Sequencing massive chloroplast genomes now attainable
Researchers have developed a sequencing methodology that enables doubtlessly a whole lot of plant chloroplast genomes to be sequenced without delay, facilitating research of molecular biology and evolution in crops. This methodology depends on environment friendly separation of chloroplast DNA utilizing brief DNA “baits” designed from already-sequenced chloroplast genomes. These molecular baits focus the chloroplast DNA earlier than sequencing, dramatically rising the variety of samples that may be sequenced.
sequencing methodology chloroplast genomes
Researchers on the University of Florida and Oberlin College have developed a sequencing methodology that can permit doubtlessly a whole lot of plant chloroplast genomes to be sequenced directly, facilitating research of molecular biology and evolution in crops.
Chloroplast is the compartment throughout the plant
Cell that’s answerable for photosynthesis and therefore offers all the sugar that a plant must develop and survive. The chloroplast is uncommon in containing its personal DNA genome, separate from the bigger and dominant genome that’s positioned in each cell’s nucleus.
Chloroplast DNA sequences are extensively utilized by plant biologists in genetic engineering and in reconstructing evolutionary relationships amongst vegetation. Until lately, although, chloroplast genome sequencing was a expensive and time-intensive endeavor, limiting its utility for plant evolutionary and molecular biologists. Instead, most researchers have been restricted to sequencing a small portion of the chloroplast genome, which in lots of instances is inadequate for figuring out evolutionary relationships, particularly in plant teams which can be evolutionarily younger.
In distinction, full chloroplast genome sequences harbor sufficient data to reconstruct each current and historic variations. New DNA sequencing applied sciences, termed “subsequent-era” sequencers, have made it significantly cheaper and simpler to sequence full chloroplast genomes. While present strategies utilizing subsequent-technology sequencers enable as much as forty eight chloroplast genomes to be sequenced at one time, the brand new technique will permit doubtlessly tons of of flowering plant chloroplast genomes to be sequenced without delay, considerably decreasing the per-pattern price of chloroplast genome sequencing.
This new methodology, reported within the February challenge of Applications in Plant Sciences, depends on environment friendly separation of chloroplast DNA from different DNA within the cell utilizing brief DNA “baits” that have been designed from chloroplast genomes which have already been sequenced. These molecular baits successfully focus the chloroplast DNA earlier than sequencing (a course of termed “focused enrichment”), dramatically growing the variety of samples that may be sequenced directly.
Greg Stull, a graduate pupil on the University of Florida and lead writer of the research, summarizes the flexibility of the brand new system: “With this methodology, it ought to be attainable for researchers to cheaply sequence tons of of chloroplast genomes for any flowering plant group of curiosity.”
The technique was particularly designed by the authors of the examine such that nearly any flowering plant chloroplast genome could be sequenced, no matter species. Flowering vegetation characterize the most important (~300,000 species) and most ecologically dominant group of land crops, and embody all main crop crops.
admin June 6th, 2014
Posted In: DNA sequencing
Tags: chloroplast genome, sequenced at once, University of Florida
Malaria control and genomics methods
Single-cell genomics might present new perception into the biology of Malaria parasites, together with their virulence and ranges of drug resistance, to finally enhance therapy and management of the illness, based on new analysis funded by the Wellcome Trust and the National Institutes of Health.
The findings are revealed in a research by researchers on the Texas Biomedical Research Institute and revealed within the journal Genome Research.
Malaria infections generally include advanced mixtures of Plasmodium parasites which trigger the illness. These mixtures, often known as a number of genotype infections (MGI’s), can alter the influence of the an infection resulting from parasites competing with each other and may drive the unfold of drug resistance. MGI’s are extraordinarily widespread in areas with excessive ranges of malaria an infection however their biology is poorly understood.
“Up to 70 per cent of infections in sub-Saharan Africa are MGI’s and we presently do not know what number of genotypes are current and whether or not parasites come from a single mosquito chew or a number of mosquito bites” says Shalini Nair, first writer on the paper.
Current genome sequencing strategies contain the chemical disintegration of samples of pink blood cells from contaminated sufferers to acquire parasite DNA, that are then sequenced. This grouped sequencing can not account for variations between particular person parasites present in cells.
Single cell genomics permits the separation and isolation of cells to extract and sequence particular person parasite DNA and decide any variations between the parasites inside an an infection.
