D)J recombinase
A multiprotein complex containing RAG-1 and RAG-2, as well as other proteins involved in cellular DNA repair.
Viability
The capability to live and develop normally. vir region (of Ti plasmid). The region of the Ti plasmid of Agrobacterium tumefaciens that contains genes encoding products required for the transfer of the T-DNA from the bacterium to plant cells.
viral vector
A viral DNA altered so that it can act as a vector for recombinant DNA.
Watson-Crick double helix
The principal higher-order structure of double-stranded DNA.
XRCC4
A protein that functions in NHEJ DNA repair by interacting with DNA ligase IV and Ku70/80 at double-strand breaks.
YACs (yeast artificial chromosomes)
Linear cloning vectors constructed from essential elements of yeast chromosomes. They can accommodate foreign DNA inserts of 200 to 500 kb in size.
Z-DNA
A left-handed double helix that forms in GC-rich DNA molecules. The Z refers to the zig-zagged paths of the sugarphosphate backbones in this form of DNA.
Initiation (of DNA, RNA, or protein synthesis)
The incorporation of the first subunit (nucleotide or amino acid) during the synthesis of a macromolecule (DNA, RNA, or polypeptide).
Termination (of DNA, RNA, or protein synthesis)
The release of a complete macromolecule (DNA, RNA, or polypeptide) after the incorporation of the final subunit (nucleotide or amino acid).
cDNA clone
Clone containing double-stranded cDNA molecules derived from the protein-coding mRNA molecules present in a cell.
Complementation screening
Screening expression libraries for cDNA or genomic clones based on their ability to rescue mutant host cells.
ESTs (expressed sequence tags)
Short cDNA sequences that are used to link physical maps and genetic (RFLP) maps.
PYHIN
A family of four intracellular sensor proteins containing an H inversion (HIN) domain in place of the LRR domain found in most other NLR proteins. The HIN domain functions in recognition of cytoplasmic dsDNA. Examples are AIM2 and IFI16.
quantitative PCR (qPCR)
A PCR procedure that allows the determination of how much of the amplified template was in the original sample.
quantitative RT-PCR (reverse transcription–polymerase chain reaction) T
echnique in which a population of mRNAs is converted into cDNAs via reverse transcription, and the cDNAs are then amplified by PCR. The quantitative part relies on a direct relationship between the rate at which the PCR product is generated and the original concentration of the mRNA species of interest.
