mrna is to translation as dna is to
Roger D. Kornberg


which are coded by DNA, which is copied to RNA, which creates proteins, which are sequences of amino acids. DNA resides in the nucleus. When a cell expresses a gene, it copies (transcribes) that gene's DNA sequence onto a messenger RNA (mRNA) sequence. mRNA is transported out of the nucleus to ribosomes. The ribosomes read the mRNA and translate the code into the right amino acid sequence to make that gene's protein. The DNA is transcribed to mRNA by an enzyme, RNA polymerase II
20197542
Sense (molecular biology)


methionine. However, the DNA sense strand itself is not used to make protein by the cell. It is the DNA antisense strand which serves as the source for the protein code, because, with bases complementary to the DNA sense strand, it is used as a template for the mRNA. Since transcription results in an RNA product complementary to the DNA template strand, the mRNA is complementary to the DNA antisense strand. The mRNA is what is used for translation (protein synthesis).Hence, a base triplet 3'-TAC-5' in the DNA
16416161
Drosophila embryogenesis


Hunchback, and Caudal proteins are transcription factors. The Bicoid protein is a morphogen as well. The Nanos protein is a translational repressor protein. Bicoid has a DNA-binding homeodomain that binds both DNA and the "nanos" mRNA. Bicoid binds a specific RNA sequence in the 3' untranslated region, called the Bicoid 3'-UTR regulatory element, of "caudal" mRNA and blocks translation. Hunchback protein levels in the early embryo are significantly augmented by new "hunchback" gene transcription and translation of the resulting zygotically produced mRNA.
14656879
Primary transcript


A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing. Pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. Pre-mRNA comprises the
1542540
Silencer (genetics)


In genetics, a silencer is a DNA sequence capable of binding transcription regulation factors, called repressors. DNA contains genes and provides the template to produce messenger RNA (mRNA). That mRNA is then translated into proteins. When a repressor protein binds to the silencer region of DNA, RNA polymerase is prevented from transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA into proteins is impossible. Thus, silencers prevent genes from being expressed as proteins. RNA polymerase, a DNA-dependent enzyme, transcribes
5779303
Central dogma of molecular biology


be copied to DNA (DNA replication), DNA information can be copied into mRNA (transcription), and proteins can be synthesized using the information in mRNA as a template (translation). The special transfers describe: RNA being copied from RNA (RNA replication), DNA being synthesised using an RNA template (reverse transcription), and proteins being synthesised directly from a DNA template without the use of mRNA. The unknown transfers describe: a protein being copied from a protein, synthesis of RNA using the primary structure of
18963388
Messenger RNA


Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. RNA polymerase transcribes primary transcript mRNA (known as pre-mRNA) into processed, mature mRNA. This mature mRNA is then translated into a polymer of amino acids: a protein, as summarized in the central dogma of molecular biology. As in DNA, mRNA genetic information is in the sequence of nucleotides, which are arranged into
48663
Sense (molecular biology)


Negative-sense (3' to 5') viral RNA is complementary to the viral mRNA and thus from it a positive-sense RNA must be produced by an RNA-dependent RNA polymerase prior to translation. Negative-sense RNA (like DNA) has a nucleotide sequence complementary to the mRNA that it encodes. Like DNA, this RNA cannot be translated into protein directly. Instead, it must first be transcribed into a positive-sense RNA that acts as an mRNA. Some viruses (Influenza, for example
16416174
4EGI-1


inhibiting only cap-dependent translation, not initiation factor-independent translation. Messenger RNAs (mRNAs) are transcribed from DNA, and serve as templates for the synthesis of proteins by ribosomal translation. Weak mRNAs contain long and highly structured untranslatable regions at their 5’ end. This lengthy region makes it difficult for enzymes to determine where transcription should begin. As a result, initiation factor proteins are required for translation of the message into protein. These weak mRNAs, or mRNAs that carry the code for proteins involved in the development
9653221
Michael Rosbash


activity the peak expression is shifted earlier for per and later for per. They transformed the period null mutation flies with a 7.2-kb piece of functional per DNA, and measured per mRNA levels at the per locus and new locus. Following transformation, per mRNA levels were rhythmic at both the original and new locus. The per locus was able to transcribe normal per mRNA and translate normal PER protein, meaning that rhythmicity was rescued by functional PER protein transcribed and translated from the 7.2-kb piece of per DNA. There is a feedback loop
17661174
Dictyate


dictyate appears to be an adaptation for efficiently removing damages in germ line DNA by homologous recombinational repair. There are a lot of mRNAs that have been transcribed but not translated during dictyate. Shortly before ovulation, the oocyte of interest activates these mRNA strains. Translation of mRNA in dictyate is partly explained by molecules binding to sites on the mRNA strain, which results in that initiation factors of translation can not bind to that site. Two such molecules, that impedes initiation factors, are CPEB and "maskin", which bind to
16090279
Cell-free protein array


. In 2006, another group refined and miniaturized this method by using multiple spotting technique to spot the DNA template and cell-free transcription and translation mixture on a high-density protein microarray with up to 13,000 spots. This was made possible by the automated system used to accurately and sequentially supply the reagents for the transcription/translation reaction occurs in a small, sub-nanolitre droplet. This method is an adaptation of mRNA display technology. PCR DNA is first transcribed to mRNA, and a single-stranded DNA oligonucleotide modified
9926925
Protein aggregation


proteins in regulatory pathways such as the refolding pathway (molecular chaperones) or the ubiquitin-proteasome pathway (ubiquitin ligases). Chaperones help with protein refolding by providing a safe environment for the protein to fold. Ubiquitin ligases target proteins for degradation through ubiquitin modification. Protein aggregation can be caused by problems that occur during transcription or translation. During transcription, DNA is copied into mRNA, forming a strand of pre-mRNA that undergoes RNA processing to form mRNA. During translation, ribosomes and tRNA help translate the mRNA sequence into
312037
DNA codon table