“Current sequencing methods actually restrict our understanding of parasite biology and malaria control, “It’s like making an attempt to grasp human genetics by making DNA from everybody in a village directly. The knowledge is all jumbled up, however what we actually need is data from people.”
The workforce used strategies of single cell-sorting and complete genome amplification to separate out particular person cells and amplify their DNA for sequencing immediately from contaminated pink blood cells. The use of single-cell genomics permits sequencing of particular person parasites straight from a affected person’s blood.
The method permits a complete description of the composition of MGIs, and can reveal data on the energy of an an infection and the event of drug-resistance, which may inform illness management interventions.
Though the expertise is presently too costly and demanding for routine use within the clinic, because the know-how matures the purposes for understanding malaria biology are huge.
Head of Genetics and Molecular Sciences mentioned: “Malaria stays one of many greatest killers on this planet at this time regardless of a long time of management efforts. Any perception into the basic genetics and total biology of the illness is efficacious to enhance future interventions and scale back charges of an infection and mortality.”
Two types of malaria parasites had been sequenced within the research; Plasmodium falciparum (liable for as much as seven-hundred, deaths per yr) and Plasmodium vivax (answerable for 20 million infections per yr).
admin May 28th, 2014
Posted In: DNA sequencing
New single cell genome sequencing method
Researchers led by bioengineers have generated essentially the most full genome sequences from single E. coli cells and particular person neurons from the brain. The breakthrough comes from a brand new single-cell genome sequencing method that confines genome amplification to fluid-crammed wells with a quantity of simply 12 nanoliters.
The research is revealed within the journal Nature Biotechnology on November 10, 2013.
“Our preliminary information recommend that neurons from the brain have completely different genetic compositions. This is a comparatively new concept, and our method will allow researchers to have a look at genomic variations between single cells with a lot finer element,” mentioned Kun Zhang, a professor within the Department of Bioengineering on the UC San Diego Jacobs School of Engineering and the corresponding creator on the paper.
The researchers report that the genome sequences of single cells generated utilizing the brand new method exhibited comparatively little “amplification bias,” which has been probably the most vital technological impediment going through single-cell genome sequencing up to now decade. This bias refers to the truth that the amplification step is uneven, with completely different areas of a genome being copied completely different numbers of instances. This imbalance complicates many downstream genomic analyses, together with meeting of genomes from scratch and figuring out DNA content material variations amongst cells from the identical particular person.
Nice curiosity to researchers: Single cell Genome Sequencing
Sequencing the genomes of single cells is of nice curiosity to researchers working in many various fields. For instance, probing the genetic make-up of particular person cells would assist researchers determine and perceive a variety of organisms that can’t be simply grown within the lab from the micro organism that reside inside our digestive tracts and on our pores and skin, to the microscopic organisms that stay in ocean water. Single-cell genetic research are additionally getting used to review most cancers cells, stem cells and the human mind, which is made up of cells that more and more seem to have vital genomic variety.
“We now have the fantastic alternative to take a better-decision have a look at genomes inside single cells, extending our understanding of genomic mosaicism throughout the mind to the extent of DNA sequence, which right here revealed new somatic adjustments to the neuronal genome. This may present new insights into the conventional in addition to irregular mind, resembling happens in Alzheimer’s and Parkinson’s illness or Schizophrenia,” mentioned Jerold Chun, a co-creator and Professor within the Dorris Neuroscience Center at The Scripps Research Institute.
For instance, the brand new sequencing method recognized positive factors or lack of single copy DNA as small as M million base pairs, the best decision to this point for single-cell sequencing approaches. Recent single-cell sequencing research have used older strategies which may solely decipher DNA copy modifications which might be no less than three to 6 million base pairs.
Amplification in Nano-Scale Wells
The 12 nanoliter (nL) quantity microwells wherein amplification takes place are a few of the smallest quantity wells for use in revealed protocols for single-cell genome sequencing.
“By decreasing amplification response volumes a thousand-fold to nanoliter ranges in 1000′s of microwells, we elevated the efficient focus of the template genome, resulting in improved amplification uniformity and diminished DNA contamination,” defined Jeff Gole, the primary creator on the paper. Gole labored on this challenge as a Ph.A. pupil in Kun Zhang’s bioengineering lab on the UC San Diego Jacobs School of Engineering. Gole is now a Scientist at Good Start Genetics in Cambridge, Mass.
