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Anucleic acid sequence is a succession ofbases within thenucleotides formingalleles within aDNA (using GACT) orRNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, thesense strand is used. Because nucleic acids are normally linear (unbranched)polymers, specifying the sequence is equivalent to defining thecovalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed theprimary structure.
The sequence representsgenetic information. Biologicaldeoxyribonucleic acid represents theinformation which directs the functions of anorganism.
Nucleic acids also have asecondary structure andtertiary structure. Primary structure is sometimes mistakenly referred to as "primary sequence". However there is no parallel concept of secondary or tertiary sequence.
Nucleic acids consist of a chain of linked units called nucleotides. Each nucleotide consists of three subunits: aphosphate group and asugar (ribose in the case ofRNA,deoxyribose inDNA) make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set ofnucleobases. The nucleobases are important inbase pairing of strands to form higher-levelsecondary andtertiary structures such as the fameddouble helix.
The possible letters areA,C,G, andT, representing the fournucleotidebases of a DNA strand –adenine,cytosine,guanine,thymine –covalently linked to aphosphodiester backbone. In the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the5' to 3' direction. With regards totranscription, a sequence is on the coding strand if it has the same order as the transcribed RNA.
One sequence can becomplementary to another sequence, meaning that they have the base on each position in the complementary (i.e., A to T, C to G) and in the reverse order. For example, the complementary sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand.
While A, T, C, and G represent a particular nucleotide at a position, there are also letters that represent ambiguity which are used when more than one kind of nucleotide could occur at that position. The rules of the International Union of Pure and Applied Chemistry (IUPAC) are as follows:[1]
For example,W means that either an adenine or a thymine could occur in that position without impairing the sequence's functionality.
| Symbol[2] | Meaning/derivation | Possible bases | Complement | ||||
|---|---|---|---|---|---|---|---|
| A | Adenine | A | 1 | T (or U) | |||
| C | Cytosine | C | G | ||||
| G | Guanine | G | C | ||||
| T | Thymine | T | A | ||||
| U | Uracil | U | A | ||||
| W | Weak | A | T | 2 | W | ||
| S | Strong | C | G | S | |||
| M | aMino | A | C | K | |||
| K | Keto | G | T | M | |||
| R | puRine | A | G | Y | |||
| Y | pYrimidine | C | T | R | |||
| B | not A (B comes after A) | C | G | T | 3 | V | |
| D | not C (D comes after C) | A | G | T | H | ||
| H | not G (H comes after G) | A | C | T | D | ||
| V | not T (V comes after T and U) | A | C | G | B | ||
| N | anyNucleotide (not a gap) | A | C | G | T | 4 | N |
| Z | Zero | 0 | Z | ||||
These symbols are also valid for RNA, except with U (uracil) replacing T (thymine).[1]
Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is5-methylcytidine (m5C). In RNA, there are many modified bases, includingpseudouridine (Ψ),dihydrouridine (D),inosine (I),ribothymidine (rT) and7-methylguanosine (m7G).[3][4]Hypoxanthine andxanthine are two of the many bases created throughmutagen presence, both of them through deamination (replacement of the amine-group with a carbonyl-group). Hypoxanthine is produced fromadenine, and xanthine is produced fromguanine.[5] Similarly, deamination ofcytosine results inuracil.
Given the two 10-nucleotide sequences, line them up and compare the differences between them. Calculate the percent difference by taking the number of differences between the DNA bases divided by the total number of nucleotides. In this case there are three differences in the 10 nucleotide sequence. Thus there is a 30% difference.
In biological systems, nucleic acids contain information which is used by a livingcell to construct specificproteins. The sequence ofnucleobases on a nucleic acid strand istranslated by cell machinery into a sequence ofamino acids making up a protein strand. Each group of three bases, called acodon, corresponds to a single amino acid, and there is a specificgenetic code by which each possible combination of three bases corresponds to a specific amino acid.
Thecentral dogma of molecular biology outlines the mechanism by which proteins are constructed using information contained in nucleic acids.DNA istranscribed intomRNA molecules, which travel to theribosome where the mRNA is used as a template for the construction of the protein strand. Since nucleic acids can bind to molecules withcomplementary sequences, there is a distinction between "sense" sequences which code for proteins, and the complementary "antisense" sequence, which is by itself nonfunctional, but can bind to the sense strand.