The standard genetic code is traditionally represented as an RNA codon table because, when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. With the rise of computational biology and genomics, most genes are now discovered at the DNA level, so a DNA codon table is becoming increasingly useful. In this context, the standard genetic code is referred to as translation table 1. The DNA codons in such tables occur on the sense DNA
17440867
Nucleic acid hybridization


between closely related organisms, higher temperatures are required to melt such DNA hybrids when compared to more distantly related organisms. A variety of different methods use hybridization to pinpoint the origin of a DNA sample, including the polymerase chain reaction (PCR). In another technique, short DNA sequences are hybridized to cellular mRNAs to identify expressed genes. Pharmaceutical drug companies are exploring the use of antisense RNA to bind to undesired mRNA, preventing the ribosome from translating the mRNA into protein. Fluorescence in situ hybridization (FISH) is a laboratory
4397261
ERCC1


in DNA repair genes cause a high risk of cancer (see inherited impairment in DNA repair increases cancer risk), somatic mutations in DNA repair genes, including "ERCC1", only occur at low levels in sporadic (non-familial) cancers. Control of ERCC1 protein level occurred at the translational level. In addition to the wild-type sequence, three splice variants of mRNA ERCC1 exist. ERCC1 mRNA is also found to have either wild-type or three alternative transcription start points. Neither the level of overall mRNA
6558809
Directionality (molecular biology)


into RNA. The 5′-flanking region contains the gene promoter, and may also contain enhancers or other protein binding sites. The 5′-"untranslated" region (5′-UTR) is a region of a gene which is transcribed into mRNA, and is located at the 5′-end of the mRNA. This region of an mRNA may or may not be translated, but is usually involved in the regulation of translation. The 5′-untranslated region is the portion of the DNA starting from the cap site and extending to the base just before the AUG translation initiation codon of
12695876
SR protein


splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. As RNA Polymerase II is transcribing DNA into RNA, SR proteins attach to newly made pre-mRNA to prevent the pre-mRNA from binding to the coding DNA strand to increase genome stabilization. Topoisomerase I and SR proteins also interact to increase genome stabilization. SR proteins can control the concentrations of specific mRNA that is successfully translated into protein by selecting for nonsense-mediated decay codons during alternative splicing. SR
11496391
Introduction to viruses


and translation. Transcription is the process where information in DNA, called the genetic code, is used to produce RNA copies called messenger RNA (mRNA). These migrate through the cell and carry the code to ribosomes where it is used to make proteins. This is called translation because the protein's amino acid structure is determined by the mRNA's code. Information is hence translated from the language of nucleic acids to the language of amino acids. Some nucleic acids of RNA viruses function directly as mRNA without further modification. For
16162390
Prokaryotic translation


the remaining codons on the mRNA as more aminoacyl-tRNA bind to the A site, until the ribosome reaches a stop codon on mRNA(UAA, UGA, or UAG). The translation machinery works relatively slowly compared to the enzyme systems that catalyze DNA replication. Proteins in prokaryotes are synthesized at a rate of only 18 amino acid residues per second, whereas bacterial replisomes synthesize DNA at a rate of 1000 nucleotides per second. This difference in rate reflects, in part, the difference between polymerizing four types of nucleotides to make nucleic
11030251
Cafeteria roenbergensis virus


RNA polymerase and it also encodes at least six transcription factors, which allows the DNA genome to be transcribed into mRNA without the use of the cell’s proteins. CroV can then translate the mRNA into DNA, again without the help of the cell, by using its own tRNA synthetase, tRNA, and translation initiation factors. CroV infects "Cafeteria roenbergensis", which is a marine zooflagellate. CroV is fatal to the host cell. This impacts coastal ecology because "Cafeteria roenbergensis" feeds on bacteria found in the water.
5339574
MRNA display


). After translation, the single-stranded mRNA portions of the fusions will be converted to heteroduplex of RNA/DNA by reverse transcriptase to eliminate any unwanted RNA secondary structures, and render the nucleic acid portion of the fusion more stable. This step is a standard reverse transcription reaction. For instance, it can be done by using Superscript II (GIBCO-BRL) following the manufacturer’s protocol. The mRNA/DNA-polypeptide fusions can be selected over immobilized selection targets for several rounds (Figure 3). There
13789600
Genomic DNA


necessary for the function of the organism. Precursor mRNA (pre-mRNA) is transcribed by RNA polymerase II in the nucleus. pre-mRNA is then processed by splicing to remove introns, leaving the exons in the mature messenger RNA (mRNA). Additional processing includes the addition of a 5' cap and a poly(A) tail to the pre-mRNA. The mature mRNA may then be transported to the cytosol and translated by the ribosome into a protein. Other types of RNA include ribosomal RNA (rRNA) and
9176411
Malignant transformation


and/or miR-146b-5p may also contribute to reduced expression of BRCA1 in these triple-negative breast cancers. Post-transcriptional regulation by microRNA occurs either through translational silencing of the target mRNA or through degradation of the target mRNA, via complementary binding, mostly to specific sequences in the three prime untranslated region of the target gene's mRNA. The mechanism of translational silencing or degradation of target mRNA is implemented through the RNA-induced silencing complex (RISC). Silencing of a DNA repair gene by hypermethylation or other epigenetic alteration appears to be
6617438
Derepression


the protein to allows access to the active domain. This lets the transcription factor bind to DNA and serve its function, thus derepressing the transcription factor. Derepression of translation increases protein production without altering the levels of mRNA in the cell. miRNAs are a common mechanism of translation repression, binding to the mRNA through complementary base pairing to silence them. Certain RNA binding proteins have been shown to target untranslated regions of the mRNAs and upregulate the translation initiation rates by alleviating the repressive miRNA effects. An example is the auxin mediated derepression
21320663
TCP-seq


