Sense (molecular biology)
In molecular biology and genetics, the sense of nucleic acid molecules (often DNA or RNA) is the nature of their roles and their complementary molecules' nucleic acid units' roles in specifying amino acids. Depending on the context within molecular biology, sense may have slightly different meanings.
Molecular biologists call a single strand of DNA sense (or positive (+)) if an RNA version of the same sequence is translated or translatable into protein. Its complementary strand is called antisense (or negative (-) sense). Sometimes the phrases coding strand (for sense) and template strand (for antisense) are encountered; however, protein coding and non-coding RNAs can be transcribed from the sense strand. Additionally, the terms "sense" and "antisense" are relative to the RNA transcript in question and not to the DNA strand as a whole. In other words, either DNA strand can serve as the sense or antisense strand for a particular RNA transcript. In some cases, RNA transcripts can be transcribed in both directions (i.e. on either strand) from a common promoter region, or be transcribed from within introns on either strand (see "ambisense" below).
The two complementary strands of double-stranded DNA (dsDNA) are usually differentiated as the "sense" strand and the "antisense" strand. The DNA sense strand looks like the messenger RNA (mRNA) and can be used to read the expected protein code; for example, ATG in the sense DNA may correspond to an AUG codon in the mRNA, encoding the amino acid 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 antisense strand can be used as a template which will result in a 5'-AUG-3' base triplet in mRNA (AUG is the codon for methionine, the start codon). The DNA sense strand will have the triplet ATG, which looks just like AUG but will not be used to make methionine because it will not be used to make mRNA. The DNA sense strand is called a "sense" strand not because it will be used to make protein (it won't be), but because it has a sequence that looks like the protein codon sequence.
Example with double-stranded DNAEdit
DNA strand 1: antisense strand (transcribed to)→ RNA strand (sense)
DNA strand 2: sense strand
Some regions within a double strand of DNA code for genes, which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites, noncoding introns, and other complicating details. For a cell to use this information, one strand of the DNA serves as a template for the synthesis of a complementary strand of RNA. The template DNA strand is called the transcribed strand with antisense sequence and the mRNA transcript is said to be sense sequence (the complement of antisense). Because the DNA is double-stranded, the strand complementary to the antisense sequence is called the non-transcribed strand and has the same sense sequence as the mRNA transcript (though T bases in DNA are substituted with U bases in RNA).
|3'CGCTATAGCGTTT 5'||DNA antisense strand (template/noncoding)||Used as a template for transcription.|
|5'GCGATATCGCAAA 3'||DNA sense strand (nontemplate/coding)||Complementary to the template strand.|
|5'GCGAUAUCGCAAA 3'||mRNA sense transcript||RNA strand that is transcribed from the noncoding (template/antisense) strand. Note1: Except for the fact that all thymines are now uracils (T-->U), it is complementary to the noncoding (template/antisense) DNA strand (identical to the coding (nontemplate/sense) DNA strand).|
|3'CGCUAUAGCGUUU 5'||mRNA antisense transcript||RNA strand that is transcribed from the coding (nontemplate/sense) strand. Note: Except for the fact that all thymines are now uracils (T-->U), it is complementary to the coding (nontemplate/sense) DNA strand (identical to the noncoding (template/antisense) DNA strand.)|
A note on the confusion between "sense" and "antisense" strands: The strand names actually depend on which direction you are writing the sequence that contains the information for proteins (the "sense" information), not on which strand is on the top or bottom (that is arbitrary). The only real biological information that is important for labeling strands is the location of the 5' phosphate group and the 3' hydroxyl group because these ends determine the direction of transcription and translation. A sequence 5' CGCTAT 3' is equivalent to a sequence written 3' TATCGC 5' as long as the 5' and 3' ends are noted. If the ends are not labeled, convention is to assume that the sequence is written from left to right in the 5' to 3' direction. Watson strand refers to 5' to 3' top strand (5' → 3'), whereas Crick strand refers to 5' to 3' bottom strand (3' ← 5'). Both Watson and Crick strands can be either sense or antisense strands depending on the gene whose sequences are displayed in the genome sequence database. For example, YEL021W, an alias of URA3 gene used in NCBI database, defines that this gene is located on the 21st open reading frame (ORF) from the centromere of the left arm (L) of Yeast (Y) chromosome number V (E), and that the expression coding strand is Watson strand (W). YKL074C defines the 74th ORF to the left of the centromere of chromosome XI and denotes coding strand from the Crick strand (C). Another confusing term referring to "Plus" and "Minus" strand is also widely used. Whether the strand is sense (positive) or antisense (negative), the default query sequence in NCBI BLAST alignment is "Plus" strand.
