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s 105 cell free fetal dna is found in the blood of the mother and can be sequenced to determine a great deal of information about the developing fetus 106 under the name of environmental dna edna has seen increased use in the natural sciences as a survey tool for ecology monitoring the movements and presence of species in water air or on land and assessing an area s biodiversity 107 108 interactions with proteins all the functions of dna depend on interactions with proteins these protein interactions can be non specific or the protein can bind specifically to a single dna sequence enzymes can also bind to dna and of these the polymerases that copy the dna base sequence in transcription and dna replication are particularly important dna binding proteins further information dna binding protein interaction of dna in orange with histones in blue these proteins basic amino acids bind to the acidic phosphate groups on dna structural proteins that bind dna are well understood examples of non specific dna protein interactions within chromosomes dna is held in complexes with structural proteins these proteins organize the dna into a compact structure called chromatin in eukaryotes this structure involves dna binding to a complex of small basic proteins called histones while in prokaryotes multiple types of proteins are involved 109 110 the histones form a disk shaped complex called a nucleosome which contains two complete turns of double stranded dna wrapped around its surface these non specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar phosphate backbone of the dna and are thus largely independent of the base sequence 111 chemical modifications of these basic amino acid residues include methylation phosphorylation and acetylation 112 these chemical changes alter the strength of the interaction between the dna and the histones making the dna more or less accessible to transcription factors and changing the rate of transcription 113 other non specific dna binding proteins in chromatin include the high mobility group proteins which bind to bent or distorted dna 114 these proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes 115 a distinct group of dna binding proteins is the dna binding proteins that specifically bind single stranded dna in humans replication protein a is the best understood member of this family and is used in processes where the double helix is separated including dna replication recombination and dna repair 116 these binding proteins seem to stabilize single stranded dna and protect it from forming stem loops or being degraded by nucleases the lambda repressor helix turn helix transcription factor bound to its dna target 117 in contrast other proteins have evolved to bind to particular dna sequences the most intensively studied of these are the various transcription factors which are proteins that regulate transcription each transcription factor binds to one particular set of dna sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters the transcription factors do this in two ways firstly they can bind the rna polymerase responsible for transcription either directly or through other mediator proteins this locates the polymerase at the promoter and allows it to begin transcription 118 alternatively transcription factors can bind enzymes that modify the histones at the promoter this changes the accessibility of the dna template to the polymerase 119 as these dna targets can occur throughout an organism s genome changes in the activity of one type of transcription factor can affect thousands of genes 120 consequently these proteins are often the targets of the signal transduction processes that control responses to environmental changes or cellular differentiation and development the specificity of these transcription factors interactions with dna come from the proteins making multiple contacts to the edges of the dna bases allowing them to read the dna sequence most of these base interactions are made in the major groove where the bases are most accessible 25 dna modifying enzymes nucleases and ligases the restriction enzyme ecorv green in a complex with its substrate dna 121 nucleases are enzymes that cut dna strands by catalyzing the hydrolysis of the phosphodiester bonds nucleases that hydrolyse nucleotides from the ends of dna strands are called exonucleases while endonucleases cut within strands the most frequently used nucleases in molecular biology are the restriction endonucleases which cut dna at specific sequences for instance the ecorv enzyme shown to the left recognizes the 6 base sequence 5 gatatc 3 and makes a cut at the horizontal line in nature these enzymes protect bacteria against phage infection by digesting the phage dna when it enters the bacterial cell acting as part of the restriction modification system 122 in technology these sequence specific nucleases are used in molecular cloning and dna fingerprinting enzymes called dna ligases can rejoin cut or broken dna strands 123 ligases are particularly important in lagging strand dna replication as they join the short segments of dna produced at the replication fork into a complete copy of the dna template they are also used in dna repair and genetic recombination 123 topoisomerases and helicases topoisomerases are enzymes with both nuclease and ligase activity these proteins change the amount of supercoiling in dna some of these enzymes work by cutting the dna helix and allowing one section to rotate thereby reducing its level of supercoiling the enzyme then seals the dna break 44 other types of these enzymes are capable of cutting one dna helix and then passing a second strand of dna through this break before rejoining the helix 124 topoisomerases are required for many processes involving dna such as dna replication and transcription 45 helicases are proteins that are a type of molecular motor they use the chemical energy in nucleoside triphosphates predominantly adenosine triphosphate atp to break hydrogen bonds between bases and unwind the dna double helix into single strands 125 these enzymes are essential for most processes where enzymes need to access the dna bases polymerases polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates the sequence of their products is created based on existing polynucleotide chains which are called templates these enzymes function by repeatedly adding a nucleotide to the 3 hydroxyl group at the end of the growing polynucleotide chain as a consequence all polymerases work in a 5 to 3 direction 126 in the active site of these enzymes the incoming nucleoside triphosphate base pairs to the template this allows polymerases to accurately synthesize the complementary strand of their template polymerases are classified according to the type of template that they use in dna replication dna dependent dna polymerases make copies of dna polynucleotide chains to preserve biological information it is essential that the sequence of bases in each copy are precisely complementary to the sequence of bases in the template strand many dna polymerases have a proofreading activity here the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides if a mismatch is detected a 3 to 5 exonuclease activity is activated and the incorrect base removed 127 in most organisms dna polymerases function in a large complex called the replisome that contains multiple accessory subunits such as the dna clamp or helicases 128 rna dependent dna polymerases are a specialized class of polymerases that copy the sequence of an rna strand into dna they include reverse transcriptase which is a viral enzyme involved in the infection of cells by retroviruses and telomerase which is required for the replication of telomeres 63 129 for example hiv reverse transcriptase is an enzyme for aids virus replication 129 telomerase is an unusual polymerase because it contains its own rna template as part of its structure it synthesizes telomeres at the ends of chromosomes telomeres prevent fusion of the ends of neighboring chromosomes and protect chromosome ends from damage 64 transcription is carried out by a dna dependent rna polymerase that copies the sequence of a dna strand into rna to begin transcribing a gene the rna polymerase binds to a sequence of dna called a promoter and separates the dna strands it then copies the gene sequence into a messenger rna transcript until it reaches a region of dna called the terminator where it halts and detaches from the dna as with human dna dependent dna polymerases rna polymerase ii the enzyme that transcribes most of the genes in the human genome operates as part of a large protein complex with multiple regulatory and accessory subunits 130 genetic recombination further information genetic recombination structure of the holliday junction intermediate in genetic recombination the four separate dna strands are coloured red blue green and yellow 131 a current model of meiotic recombination initiated by a double strand break or gap followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process repair of the gap can lead to crossover co or non crossover nco of the flanking regions co recombination is thought to occur by the double holliday junction dhj model illustrated on the right above nco recombinants are thought to occur primarily by the synthesis dependent strand annealing sdsa model illustrated on the left above most recombination events appear to be the sdsa type a dna helix usually does not interact with other segments of dna and in human cells the different chromosomes even occupy separate areas in the nucleus called chromosome territories 132 this physical separation of different chromosomes is important for the ability of dna to function as a stable repository for information as one of the few times chromosomes interact is in chromosomal crossover which occurs during sexual reproduction when genetic recombination occurs chromosomal crossover is when two dna helices break swap a section and then rejoin recombination allows chromosomes to exchange genetic information and produces new combinations of genes which 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 rese...
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