Translation complex profile sequencing (TCP-seq) is a molecular biology method for obtaining snapshots of momentary distribution of protein synthesis complexes along messenger RNA (mRNA) chains. Expression of genetic code in all life forms consists of two major processes, synthesis of copies of the genetic code recorded in DNA into the form of mRNA (transcription), and protein synthesis itself (translation), whereby the code copies in mRNA are decoded into amino acid sequences of the respective proteins. Both transcription and translation are highly regulated processes essentially controlling
5941087
Three prime untranslated region


In molecular genetics, the three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. An mRNA molecule is transcribed from the DNA sequence and is later translated into protein. Several regions of the mRNA molecule are not translated into protein including the 5' cap, 5' untranslated region, 3' untranslated region, and the poly(A) tail. The 3'-UTR often contains regulatory regions that post-transcriptionally influence gene expression. Regulatory regions within the 3'-untranslated region can influence
707308
Phycodnaviridae


of infection, host chromosomal degradation occurs, inhibiting host transcription. At 20 minutes post infection, most of the mRNAs in the infected cell are viral mRNAs. The proteins translated from the early stage of transcription are involved in initiating viral DNA replication, occurring 60–90 minutes post infection. The second phase of proteins are translated in the cytoplasm and the assembly of virus capsids begins about 2–3 hours post infection. Mature virions are formed with the addition of newly-replicated viral DNA from the host nucleus, likely facilitated by a virus encoded
16722416
Protein sequencing


also requires peptide amounts of 1 picomole or above for discernible results, making it less sensitive than mass spectrometry. In biology, proteins are produced by translation of messenger RNA (mRNA) with the protein sequence deriving from the sequence of codons in the mRNA. The mRNA is itself formed by the transcription of genes and may be further modified. These processes are sufficiently understood to use computer algorithms to automate predictions of protein sequences from DNA sequences, such as from whole-genome DNA-sequencing projects, and have led to the
2561732
Operon


In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be "co-transcribed" to define an operon
10290750
Progeroid syndromes


a step necessary in DNA repair and DNA replication. Since WRNp's function depends on DNA, it is only functional when localized to the nucleus. Mutations that cause Werner syndrome only occur at the regions of the gene that encode for protein and not at non-coding regions. These mutations can have a range of effects. They may decrease the stability of the transcribed messenger RNA (mRNA), which increases the rate at which they are degraded. With fewer mRNA, fewer are available to be translated into the WRNp protein
18668868
Gene prediction


RNA (mRNA), protein products, and homologous or orthologous sequences. Given an mRNA sequence, it is trivial to derive a unique genomic DNA sequence from which it had to have been transcribed. Given a protein sequence, a family of possible coding DNA sequences can be derived by reverse translation of the genetic code. Once candidate DNA sequences have been determined, it is a relatively straightforward algorithmic problem to efficiently search a target genome for matches, complete or partial, and exact or inexact. Given a sequence, local alignment
14194320
Thyroid hormone receptor


12 of the TR transactivation domain, which displaces the corepressors from the receptor/DNA complex. Coactivator proteins are recruited, forming a DNA/TR/coactivator complex. One coactivator recruited to the site is nuclear receptor co-activator 1 (NCoA-1). RNA polymerase is recruited to the site and transcribes downstream DNA into messenger RNA (mRNA). The mRNA generated is then translated into the corresponding proteins. The protein products from this process drive the changes in cell function observed in the presence of thyroid hormone. Non-
16590744
Chimeric RNA


tRNA). Through a series of experiments involving E. coli and the T4 phage in 1960, it was shown that messenger RNA (mRNA) carriers information from DNA to the ribosomal sites of protein synthesis. The tRNA-amino acid precursors are brought into position by ribosomes where they can read the information provided mRNA templates to synthesize protein. Creating a protein consists of two main steps: transcription of DNA into RNA and translation of RNA into protein. After DNA is transcribed into RNA, the molecule is known as pre-messenger
20630853
Reading frame


viral, prokaryote, and mitochondrial genomes. Some viruses, e.g. hepatitis B virus and BYDV, use several overlapping genes in different reading frames. In rare cases, a ribosome may shift from one frame to another during translation of an mRNA (translational frameshift). This causes the first part of the mRNA to be translated in one reading frame, and the latter part to be translated in a different reading frame. This is distinct from a frameshift mutation, as the nucleotide sequence (DNA or RNA) is not altered—
21250559
RNA


, the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon) corresponds to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its introns—non-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic
6211800
Genetic code


The genetic code is the set of rules used by living cells to translate information encoded within genetic material (DNA or mRNA sequences) into proteins. Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide
12022036
Gene product


