A nucleic acid sequence is a succession of letters denoting a nucleotide sequence forming an allele in DNA (using GACT) or RNA (GACU) molecules. By convention, the order is usually presented from the 5 'end to the 3' end. For DNA, sensory strands are used. Since nucleic acids are usually linear (not branched) polymers, determining their sequence is equivalent to defining the covalent structure of all molecules. For this reason, the nucleic acid sequence is also called the primary structure.
The sequence has the capacity to represent information. The biological deoxyribonucleic acid is the information that directs the function of living things.
Nucleic acid also has a secondary structure and tertiary structure. The main structure is sometimes mistakenly referred to as the main sequence . Conversely, there is no concept of secondary or tertiary sequence parallel.
Video Nucleic acid sequence
Nukleotida
Nucleic acid consists of a chain of related units called nucleotides. Each nucleotide consists of three subunits: the phosphate group and the sugar (ribose in the case of RNA, deoxyribose in DNA) form the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases. Nucleobase is important in pair pairs of strands to form high-level secondary and tertiary structures such as the famous double helix.
The possible letters are A , C , G , and T , representing four nucleotide bases of DNA strand - adenine, cytosine, guanine, thymine - covalent associated with the phosphodiester backbone. In a typical case, the printed sequence abuts without a gap, as in the AAAGTCTGAC sequence, read left to right in the 5 'to 3' direction. With respect to transcription, the sequence is on the encoding string if it has the same sequence as the transcribed RNA.
One sequence can complement other sequences, meaning that they have a base on each position in the complement (ie A through T, C to G) and in reverse order. For example, the complementary order for TTAC is GTAA. If a single strand of double-stranded DNA is considered a thread of senses, then the other strands, regarded as antisense strands, will have a complementary sequence on the sensory strands.
Notation
Compare and determine the% difference between two nucleotide sequences.
- AA T CC GC TAG
- AA A CC CT TAG
- Given two 10-nucleotide sequences, line them and compare the differences between them. Calculate the percent equation by taking the number of different DNA bases divided by the total number of nucleotides. In the above case, there are three differences in the 10 nucleotide sequences. Therefore, divide 7/10 to get a 70% resemblance and subtract from 100% to get 30% difference.
While A, T, C, and G represent certain nucleotides in position, there are also letters representing the ambiguities used when more than one nucleotide type may occur in that position. The International Union of Pure and Applied Chemistry (IUPAC) is as follows:
- A = adenine
- C = cytosine
- G = guanin
- T = mute
- R = G A (purine)
- Y = T C (pyrimidine)
- K = G T (for)
- M = A C (amino)
- S = G C (strong bond)
- W = A T (weak bonds)
- B = G T C (all but A)
- D = G A T (all except C)
- H = A C T (all but G)
- V = G C A (all except T)
- N = A G C T (exists)
This symbol also applies to RNA, except with U (uracil) replacing T (timin).
In addition to 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 is formed. In DNA, the most common modified base is 5-methylcytidine (m5C). In RNA, there are many modified bases, including pseudouridine (?), Dihydrouridine (D), inosine (I), ribothymidine (rT) and 7-methylguanosine (m7G). Hypoxanthine and xanthine are two of the many bases created through the presence of mutagen, both by deamination (replacement of amine groups with carbonyl groups). Hypoxanthine is produced from adenine, xanthine from guanine. Similarly, the deamination of cytosine results in uracil.
Maps Nucleic acid sequence
Biological significance
In biological systems, nucleic acids contain information used by living cells to build specific proteins. The nucleobase sequence on the nucleic acid strand is translated by the cell machinery into a sequence of amino acids forming a protein strand. Each group of three bases, called codons, corresponds to a single amino acid, and there is a specific genetic code that allows any combination of three bases to correspond to certain amino acids.
The central dogma of molecular biology describes the mechanism by which proteins are built using information contained in nucleic acids. DNA is transcribed into mRNA molecules, which move to the ribosomes where mRNA is used as a template for the construction of protein strands. Since nucleic acids can bind to molecules with complementary sequences, there is a distinction between the "sensory" sequences that encode proteins, and complementary complementary "antisense" sequences that are not functioning, but may bind to the sense strands.
Ordering
DNA sequencing is the process of determining the sequence of nucleotides from a given DNA fragment. The DNA sequence of living things encodes the information necessary for the living beings to survive and reproduce. Therefore, determining this sequence is useful in fundamental research on why and how living organisms, as well as in applied subjects. Because of the importance of DNA to living things, knowledge of DNA sequences may be useful in almost all biological research. For example, in medical science can be used to identify, diagnose, and potentially develop treatments for genetic diseases. Similarly, research on pathogens may lead to treatment for infectious diseases. Biotechnology is an evolving discipline, with the potential for many useful products and services.
