Sense (molecular biology)

Property of nucleic acid strands with respect to their translatability into protein

In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, sense may have slightly different meanings. For example, the negative sense strand of DNA is equivalent to the template strand, whereas the positive sense strand is the non template strand whose nucleotide sequence is equivalent to the sequence of the mRNA transcript.

Because of the complementary nature of base pairing between nucleic acid polymers, a double stranded DNA molecule will be composed of two strands with sequences that are reverse complements of each other. To help molecular biologists specifically identify each strand individually, the two strands are usually differentiated as the "sense" strand and the "antisense" strand. An individual strand of DNA is referred to as positive sense (also positive (+) or simply sense) if its nucleotide sequence corresponds directly to the sequence of an RNA transcript which is translated or translatable into a sequence of amino acids (provided that any thymine bases in the DNA sequence are replaced with uracil bases in the RNA sequence). The other strand of the double stranded DNA molecule is referred to as negative sense (also negative (−) or antisense), and is reverse complementary to both the positive sense strand and the RNA transcript. It is actually the antisense strand that is used as the template from which RNA polymerases construct the RNA transcript, but the complementary base pairing by which nucleic acid polymerization occurs means that the sequence of the RNA transcript will look identical to the positive sense strand, apart from the RNA transcript's use of uracil instead of thymine. Sometimes the phrases coding strand and template strand are encountered in place of sense and antisense, respectively, and in the context of a double stranded DNA molecule the usage of these terms is essentially equivalent. However, the coding/sense strand need not always contain a code that is used to make a protein; both protein coding and non coding RNAs may be transcribed. The terms "sense" and "antisense" are relative only to the particular 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. Most organisms with sufficiently large genomes make use of both strands, with each strand functioning as the template strand for different RNA transcripts in different places along the same DNA molecule. 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 DNA sense strand looks like the messenger RNA (mRNA) transcript, and can therefore be used to read the expected codon sequence that will ultimately be used during translation (protein synthesis) to build an amino acid sequence and then a protein. For example, the sequence "ATG" within a DNA sense strand corresponds to an "AUG" codon in the mRNA, which codes for the amino acid methionine. However, the DNA sense strand itself is not used as the template for the mRNA; it is the DNA antisense strand that 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. Hence, a base triplet 3′ TAC 5′ in the DNA antisense strand (complementary to the 5′ ATG 3′ of the DNA sense strand) is used as the template which results in a 5′ AUG 3′ base triplet in the mRNA. The DNA sense strand will have the triplet ATG, which looks similar to the mRNA triplet AUG but will not be used to make methionine because it will not be directly 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 corresponds directly to the RNA codon sequence. By this logic, the RNA transcript itself is sometimes described as "sense".

A single stranded genome that is used in both positive sense and negative sense capacities is said to be ambisense. Some viruses have ambisense genomes. Bunyaviruses have three 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 three fragments that are mainly negative sense except for part of the 5′ ends of the large and small segments of their genome.

An RNA sequence that is complementary to an endogenous mRNA transcript is sometimes called "antisense RNA". In other words, it is a non coding strand complementary to the coding sequence of RNA; this is similar to negative sense viral RNA. When mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This process is related to RNA interference. Cells can produce antisense RNA molecules naturally, called microRNAs, which interact with complementary mRNA molecules and inhibit their expression. The concept has also been exploited as a molecular biology technique, by artificially introducing a transgene coding for antisense RNA in order to block the expression of a gene of interest. Radioactively or fluorescently labelled antisense RNA can be used to show the level of transcription of genes in various cell types. Some alternative antisense structural types have been experimentally applied as antisense therapy. In the United States, the Food and Drug Administration (FDA) has approved the phosphorothioate antisense oligonucleotides fomivirsen (Vitravene) and mipomersen (Kynamro) for human therapeutic use.

In virology, the term "sense" has a slightly different meaning. 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 terms such as "positive strand" equivalent to "positive sense", and "plus strand" equivalent to "plus sense". Whether a viral 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 viral proteins (e. g., those needed for viral replication). 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—the RNA polymerase will be one of the first proteins produced by the host cell, since it is needed in order for the virus's genome to be replicated.

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. Like DNA, negative sense RNA has a nucleotide sequence complementary to the mRNA that it encodes; also 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 (e. g. influenza viruses) 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 to 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.