, as well as mRNA which carry the instructions for creating the protein product. One type of functional RNA involved in regulation are microRNA (miRNA), which works by repressing translation. These miRNAs work by binding to a complementary target mRNA sequence to prevent translation from occurring. Short-interfering RNA (siRNA) also work by negative regulation of transcription. These siRNA molecules work in RNA-induced silencing complex (RISC) during RNA interference by binding to a target DNA sequence to prevent transcription of a specific mRNA. Proteins are
1730074
Untranslated region


a cell. The mRNA is initially transcribed from the corresponding DNA sequence and then translated into protein. However, several regions of the mRNA are usually not translated into protein, including the 5' and 3' UTRs. Although they are called untranslated regions, and do not form the protein-coding region of the gene, uORFs located within the 5' UTR can be translated into peptides. The 5' UTR is upstream from the coding sequence. Within the 5' UTR is a sequence that is recognized by the ribosome
9291282
Mir-126


the suppression of the various targets of mir-126. The frequency of the SNP varies between different ethnic backgrounds and potentially is related to the differential acquisition of human disease. miRNA binds to target sequences reducing the expression of the target gene. miRNA can bind either directly to DNA preventing transcription or to transcribed mRNA preventing translation and directing the mRNA for degradation. One of the main targets of mir-126 is the host gene EGFL7. Transcription of both occur, however mature mir-126 binds to a complementary sequence within EGFL7 preventing translation of the mRNA resulting
6951279
Sense strand


cap at the 5' end, and the addition of a poly-A tail at the 3' end. This deletion process is known as splicing. The end product is known as a mature mRNA. Prokaryotic mRNA does not undergo the same process. Strictly speaking, only the mRNA makes "sense" with the genetic code, as the translated protein peptide sequence can be directly inferred from this strand. The "antisense" strand of DNA is complementary to the "sense" strand and is the actual template for mRNA
18562089
Messenger RNA


by Jacob, Sydney Brenner and Matthew Meselson at the California Institute of Technology in 1961. It should not be confused with mitochondrial DNA. The brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, an mRNA molecule may also be processed, edited, and transported prior to translation. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not. A molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when
48665
Repressor


In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. A DNA-binding repressor blocks the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes into messenger RNA. An RNA-binding repressor binds to the mRNA and prevents translation of the mRNA into protein. This blocking of expression is called repression. If an inducer, a molecule that initiates the gene expression, is present, then it
7214092
LIG3


is involved in meiotic recombination and/or DNA repair in haploid sperm but this has not been definitively demonstrated. Although an internal ATG is the preferred site for translation initiation within the DNA ligase III open reading frame, translation initiations does also occur at the first ATG within the open reading frame, resulting in the synthesis of a polypeptide with an N-terminal mitochondrial targeting sequence. As mentioned above, DNA ligase III-alpha mRNA encodes nuclear and mitochondrial versions of DNA ligase III-alpha. Nuclear DNA ligase III-alpha exists and
8641366
MRNA display


T7 RNA polymerase transcription site and a ribosomal binding site at the 5’ end. The T7 promoter region allows large-scale "in vitro" T7 transcription to transcribe the DNA library into an mRNA library, which provides templates for the "in vitro" translation reaction later. The ribosomal binding site in the 5’-untranslated region (5’ UTR) is designed according to the "in vitro" translation system to be used. There are two popular commercially available "in vitro" translation systems. One is "E. Coli"
13789597
Reading frame


is formed in the 5′ to 3′ direction. The mRNA is single-stranded and therefore only contains three possible reading frames, of which only one is translated. The codons of the mRNA reading frame are translated in the 5′→3′ direction into amino acids by a ribosome to produce a polypeptide chain. An open reading frame (ORF) is a reading frame that has the potential to be transcribed into RNA and translated into protein. It requires a continuous sequence of DNA from a start codon, through a subsequent region which usually has
21250557
TisB-IstR toxin-antitoxin system


rather than cell death, in response to DNA damage, allowing time for repair processes to occur. TisB translation is under LexA control, so it is induced by DNA damage as part of the SOS response. Under normal conditions, very little "tisB" mRNA is synthesised and translation is inhibited, but when DNA damage occurs "tisAB" is strongly induced causing overexpression, which overrides inhibition by depleting the IstR-1 pool. Experimental data has shown effects of TisB to be decreases in transcription, translation and replication, RNA degradation and
8920971
Cell nucleus


DNA is used as a template to produce RNA. In the case of genes encoding proteins, that RNA produced from this process is messenger RNA (mRNA), which then needs to be translated by ribosomes to form a protein. As ribosomes are located outside the nucleus, mRNA produced needs to be exported. Since the nucleus is the site of transcription, it also contains a variety of proteins that either directly mediate transcription or are involved in regulating the process. These proteins include helicases, which unwind the double-stranded DNA
6416570
Ribosome-binding site


5′-GGTG-3′ regions, 5 basepairs upstream of the start site. Additionally, some bacterial initiation regions, such as rpsA in E.coli completely lack identifiable SD sequences. Prokaryotic ribosomes begin translation of the mRNA transcript while DNA is still being transcribed. Thus translation and transcription are parallel processes. Bacterial mRNA are usually polycistronic and contain multiple ribosome binding sites. Translation initiation is the most highly regulated step of protein synthesis in prokaryotes. The rate of translation depends on two factors: The RBS sequence affects both of these factors. The ribosomal protein S1
1943204
Central dogma of molecular biology


which the information contained in a section of DNA is replicated in the form of a newly assembled piece of messenger RNA (mRNA). Enzymes facilitating the process include RNA polymerase and transcription factors. In eukaryotic cells the primary transcript is pre-mRNA. Pre-mRNA must be processed for translation to proceed. Processing includes the addition of a 5' cap and a poly-A tail to the pre-mRNA chain, followed by splicing. Alternative splicing occurs when appropriate, increasing the diversity of the proteins that any single
18963391
Human mitochondrial genetics


TFAM, and TFB1M or TFB2M assemble at the mitochondrial promoters and begin transcription. The actual molecular events that are involved in initiation are unknown, but these factors make up the basal transcription machinery and have been shown to function in vitro. Mitochondrial translation is still not very well understood. In vitro translations have still not been successful, probably due to the difficulty of isolating sufficient mt mRNA, functional mt rRNA, and possibly because of the complicated changes that the mRNA undergoes before it is translated. The Mitochondrial DNA Polymerase
21435791
Protein metabolism


