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h increases the efficiency of natural selection and can be important in the rapid evolution of new proteins 133 genetic recombination can also be involved in dna repair particularly in the cell s response to double strand breaks 134 the most common form of chromosomal crossover is homologous recombination where the two chromosomes involved share very similar sequences non homologous recombination can be damaging to cells as it can produce chromosomal translocations and genetic abnormalities the recombination reaction is catalyzed by enzymes known as recombinases such as rad51 135 the first step in recombination is a double stranded break caused by either an endonuclease or damage to the dna 136 a series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one holliday junction in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix the holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes swapping one strand for another the recombination reaction is then halted by cleavage of the junction and re ligation of the released dna 137 only strands of like polarity exchange dna during recombination there are two types of cleavage east west cleavage and north south cleavage the north south cleavage nicks both strands of dna while the east west cleavage has one strand of dna intact the formation of a holliday junction during recombination makes it possible for genetic diversity genes to exchange on chromosomes and expression of wild type viral genomes evolution further information origin of dna and rna world hypothesis dna contains the genetic information that allows all forms of life to function grow and reproduce however it is unclear how long in the 4 billion year history of life dna has performed this function as it has been proposed that the earliest forms of life may have used rna as their genetic material 138 139 rna may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes 140 this ancient rna world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases this would occur since the number of different bases in such an organism is a trade off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes 141 however there is no direct evidence of ancient genetic systems as recovery of dna from most fossils is impossible because dna survives in the environment for less than one million years and slowly degrades into short fragments in solution 142 claims for older dna have been made most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old 143 but these claims are controversial 144 145 building blocks of dna adenine guanine and related organic molecules may have been formed extraterrestrially in outer space 146 147 148 complex dna and rna organic compounds of life including uracil cytosine and thymine have also been formed in the laboratory under conditions mimicking those found in outer space using starting chemicals such as pyrimidine found in meteorites pyrimidine like polycyclic aromatic hydrocarbons pahs the most carbon rich chemical found in the universe may have been formed in red giants or in interstellar cosmic dust and gas clouds 149 ancient dna has been recovered from ancient organisms at a timescale where genome evolution can be directly observed including from extinct organisms up to millions of years old such as the woolly mammoth 150 151 uses in technology genetic engineering further information molecular biology nucleic acid methods and genetic engineering methods have been developed to purify dna from organisms such as phenol chloroform extraction and to manipulate it in the laboratory such as restriction digests and the polymerase chain reaction modern biology and biochemistry make intensive use of these techniques in recombinant dna technology recombinant dna is a man made dna sequence that has been assembled from other dna sequences they can be transformed into organisms in the form of plasmids or in the appropriate format by using a viral vector 152 the genetically modified organisms produced can be used to produce products such as recombinant proteins used in medical research 153 or be grown in agriculture 154 155 dna profiling further information dna profiling forensic scientists can use dna in blood semen skin saliva or hair found at a crime scene to identify a matching dna of an individual such as a perpetrator 156 this process is formally termed dna profiling also called dna fingerprinting in dna profiling the lengths of variable sections of repetitive dna such as short tandem repeats and minisatellites are compared between people this method is usually an extremely reliable technique for identifying a matching dna 157 however identification can be complicated if the scene is contaminated with dna from several people 158 dna profiling was developed in 1984 by british geneticist sir alec jeffreys 159 and first used in forensic science to convict colin pitchfork in the 1988 enderby murders case 160 the development of forensic science and the ability to now obtain genetic matching on minute samples of blood skin saliva or hair has led to re examining many cases evidence can now be uncovered that was scientifically impossible at the time of the original examination combined with the removal of the double jeopardy law in some places this can allow cases to be reopened where prior trials have failed to produce sufficient evidence to convince a jury people charged with serious crimes may be required to provide a sample of dna for matching purposes the most obvious defense to dna matches obtained forensically is to claim that cross contamination of evidence has occurred this has resulted in meticulous strict handling procedures with new cases of serious crime dna profiling is also used successfully to positively identify victims of mass casualty incidents 161 bodies or body parts in serious accidents and individual victims in mass war graves via matching to family members dna profiling is also used in dna paternity testing to determine if someone is the biological parent or grandparent of a child with the probability of parentage is typically 99 99 when the alleged parent is biologically related to the child usually dna sequencing are carried out after birth but there are new methods to test paternity while a mother is still pregnant 162 dna enzymes or catalytic dna further information deoxyribozyme deoxyribozymes also called dnazymes or catalytic dna were first discovered in 1994 163 they are mostly single stranded dna sequences isolated from a large pool of random dna sequences through a combinatorial approach called in vitro selection or systematic evolution of ligands by exponential enrichment selex dnazymes catalyze variety of chemical reactions including rna dna cleavage rna dna ligation amino acids phosphorylation dephosphorylation carbon carbon bond formation etc dnazymes can enhance catalytic rate of chemical reactions up to 100 000 000 000 fold over the uncatalyzed reaction 164 the most extensively studied class of dnazymes is rna cleaving types which have been used to detect different metal ions and designing therapeutic agents several metal specific dnazymes have been reported