RNA is not sorted directly. Instead, it is copied to DNA by reverse transcriptase, and the DNA is then sorted.
The current sequencing method depends on the discriminatory ability of the DNA polymerase, and therefore can only distinguish four bases. Inosine (made from adenosine during RNA editing) is read as G, and 5-methyl-cytosine (made from cytosine by DNA methylation) is read as C. With current technology, it is difficult to sequence small amounts of DNA, because the signal is too weak to measure. This is overcome by the amplification of polymerase chain reaction (PCR).
Digital Representation
After a sequence of nucleic acids has been obtained from an organism, it is stored in silico in digital format. The digital genetic sequence can be stored in the sequence database, analyzed (see Sequence analysis below), converted digitally and used as a template to create new actual DNA using synthesized artificial genes.
Sequence analysis
The digital genetic sequence can be analyzed using a bioinformatics tool to try to determine its function.
Genetic testing
DNA in the genomes of organisms can be analyzed to diagnose susceptibility to inherited diseases, and can also be used to determine a child's father (genetic father) or a person's ancestor. Typically, each person carries two variations of each gene, one inherited from their mother, the other inherited from their father. The human genome is believed to contain about 20,000 - 25,000 genes. In addition to studying chromosomes to individual gene levels, genetic testing in a broader sense includes biochemical tests for possible genetic diseases, or mutant gene forms associated with an increased risk of developing a genetic disorder.
Genetic testing identifies changes in chromosomes, genes, or proteins. Typically, testing is used to find changes related to inherited interruptions. Genetic test results can confirm or rule out a suspected genetic condition or help determine a person's chances of developing or passing on genetic disorders. Several hundred genetic tests are in use, and more are being developed.
Order alignment
In bioinformatics, alignment of sequences is a way of arranging DNA, RNA, or protein sequences to identify areas of possible similarity due to functional, structural, or evolutionary relationships between sequences. If two sequences in harmony share a common ancestor, mismatches can be interpreted as point mutations and gaps as the insertion or deletion of mutations (indels) introduced in one or both lineages in time because they deviate from each other. In the sequence of protein alignments, the degree of similarity between the amino acids that occupy a particular position in the sequence can be interpreted as a rough measure of how to preserve a particular region or motive sequence among lineages. The absence of substitution, or the presence of only very conservative substitutions (ie, substitution of amino acids whose side chains have similar biochemical properties) in certain regions of the series, indicates that this region has structural or functional importance. Although nucleotide bases of DNA and RNA are more similar to each other than amino acids, the conservation of base pairs may indicate similar functional or structural roles.
Computational phylogenetics makes extensive use of sequential alignments in the construction and interpretation of phylogenetic trees, which are used to classify evolutionary relationships between homologous genes represented in the genomes of different species. The rate at which the order in the query sets differ is qualitatively related to the evolutionary distance sequences of each other. Roughly speaking, high order identities indicate that the sequence in question has a relatively young common ancestor recently, while low identities suggest that the differences are more ancient. This approach, which reflects the hypothesis of "molecular clock" that a constant rate of evolutionary change can be used to extrapolate the elapsed time since the first two genes deviate (ie, time of integration), assumes that mutation and selection effects are constant in the lineage sequence. Therefore, this does not take into account possible differences between organisms or species in the degree of DNA repair or the possible functional conservation of a particular area in sequence. (In the case of a nucleotide sequence, the molecular clock hypothesis in its most basic form also discounts the difference in the rate of acceptability between the stationary mutations that do not alter the meaning of the given codon and other mutations that produce different amino acids incorporated into proteins.) More accurate methods statistically allowing the rate of evolution in each branch of the phylogenetic tree to vary, resulting in better approximation of time of incorporation for the gene.
Order motive
Often the main structure encodes motives that have functional importance. Some examples of sequential motifs are: C/D and H/ACA boxes of snoRNA, Sm bond sites found in RNA spliceosomes such as U1, U2, U4, U5, U6, U12 and U3, Shine-Dalgarno sequences, Kozak consensus sequences and terminators RNA polymerase III.
Remote correlation
Peng et al found a long-range correlation in the sequence of non-coding base pairs of DNA. On the contrary, the correlation does not appear to be encoded in DNA sequencing.
Entropy order
In Bioinformatics, sequence entropy, also known as sequence complexity or information profile, is a numerical sequence that provides a quantitative measure of the local complexity of a DNA sequence, regardless of the direction of processing. The manipulation of the profile information allows sequence analysis using alignment free techniques, such as in the motive and re-arrangement of detection.
See also
- Gene structure
- Quarter number system
- Single nucleotide polymorphism (SNP)
References
External links
- Bibliography of features, patterns, correlations in DNA texts and proteins
Source of the article : Wikipedia
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