Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, library construction and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression, or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Each DNA spot contains picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore-, silver-, or chemiluminescence-labeled targets to determine relative abundance of nucleic acid sequences in the target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown.
The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and a modified Met (fMet) in prokaryotes. The most common start codon is AUG.
Modern pharmaceutical manufacturing techniques frequently rely upon biotechnology.
The C0299 RNA family consists of a group of Shigella flexneri and Escherichia coli RNA genes which are 78 bases in length and are found between the hlyE and umuD genes. The function of this RNA is unknown.
The C0343 RNA is a bacterial non-coding RNA of 74 nucleotides in length that is found between the ydaN and dbpA genes in the genomes of Escherichia coli and Shigella flexneri, Salmonella enterica and Salmonella typhimurium. This ncRNA was originally identified in E.coli using high-density oligonucleotide probe arrays (microarray). The function of this ncRNA is unknown.
The C0465 RNA is a bacterial non-coding RNA of 78 nucleotides in length that is found between the tar and cheW genes in the genomes of Escherichia coli and Shigella flexneri. This ncRNA was originally identified in E.coli using high-density oligonucleotide probe arrays (microarray). The function of this ncRNA is unknown.
GadY RNA is a non-coding RNA. The GadY gene is located on between and on the opposite strand to the GadX and GadW genes. GadY can form base pairs with the 3' UTR of its target mRNA gadX, this pairing is thought to confer increased stability to the transcript, allowing accumulation of gadX and therefore increased expression of downstream acid resistance genes. The GadY gene produces three overlapping transcripts that differ in length. The long form is 105 nucleotides in length and two processed versions are 59 and 90 nucleotides in length. It has been shown that all three forms of GadY bind to the Hfq protein.
The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well as amino acid biosynthetic genes. The GcvB gene is found in enteric bacteria such as Escherichia coli. GcvB regulates genes by acting as an antisense binding partner of the mRNAs for each regulated gene. This binding is dependent on binding to a protein called Hfq. Transcription of the GcvB RNA is activated by the adjacent GcvA gene and repressed by the GcvR gene. A deletion of GcvB RNA from Y. pestis changed colony shape as well as reducing growth. It has been shown by gene deletion that GcvB is a regulator of acid resistance in E. coli. GcvB enhances the ability of the bacterium to survive low pH by upregulating the levels of the alternate sigma factor RpoS. A polymeric form of GcvB has recently been identified. Interaction of GcvB with small RNA SroC triggers the degradation of GcvB by RNase E, lifting the GcvB-mediated mRNA repression of its target genes.
The IS102 RNA is a non-coding RNA that is found in bacteria such as Shigella flexneri and Escherichia coli. The RNA is 208 nucleotides in length and found between the yeeP and flu genes. This RNA was identified in a computational screen of E. coli. The function of this RNA is unknown.
The IS128 RNA is a non-coding RNA found in bacteria such as Escherichia coli and Shigella flexneri. The RNA is 209 nucleotides in length. It is found between the sseA and sseB genes. The IS128 RNA was initially identified in a computational screen of the E. coli genome. The function of this RNA is unknown.
Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in Escherichia coli intergenic regions. The family was later renamed Sib when it was discovered that the number of repeats is variable in other species and in other E. coli strains.
RyhB RNA is a 90 nucleotide RNA that down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur.
The SraB RNA is a small non-coding RNA discovered in E. coli during a large scale experimental screen. The 14 novel RNAs discovered were named 'sra' for small RNA, examples include SraC, SraD and SraG. This ncRNA was found to be expressed only in stationary phase. The exact function of this RNA is unknown but it has been shown to affect survival of Salmonella enterica to antibiotic administration in egg albumin. The authors suggest this may be due to SraB regulating a response to components in albumin.
The T44 RNA family consists of a number of bacterial RNA genes of between 135 and 170 bases in length. The t44 gene has been identified in several species of enteric bacteria but homologs have also been identified in Pseudomonas and Coxiella species. The t44 gene is found between the map and rpsB genes in all species in the full alignment apart from Shigella flexneri. The function of this RNA is unknown.
The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 20 common naturally-encoded proteinogenic amino acids.
FnrS RNA is a family of Hfq-binding small RNA whose expression is upregulated in response to anaerobic conditions. It is named FnrS because its expression is strongly dependent on fumarate and nitrate reductase regulator (FNR), a direct oxygen availability sensor.
Escherichia coli contains a number of small RNAs located in intergenic regions of its genome. The presence of at least 55 of these has been verified experimentally. 275 potential sRNA-encoding loci were identified computationally using the QRNA program. These loci will include false positives, so the number of sRNA genes in E. coli is likely to be less than 275. A computational screen based on promoter sequences recognised by the sigma factor sigma 70 and on Rho-independent terminators predicted 24 putative sRNA genes, 14 of these were verified experimentally by northern blotting. The experimentally verified sRNAs included the well characterised sRNAs RprA and RyhB. Many of the sRNAs identified in this screen, including RprA, RyhB, SraB and SraL, are only expressed in the stationary phase of bacterial cell growth. A screen for sRNA genes based on homology to Salmonella and Klebsiella identified 59 candidate sRNA genes. From this set of candidate genes, microarray analysis and northern blotting confirmed the existence of 17 previously undescribed sRNAs, many of which bind to the chaperone protein Hfq and regulate the translation of RpoS. UptR sRNA transcribed from the uptR gene is implicated in suppressing extracytoplasmic toxicity by reducing the amount of membrane-bound toxic hybrid protein.