Protein metabolism denotes the various biochemical processes responsible for the synthesis of proteins and amino acids (anabolism), and the breakdown of proteins by catabolism. The steps of protein synthesis include transcription, translation, and post translational modifications. During transcription, RNA polymerase transcribes a coding region of the DNA in a cell producing a sequence of RNA, specifically messenger RNA (mRNA). This mRNA sequence contains codons: 3 nucleotide long segments that code for a specific amino acid. Ribosomes translate the codons to their respective amino acids. In
9119646
Gene expression


, such as tRNA or a ribozyme. An expression system consists of a gene, normally encoded by DNA, and the molecular machinery required to transcribe the DNA into mRNA and translate the mRNA into protein using the reagents provided. In the broadest sense this includes every living cell but the term is more normally used to refer to expression as a laboratory tool. An expression system is therefore often artificial in some manner. Expression systems are, however, a fundamentally natural process. Viruses are an excellent example where they replicate by using
791928
Gene silencing


dependent oligonucleotides cause the target mRNA molecules to be degraded, while steric-blocker oligonucleotides prevent translation of the mRNA molecule. The majority of antisense drugs function through the RNase H-dependent mechanism, in which RNase H hydrolyzes the RNA strand of the DNA/RNA heteroduplex. This mechanism is thought to be more efficient, resulting in an approximately 80% to 95% decrease in the protein and mRNA expression. Ribozymes are catalytic RNA molecules used to inhibit gene expression. These molecules work by cleaving mRNA molecules, essentially silencing the
10533334
Messenger RNA


, but recent studies have shown that short stretches of uridine (oligouridylation) are also common. The poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, and translation. mRNA can also be polyadenylated in prokaryotic organisms, where poly(A) tails act to facilitate, rather than impede, exonucleolytic degradation. Polyadenylation occurs during and/or immediately after transcription of DNA into RNA. After transcription has been terminated, the mRNA
48670
Complementary DNA


. They typically also contain a strong promoter to drive transcription of the target cDNA into mRNA, which is then translated into protein. On June 13, 2013, the United States Supreme Court ruled in the case of "Association for Molecular Pathology v. Myriad Genetics" that while naturally occurring human genes cannot be patented, cDNA is patent eligible because it does not occur naturally. Some viruses also use cDNA to turn their viral RNA into mRNA (viral RNA → cDNA → mRNA). The mRNA is used to make viral
7538608
Degradosome


"coding DNA sequence" (CDS). Firstly, to attach sRNA to targeted mRNA a Hfq (chaperone protein) is needed. Once the attachment is done, if the complex Hfq-sRna ends on TIR, it blocks "ribosome binding site" (RBS) so ribosomes can not translate, and activates nucleases (RNase E) to eliminate mRNA. Another possibility is ending on another region, that makes the complex work as a finisher point of the translation. This way, the ribosomes can do their job of
20932884
Discovery and development of HIV-protease inhibitors


first virally encoded enzyme, the reverse transcriptase. The viral DNA enters the nucleus where it is integrated into the genetic material of the cell by the integrase, a second virally encoded enzyme. Activation of the host cell leads to the transcription of the viral DNA into mRNA. The mRNA is then translated into viral proteins and the third virally encoded enzyme, namely HIV protease, is required to cleave a viral polyprotein precursor into individual mature proteins. The viral RNA and viral proteins assemble at the surface of the cell into new virions
19437337
Protein microarray


the technology developed for DNA microarrays, which have become the most widely used microarrays. Protein microarrays were developed due to the limitations of using DNA microarrays for determining gene expression levels in proteomics. The quantity of mRNA in the cell often doesn't reflect the expression levels of the proteins they correspond to. Since it is usually the protein, rather than the mRNA, that has the functional role in cell response, a novel approach was needed. Additionally post-translational modifications, which are often critical for determining protein function, are
7653148
Recombinant DNA


may not be expressed. That is, the DNA may simply be replicated without expression, or it may be transcribed and translated and a recombinant protein is produced. Generally speaking, expression of a foreign gene requires restructuring the gene to include sequences that are required for producing an mRNA molecule that can be used by the host's translational apparatus (e.g. promoter, translational initiation signal, and transcriptional terminator). Specific changes to the host organism may be made to improve expression of the ectopic gene. In addition, changes may be
16914023
Gene silencing


molecules or by miRNA molecules that suppress translation of the mRNA molecule. With the cleavage or translational repression of the mRNA molecules, the genes that form them are essentially inactive. RNAi is thought to have evolved as a cellular defense mechanism against invaders, such as RNA viruses, or to combat the proliferation of transposons within a cell's DNA. Both RNA viruses and transposons can exist as double-stranded RNA and lead to the activation of RNAi. Currently, siRNAs are being widely used to suppress specific gene expression and to assess
10533340
60S ribosomal protein L7


sub-motif RNP2. In vitro the BZIP-like domain mediates homodimerization and stable binding to DNA and RNA, with a preference for 28S rRNA and mRNA. The protein can inhibit cell-free translation of mRNAs, suggesting that it plays a regulatory role in the translation apparatus. It is located in the cytoplasm. The protein has been shown to be an autoantigen in patients with systemic autoimmune diseases, such as systemic lupus erythematosus. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene
21216360
Cell (biology)


the modulation and maintenance of cellular activities. This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two major steps: transcription and translation. Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol,
3756015
Mimivirus