including the gr 5 dnazyme lead specific 163 the ca1 3 dnazymes copper specific 165 the 39e dnazyme uranyl specific and the naa43 dnazyme sodium specific 166 the naa43 dnazyme which is reported to be more than 10 000 fold selective for sodium over other metal ions was used to make a real time sodium sensor in cells bioinformatics further information bioinformatics bioinformatics involves the development of techniques to store data mine search and manipulate biological data including dna nucleic acid sequence data these have led to widely applied advances in computer science especially string searching algorithms machine learning and database theory 167 string searching or matching algorithms which find an occurrence of a sequence of letters inside a larger sequence of letters were developed to search for specific sequences of nucleotides 168 the dna sequence may be aligned with other dna sequences to identify homologous sequences and locate the specific mutations that make them distinct these techniques especially multiple sequence alignment are used in studying phylogenetic relationships and protein function 169 data sets representing entire genomes worth of dna sequences such as those produced by the human genome project are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome regions of dna sequence that have the characteristic patterns associated with protein or rna coding genes can be identified by gene finding algorithms which allow researchers to predict the presence of particular gene products and their possible functions in an organism even before they have been isolated experimentally 170 entire genomes may also be compared which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events dna nanotechnology further information dna nanotechnology the dna structure at left schematic shown will self assemble into the structure visualized by atomic force microscopy at right dna nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of dna molecules 171 dna nanotechnology uses the unique molecular recognition properties of dna and other nucleic acids to create self assembling branched dna complexes with useful properties 172 dna is thus used as a structural material rather than as a carrier of biological information this has led to the creation of two dimensional periodic lattices both tile based and using the dna origami method and three dimensional structures in the shapes of polyhedra 173 nanomechanical devices and algorithmic self assembly have also been demonstrated 174 and these dna structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins 175 dna and other nucleic acids are the basis of aptamers synthetic oligonucleotide ligands for specific target molecules used in a range of biotechnology and biomedical applications 176 history and anthropology further information phylogenetics and genetic genealogy because dna collects mutations over time which are then inherited it contains historical information and by comparing dna sequences geneticists can infer the evolutionary history of organisms their phylogeny 177 this field of phylogenetics is a powerful tool in evolutionary biology if dna sequences within a species are compared population geneticists can learn the history of particular populations this can be used in studies ranging from ecological genetics to anthropology information storage main article dna digital data storage dna as a storage device for information has enormous potential since it has much higher storage density compared to electronic devices however high costs slow read and write times memory latency and insufficient reliability has prevented its practical use 178 179 history further information history of molecular biology maclyn mccarty left shakes hands with francis crick and james watson co originators of the double helix model based on the x ray diffraction data and insights of rosalind franklin and raymond gosling dna was first isolated by the swiss physician friedrich miescher who in 1869 discovered a microscopic substance in the pus of discarded surgical bandages as it resided in the nuclei of cells he called it nuclein 180 181 in 1878 albrecht kossel isolated the non protein component of nuclein nucleic acid and later isolated its five primary nucleobases 182 183 in 1909 phoebus levene identified the base sugar and phosphate nucleotide unit of rna then named yeast nucleic acid 184 185 186 in 1929 levene identified deoxyribose sugar in thymus nucleic acid dna 187 levene suggested that dna consisted of a string of four nucleotide units linked together through the phosphate groups tetranucleotide hypothesis levene thought the chain was short and the bases repeated in a fixed order in 1927 nikolai koltsov proposed that inherited traits would be inherited via a giant hereditary molecule made up of two mirror strands that would replicate in a semi conservative fashion using each strand as a template 188 189 in 1928 frederick griffith in his experiment discovered that traits of the smooth form of pneumococcus could be transferred to the rough form of the same bacteria by mixing killed smooth bacteria with the live rough form 190 191 this system provided the first clear suggestion that dna carries genetic information in 1933 while studying virgin sea urchin eggs jean brachet suggested that dna is found in the cell nucleus and that rna is present exclusively in the cytoplasm at the time yeast nucleic acid rna was thought to occur only in plants while thymus nucleic acid dna only in animals the latter was thought to be a tetramer with the function of buffering cellular ph 192 193 in 1937 william astbury produced the first x ray diffraction patterns that showed that dna had a regular structure 194 in 1943 oswald avery along with co workers colin macleod and maclyn mccarty identified dna as the transforming principle supporting griffith s suggestion avery macleod mccarty experiment 195 erwin chargaff developed and published observations now known as chargaff s rules stating that in dna from any species of any organism the amount of guanine should be equal to cytosine and the amount of adenine should be equal to thymine 196 197 a blue plaque outside the eagle pub in cambridge england commemorating crick and watson by 1951 alec todd and collaborators at the university of cambridge had determined by biochemical methods how the backbone of dna is structured via the successive linking of carbon atoms 3 and 5 of the sugar to phosphates this would help to corroborate watson and crick s later x ray structural work 198 todd would later be awarded the 1957 nobel prize in chemistry for this and other discoveries related to dna 199 late in 1951 francis crick started working with james watson at the cavendish laboratory within the university of cambridge dna s role in heredity was confirmed in 1952 when alfred hershey and martha chase in the hershey chase experiment showed that dna is the genetic material of the enterobacteria phage t2 200 photo 51 showing x ray diffraction pattern of dna in may 1952 raymond gosling a graduate student working under the supervision of rosalind franklin...
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