A single-stranded genome that contains both positive-sense and negative-sense is said to be ambisense. Bunyaviruses have 3 single-stranded RNA (ssRNA) fragments, some of them containing both positive-sense and negative-sense sections; arenaviruses are also ssRNA viruses with an ambisense genome, as they have 2 fragments that are mainly negative-sense except for part of the 5' ends of the large and small segments of their genome.
Antisense RNA is an RNA transcript that is complementary to endogenous mRNA. In other words, it is a non-coding strand complementary to the coding sequence of RNA; this is similar to negative-sense viral RNA. Introducing a transgene coding for antisense RNA is a technique used to block expression of a gene of interest. Radioactively-labelled antisense RNA can be used to show the level of transcription of genes in various cell types. Some alternative antisense structural types are being experimentally applied as antisense therapy, with at least one antisense therapy approved for use in humans.
When mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This process is related to RNA interference.
Antisense nucleic acid molecules have been used experimentally to bind to mRNA and prevent expression of specific genes. Antisense therapies are also in development; in the US, the Food and Drug Administration (FDA) has approved phosphorothioate antisense oligos fomivirsen (Vitravene) and mipomersen (Kynamro) for human therapeutic use.
RNA sense in virusesEdit
In virology, the genome of an RNA virus can be said to be either positive-sense, also known as a "plus-strand", or negative-sense, also known as a "minus-strand". In most cases, the terms sense and strand are used interchangeably, making such terms as positive-strand equivalent to positive-sense, and plus-strand equivalent to plus-sense. Whether a virus genome is positive-sense or negative-sense can be used as a basis for classifying viruses.
Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may be directly translated into the desired viral proteins. Therefore, in positive-sense RNA viruses, the viral RNA genome can be considered viral mRNA, and can be immediately translated by the host cell. Unlike negative-sense RNA, positive-sense RNA is of the same sense as mRNA. Some viruses (e.g., Coronaviridae) have positive-sense genomes that can act as mRNA and be used directly to synthesize proteins without the help of a complementary RNA intermediate. Because of this, these viruses do not need to have an RNA polymerase packaged into the virion.
Negative-sense (3' to 5') viral RNA is complementary to the viral mRNA, thus a positive-sense RNA must be produced by an RNA-dependent RNA polymerase from it 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) have negative-sense genomes and so must carry an RNA polymerase inside the virion.
Gene silencing can be achieved by introducing into cells a short "antisense oligonucleotide" that is complementary to an RNA target. This experiment was first done by Zamecnik and Stephenson in 1978 and continues to be a useful approach, both for laboratory experiments and potentially for clinical applications (antisense therapy). Several viruses such as influenza viruses, Respiratory syncytial virus (RSV) and SARS coronavirus (SARS-CoV) have been targeted using antisense oligonucleotides to inhibit their replication in host cells.
If the antisense oligonucleotide contains a stretch of DNA or a DNA mimic (phosphorothioate DNA, 2'F-ANA, or others) it can recruit RNase H to degrade the target RNA. This makes the mechanism of gene silencing catalytic. Double-stranded RNA can also act as a catalytic, enzyme-dependent antisense agent through the RNAi/siRNA pathway, involving target mRNA recognition through sense-antisense strand pairing followed by target mRNA degradation by the RNA-induced silencing complex (RISC). The R1 plasmid hok/sok system provides yet another example of an enzyme-dependent antisense regulation process through enzymatic degradation of the resulting RNA duplex.
Other antisense mechanisms are not enzyme-dependent, but involve steric blocking of their target RNA (e.g. to prevent translation or induce alternative splicing). Steric blocking antisense mechanisms often use oligonucleotides that are heavily modified. Since there is no need for RNase H recognition, this can include chemistries such as 2'-O-alkyl, peptide nucleic acid (PNA), locked nucleic acid (LNA), and Morpholino oligomers.
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