so this features may also be present in mimivirus. Several mRNA transcripts can be recovered from purified virions. Like other NCLDVs, transcripts for DNA polymerase, a capsid protein and a TFII-like transcription factor were found. However, three distinct aminoacyl tRNA synthetase enzyme transcripts and four unknown mRNA molecules specific to mimivirus were also found. These pre-packaged transcripts can be translated without viral gene expression and are likely to be necessary to Mimivirus for replication. Other DNA viruses, such as the "Human cytomegalovirus" and "Herpes
4535825
DNA oxidation


damages RNAs, and each attack bring problems to the normal cellular metabolism. Although alteration of genetic information on mRNA is relatively rare, oxidation on mRNAs in vitro and in vivo results in low translation efficiency and aberrant protein products. Though the oxidation strikes the nucleic strands randomly, particular residues are more susceptible to ROS, such hotspot sites being hit by ROS at a high rate. Among all the lesions discovered thus far, one of the most abundant in DNA and RNA is the 8-hydroxyguanine. Moreover, 8-hydroxyguanine is the only one
7863481
Terminator (genetics)


activity, to disrupt the mRNA-DNA-RNA polymerase transcriptional complex. Rho-dependent terminators are found in bacteria and phages. The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich sequence on the mRNA known as a Rho utilization site ("rut") for which a consensus sequence has not been identified, and a downstream transcription stop point ("tsp"). The "rut" serves as a mRNA loading site and as an activator for Rho; activation
18787710
Regulatory sequence


polymerase from forming a productive complex with the transcriptional initiation region (promoter), while activators facilitate formation of a productive complex. Furthermore, DNA motifs have been shown to be predictive of epigenomic modifications, suggesting that transcription factors play a role in regulating the epigenome. In RNA, regulation may occur at the level of protein biosynthesis (translation), RNA cleavage, RNA splicing, or transcriptional termination. Regulatory sequences are frequently associated with messenger RNA (mRNA) molecules, where they are used to control mRNA biogenesis or translation.
10219733
Coding region


AUG initiation codon in eukaryotes and stop at one of the three stop codons (UAA, UGA, UAG). While identification of open reading frames within a DNA sequence is straightforward, identifying coding sequences is not, because the cell translates only a subset of all open reading frames to proteins. Currently CDS prediction uses sampling and sequencing of mRNA from cells, although there is still the problem of determining which parts of a given mRNA are actually translated to protein. CDS prediction is a subset of gene prediction, the latter also
20295867
Capping enzyme


called the capping enzymes, are only able to catalyze their respective reactions when attached to RNA polymerase II, an enzyme necessary for the transcription of DNA into pre-mRNA. When this complex of RNA polymerase II and the capping enzymes is achieved, the capping enzymes are able to add the cap to the mRNA while it is produced by RNA polymerase II. Eukaryotic RNA must undergo a series of modifications in order to be exported from the nucleus and successfully translated into function proteins, many of which are dependent on mRNA capping,
7376703
Toxin-antitoxin system


For example, the "ccdAB" system encoded in the chromosome of has been shown to be under negative selection, albeit at a slow rate due to its addictive properties. Type I toxin-antitoxin systems rely on the base-pairing of complementary antitoxin RNA with the toxin mRNA. Translation of the mRNA is then inhibited either by degradation via RNase III or by occluding the Shine-Dalgarno sequence or ribosome binding site of the toxin mRNA. Often the toxin and antitoxin are encoded on opposite strands of DNA. The 5'
9062503
Eukaryotic transcription


transcription. For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (in which translation occurs) by the nuclear membrane. This allows for the temporal regulation of gene expression through the sequestration of the RNA in the nucleus, and allows for selective transport of mature RNAs to the cytoplasm. Bacteria do not have a distinct nucleus that separates DNA from ribosome and mRNA is translated into protein as soon as it is transcribed. The
10443826
SymE-SymR toxin-antitoxin system


. Further study led to the renaming of both "yjiW" and RyjC to SymE (SOS-induced yjiW gene with similarity to MazE) and SymR (symbiotic RNA) respectively. SymR blocks translation of SymE by antisense binding. SymE exhibits its toxicity by repressing global translation within the cell, cleaving mRNA in a similar manner to MazF, another toxin. Quantitative Northern blot experiments showed that SymR RNA is present in cells at 10 times the concentration of SymE mRNA (0.02 fmol μg and 0.2 fmol μg). Following DNA
13183061
Open reading frame


If transcription were to cease before the stop codon, an incomplete protein would be made during translation. In eukaryotic genes with multiple exons, introns are removed and exons are then joined together after transcription to yield the final mRNA for protein translation. In the context of gene finding, the start-stop definition of an ORF therefore only applies to spliced mRNAs, not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF is a sequence that has a length divisible
15815749
Stem-loop


is required for self-cleavage activity. Hairpin loops are often elements found within the 5'UTR of prokaryotes. These structures are often bound by proteins or cause the attenuation of a transcript in order to regulate translation. The mRNA stem-loop structure forming at the ribosome binding site may control an initiation of translation. Stem-loop structures are also important in prokaryotic rho-independent transcription termination. The hairpin loop forms in an mRNA strand during transcription and causes the RNA polymerase to become dissociated from the DNA template strand. This process
3783043
PD-L1