DNA sequencing is the process of determining thenucleotide sequence of a givenDNA fragment. The sequence of the DNA of a living thing encodes the necessary information for that living thing to survive and reproduce. Therefore, determining the sequence is useful in fundamental research into why and how organisms live, as well as in applied subjects. Because of the importance of DNA to living things, knowledge of a DNA sequence may be useful in practically any biologicalresearch. For example, inmedicine it can be used to identify,diagnose and potentially developtreatments forgenetic diseases. Similarly, research intopathogens may lead to treatments for contagious diseases.Biotechnology is a burgeoning discipline, with the potential for many useful products and services.
RNA is not sequenced directly. Instead, it is copied to a DNA byreverse transcriptase, and this DNA is then sequenced.
Current sequencing methods rely on the discriminatory ability of DNA polymerases, and therefore can only distinguish four bases. An inosine (created from adenosine duringRNA editing) is read as a G, and 5-methyl-cytosine (created from cytosine byDNA methylation) is read as a C. With current technology, it is difficult to sequence small amounts of DNA, as the signal is too weak to measure. This is overcome bypolymerase chain reaction (PCR) amplification.
Once a nucleic acid sequence has been obtained from an organism, it is storedin silico in digital format. Digital genetic sequences may be stored insequence databases, be analyzed (seeSequence analysis below), be digitally altered and be used as templates for creating new actual DNA usingartificial gene synthesis.
Digital genetic sequences may be analyzed using the tools ofbioinformatics to attempt to determine its function.
The DNA in an organism'sgenome can be analyzed todiagnose vulnerabilities to inheriteddiseases, and can also be used to determine a child's paternity (genetic father) or a person'sancestry. Normally, every person carries two variations of everygene, one inherited from their mother, the other inherited from their father. Thehuman genome is believed to contain around 20,000–25,000 genes. In addition to studyingchromosomes to the level of individual genes, genetic testing in a broader sense includesbiochemical tests for the possible presence ofgenetic diseases, or mutant forms of genes associated with increased risk of developing genetic disorders.
Genetic testing identifies changes in chromosomes, genes, or proteins.[6] Usually, testing is used to find changes that are associated with inherited disorders. The results of a genetic test can confirm or rule out a suspected genetic condition or help determine a person's chance of developing or passing on a genetic disorder. Several hundred genetic tests are currently in use, and more are being developed.[7][8]
In bioinformatics, a sequence alignment is a way of arranging the sequences ofDNA,RNA, orprotein to identify regions of similarity that may be due to functional,structural, orevolutionary relationships between the sequences.[9] If two sequences in an alignment share a common ancestor, mismatches can be interpreted aspoint mutations and gaps asinsertion ordeletion mutations (indels) introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the degree of similarity betweenamino acids occupying a particular position in the sequence can be interpreted as a rough measure of howconserved a particular region orsequence motif is among lineages. The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whoseside chains have similar biochemical properties) in a particular region of the sequence, suggest[10] that this region has structural or functional importance. Although DNA and RNAnucleotide bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role.[11]
Computational phylogenetics makes extensive use of sequence alignments in the construction and interpretation ofphylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The degree to which sequences in a query set differ is qualitatively related to the sequences' evolutionary distance from one another. Roughly speaking, high sequence identity suggests that the sequences in question have a comparatively youngmost recent common ancestor, while low identity suggests that the divergence is more ancient. This approximation, which reflects the "molecular clock" hypothesis that a roughly constantrate of evolutionary change can be used to extrapolate the elapsed time since two genes first diverged (that is, thecoalescence time), assumes that the effects of mutation andselection are constant across sequence lineages. Therefore, it does not account for possible differences among organisms or species in the rates ofDNA repair or the possible functional conservation of specific regions in a sequence. (In the case of nucleotide sequences, the molecular clock hypothesis in its most basic form also discounts the difference in acceptance rates betweensilent mutations that do not alter the meaning of a givencodon and other mutations that result in a differentamino acid being incorporated into the protein.) More statistically accurate methods allow the evolutionary rate on each branch of the phylogenetic tree to vary, thus producing better estimates of coalescence times for genes.
Frequently the primary structure encodes motifs that are of functional importance. Some examples of sequence motifs are: the C/D[12]and H/ACA boxes[13]ofsnoRNAs,Sm binding site found in spliceosomal RNAs such asU1,U2,U4,U5,U6,U12 andU3, theShine-Dalgarno sequence,[14]theKozak consensus sequence[15]and theRNA polymerase III terminator.[16]
Inbioinformatics, a sequence entropy, also known as sequence complexity or information profile,[17] is a numerical sequence providing a quantitative measure of the local complexity of a DNA sequence, independently of the direction of processing. The manipulations of the information profiles enable the analysis of the sequences using alignment-free techniques, such as for example in motif and rearrangements detection.[17][18][19]