It was also shown that PD-L1 is constituvely expressed on mouse Ly6C nonclassical monocytes in steady state. Resting human cholangiocytes express PD-L1 mRNA, but not the protein, due to translational suppression by microRNA miR-513. Upon treatment with interferon-gamma, miR-513 was down-regulated, thereby lifting suppression of PD-L1 protein. In this way, interferon-gamma can induce PD-L1 protein expression by inhibiting gene-mediated suppression of mRNA translation. PD-L1 promoter DNA methylation may predict survival in some cancers
6815901
Directionality (molecular biology)


the message. It may also contain enhancers or other sites to which proteins may bind. The 3′-"untranslated" region (3′-UTR) is a region of the DNA which "is" transcribed into mRNA and becomes the 3′-end of the message, but which does not contain protein coding sequence. Everything between the stop codon and the polyA tail is considered to be 3′-untranslated. The 3′-untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly(A
12695880
Virus


is complementary to mRNA and thus must be converted to positive-sense RNA by an RNA-dependent RNA polymerase before translation. DNA nomenclature for viruses with single-sense genomic ssDNA is similar to RNA nomenclature, in that positive-strand viral ssDNA is identical in sequence to the viral mRNA and is thus a coding strand, while negative-strand viral ssDNA is complementary to the viral mRNA and is thus a template strand. Several types of ssDNA and ssRNA viruses have genomes that are ambisense in that transcription can occur off both
5611918
T-even bacteriophages


the cell. Biosynthesis After the bacterial DNA is inserted into the cell, the process of biosynthesis is initiated. Biosynthesis involves the utilization of the host cells' nucleotides and enzymes to make copies of the phage DNA. The mRNA in the cytoplasm are transcribed from the phage DNA being involved in the biosynthesis of phage enzymes and capsids proteins. Therefore, the ribosomes, enzymes, and amino acids of the host are involved in translation. Maturation Maturation is submitted by the assembly of bacteriophage DNA and capsids into virions. Late proteins are
19442988
Reverse transcriptase


, and characterise RNA. Reverse transcriptase has also been employed in insulin production. By inserting eukaryotic mRNA for insulin production along with reverse transcriptase into bacteria, the mRNA could be inserted into the prokaryote's genome. Large amounts of insulin can then be created, sidestepping the need to harvest pig pancreas and other such traditional sources. Directly inserting eukaryotic DNA into bacteria would not work because it carries introns, so would not translate successfully using the bacterial ribosomes. Processing in the eukaryotic cell during mRNA production removes these introns to provide a
6598653
Human genome


per base pair. The content of the human genome is commonly divided into coding and noncoding DNA sequences. Coding DNA is defined as those sequences that can be transcribed into mRNA and translated into proteins during the human life cycle; these sequences occupy only a small fraction of the genome (<2%). Noncoding DNA is made up of all of those sequences (ca. 98% of the genome) that are not used to encode proteins. Some noncoding DNA contains genes for RNA molecules with important biological functions (noncoding
20381791
Protein metabolism


Proteins bound to these regions can either directly halt or allow RNA polymerase to read the DNA strand or can signal other proteins to halt or allow RNA polymerase reading. During translation, ribosomes convert a sequence of mRNA (messenger RNA) to an amino acid sequence. Each 3-base-pair-long segment of mRNA is a codon which corresponds to one amino acid or stop signal. Amino acids can have multiple codons that correspond to them. Ribosomes do not directly attach amino acids to mRNA codons. They must utilize tRNAs (transfer
9119652
Untranslated region


In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5' side, it is called the 5' UTR (or leader sequence), or if it is found on the 3' side, it is called the 3' UTR (or trailer sequence). mRNA is RNA that carries information from DNA to the ribosome, the site of protein synthesis (translation) within
9291281
Molluscum contagiosum virus


nucleus, this virus has to bring or encode for all of the proteins needed for replication. Each virion sets up a region in the cytoplasm, called a 'viral factory' where DNA replication, transcription, and translation all occur sequentially. There are three phases of DNA transcription. During the early phase, genes that encode for transcription factors, viral DNA and RNA polymerases, and proteins that stimulate host cell mitosis are transcribed by DNA dependent RNA polymerase that the virion carries with it. The mRNA produced in the early phase
16960742
Lytic cycle


be translated destroys the host's DNA. In retroviruses (which inject an RNA strand), a unique enzyme called reverse transcriptase transcribes the viral RNA into DNA, which is then transcribed again into RNA. Once the viral DNA has taken control it induces the host cell's machinery to synthesize viral DNA, protein and starts multiplying. The biosynthesis is (e.g. T4) regulated in three phases of mRNA production followed by a phase of protein production. About 25 minutes after initial infection, approximately 200 new bacteriophages (virions) are
2001293
Werner syndrome helicase


in DNA repair, recombination, or replication, as well as resolution of DNA secondary structures. It is involved in branch migration at Holliday junctions, and it interacts with other DNA replication intermediates. mRNA that codes for WRN has been identified in most human tissues. Phosphorylation of WRN at serine/threonine inhibits helicase and exonuclease activities which are important to post-replication DNA repair. De-phosphorylation at these sites enhances the catalytic activities of WRN. Phosphorylation may affect other post-translational modifications, including sumoylation and acetylation. Methylation
8532915
Adenoviridae


DNA replication process into two phases: an early and a late phase. In both phases, a primary transcript that is alternatively spliced to generate monocistronic mRNAs compatible with the host’s ribosome is generated, allowing for the products to be translated. The early genes are responsible for expressing mainly non-structural, regulatory proteins. The goal of these proteins is threefold: to alter the expression of host proteins that are necessary for DNA synthesis; to activate other virus genes (such as the virus-encoded DNA polymerase); and
8441279
Chimeric cytoplasmic capping-prone phage polymerase expression system


When assembled these two components synthesize high levels of mature messenger RNA and/or non-coding RNA in the host-cell cytoplasm without using the host cell transcriptional machinery. In its first generation, the C3P3 enzyme would be a single-subunit protein made by the fusion of the African swine fever virus (AFSV) capping enzyme with a mutant DNA-dependent RNA polymerase from the K1E bacteriophage. Such C3P3 enzyme produces mRNA capping modifications, which are found at the 5’-ends of mRNA and are strictly required for the translation of eukaryotic mRNA
3628393
Bacterial DNA binding protein


H-NS can affect translation as well by binding to mRNA and causing its degradation. HU is a small (10 kDa) bacterial histone-like protein that resembles the eukaryotic Histone H2B. HU acts similarly to a histone by inducing negative supercoiling into circular DNA with the assistance of topoisomerase. The protein has been implicated in DNA replication, recombination, and repair. With an α-helical hydrophobic core and two positively charged β-ribbon arms, HU binds non-specifically to dsDNA with low affinity but binds to altered DNA
18485975
Reading frame


can be translated using multiple, overlapping reading frames. There is one known example of overlapping reading frames in mammalian mitochondrial DNA: coding portions of genes for 2 subunits of ATPase overlap. DNA encodes protein sequence by a series of three-nucleotide codons. Any given sequence of DNA can therefore be read in six different ways: Three reading frames in one direction (starting at different nucleotides) and three in the opposite direction. During transcription, the RNA polymerase read the template DNA strand in the 3′→5′ direction, but the mRNA
21250556
Antisense therapy


Antisense therapy is a form of treatment for genetic disorders or infections. When the genetic sequence of a particular gene is known to cause a particular disease, it is possible to synthesize a strand of nucleic acid (DNA, RNA or a chemical analogue) that will bind to the messenger RNA (mRNA) produced by that gene and inactivate it, effectively turning that gene "off". This is because mRNA has to be single stranded for it to be translated. Alternatively, the strand might be targeted to bind a splicing
11115358
Coding region


The coding region of a gene, also known as the CDS (from "coding sequence"), is that portion of a gene's DNA or RNA that codes for protein. The region usually begins at the 5' end by a start codon and ends at the 3' end with a stop codon. The coding region in an mRNA is flanked by the five prime untranslated region (5'-UTR) and the three prime untranslated region (3'-UTR). The CDS is that portion of an mRNA transcript that is translated by
20295865
Virus


. For most viruses with RNA genomes and some with single-stranded DNA genomes, the single strands are said to be either positive-sense (called the "plus-strand") or negative-sense (called the "minus-strand"), depending on if they are complementary to the viral messenger RNA (mRNA). Positive-sense viral RNA is in the same sense as viral mRNA and thus at least a part of it can be immediately translated by the host cell. Negative-sense viral RNA
5611917
Gene structure


Gene structure is the organisation of specialised sequence elements within a gene. Genes contain the information necessary for living cells to survive and reproduce. In most organisms, genes are made of DNA, where the particular DNA sequence determines the function of the gene. A gene is transcribed (copied) from DNA into RNA, which can either be non-coding (ncRNA) with a direct function, or an intermediate messenger (mRNA) that is then translated into protein. Each of these steps is controlled by specific sequence elements,
1637787
Sense strand


In genetics, a sense strand, or coding strand, is the segment within double-stranded DNA that runs from 5' to 3', and which is complementary to the antisense strand of DNA, or template strand, which runs from 3' to 5'. The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein. The antisense strand is thus responsible
18562086
Biotechnology in pharmaceutical manufacturing


human growth hormone. The "two DNA fragments... [were] combined to form a synthetic-natural 'hybrid' gene." The use of entirely synthetic methods of DNA production to produce a gene that would be translated to human growth hormone in escherichia coli would have been exceedingly laborious due to the significant length of the amino acid sequence in human growth hormone. However, if the cDNA reverse transcribed from the mRNA for human growth hormone were inserted directly into the plasmid inserted into the escherichia coli, the bacteria would translate
10908106
BLAT (bioinformatics)


attempts to rapidly detect short sequences which are more likely to be homologous, and then it aligns and further extends the homologous regions. It is similar to the heuristic BLAST family of algorithms, but each tool has tried to deal with the problem of aligning biological sequences in a timely and efficient manner by attempting different algorithmic techniques. BLAT can be used to align DNA sequences as well as protein and translated nucleotide (mRNA or DNA) sequences. It is designed to work best on sequences with great similarity. The DNA search is
599455
Ribosomal DNA


Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. Ribosomes are assemblies of proteins and rRNA molecules that translate mRNA molecules to produce proteins. As shown in the figure, rDNA of eukaryotes consists of a tandem repeat of a unit segment, an operon, composed of NTS, ETS, 18S, ITS1, 5.8S, ITS2, and 28S tracts. rDNA has another gene, coding for 5S rRNA, located in the genome in most eukaryotes. 5S rDNA is also present in tandem repeats as in "
7831337
Enterobacter virus CC31


regions are susceptible to damage, resulting in frame shifts, minute deletions, immunity regions, and silent genetic regions. These modifications, patterned with horizontal gene transfer between "E. coli" DNA and "CC30" DNA, allow for evolution to occur for the virus and bacterium. This patience illustrated by the virus allows for it to amplify its genetic material significantly through many "E. coli" generations. Also, as the integrated viral DNA is translated into mRNA, proteins are synthesized and are readily available for future virion formation.
7920931
Lac operon


the experimental bacteria on agar with lactose available on it. If they do not, the gene they are trying to express will not be expressed as the repressor protein is still blocking RNAP from binding to the promoter and transcribing the gene. Once the repressor is removed, RNAP then proceeds to transcribe all three genes ("lacZYA") into mRNA. Each of the three genes on the mRNA strand has its own Shine-Dalgarno sequence, so the genes are independently translated. The DNA sequence of the "E. coli"
20669115
Nucleic acid analogue


can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. Earlier, the artificial strings of DNA did not encode for anything, but scientists speculated they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses. Transcription of DNA containing unnatural base pair and translation of corresponding mRNA were actually achieved recently. On November 2017, the same team at the Scripps Research Institute that first introduced two extra nucleobases into bacterial DNA
3866086