Compared to essentially the most full beforehand printed single D. coli genome knowledge set, the brand new strategy recovered 50 p.c extra of the W. coli genome with A to thirteen-fold much less sequencing knowledge.
“The outcomes exhibit that MIDAS gives a way more environment friendly technique to assemble entire bacterial genomes from single cells with out tradition,” the authors write within the Nature Biotechnology paper.
Multidisciplinary Research
The genomics researchers collaborated with supplies science graduate scholar Yu-Jui (Roger) Chiu on the microfabrication required to create the arrays of microwells. Chiu is engaged on his Ph.A. within the lab of UC San Diego electrical engineering professor Yu-Hwa Lo, who additionally directs the Nano3 Labs in UC San Diego’s Qualcomm Institute, the place microfabrication befell.
“This venture wouldn’t have succeeded with out the fabrication and instrumentation assist accessible on the Jacobs School and the Qualcomm Institute,” mentioned Zhang. “We are very enthusiastic about our preliminary outcomes in addition to the likelihood that researchers all over the world will be capable of use this strategy in many various contexts.”
admin May 28th, 2014
Posted In: DNA sequencing
Tags: genome sequencing, technique
Bacterias can change genes into the human genome
A staff of scientists from the University of Maryland School of Medicine has discovered the strongest proof but that micro organism sometimes switch their genes into the human genome, discovering bacterial DNA sequences in a few third of wholesome human genomes and in a far larger proportion of most cancers cells. The outcomes, printed right this moment (20 June) in PLOS Computational Biology, counsel that gene switch from micro organism to people isn’t solely potential, but additionally in some way linked to over-proliferation: both most cancers cells are inclined to those intrusions or the incoming bacterial genes assist to kick-begin the transformation from wholesome cells into cancerous ones.
“It actually does appear that the human genome sequence knowledge from somatic cells present indicators of LGT occasions from micro organism, and so do most cancers cells,” mentioned Jonathan Eisen from University of California, Davis, who coordinated the peer evaluation of the brand new research however was not concerned within the work. “Wild stuff does occur.”
The trillions of micro organism in our our bodies recurrently change DNA with one another, however the concept their genes may find yourself in human DNA has been very controversial. In 2001, the staff that sequenced the primary human genome claimed to have discovered 113 instances of such lateral gene transfers (LGT), however their conclusion was later refuted.
This excessive-profile error “had a chilling impact on the sphere,” in line with Julie Dunning Hotopp who led the brand new research. Although her crew has since discovered a number of instances of LGT between bacteria and invertebrates, “it’s nonetheless troublesome to persuade those who it could be taking place within the human genome,” she stated.
Rather than in search of bacterial genes that had grow to be everlasting elements of the human genome, Dunning Hotopp’s group looked for traces of microbial DNA in somatic cells—the cells of the physique that don’t type gametes.
Lab members David Riley and Karsten Sieber scanned publicly accessible knowledge from the one thousand Genomes Project and located greater than S,000 situations of LGT from micro organism, affecting round a 3rd of the folks they studied. When they analyzed sequences from the Cancer Genome Atlas, they found 691,000 extra situations of LGT ninety nine.N % of those got here from tumor samples moderately than regular tissues.
Acute myeloid leukaemia cells had been notably rife with bacterial sequences. A third of the microbial genes got here from a genus referred to as Acinetobacter, and had been inserted into the mitochondrial genome.
Stomach most cancers cells additionally contained numerous bacterial DNA, particularly from Pseudomonas. Most of this DNA had been inserted into 5 genes, 4 of which have been already identified to be proto-oncogenes that can provide rise to most cancers, emphasizing a potential hyperlink between LGT and cancerous progress. “Finding these integrations in a number of people, in addition to within the proto-oncogenes, actually spoke to how important this could be,” mentioned Dunning Hotopp.
“We know already that a important proportion of cancers are attributable to insertion of genetic materials from viruses,” stated Etienne Danchin from the French National Institute for Agricultural Research, who reviewed the paper. “But that is the primary time, so far as I know, that HGT from micro organism might be suspected as a reason for most cancers.”
However, Dunning Hotopp could be very clear that her outcomes inform us nothing about whether or not the inserted bacterial DNA contributed to inflicting the cancers, or had been simply alongside for the trip. To get on the query of causation, researchers might intentionally add bacterial DNA into the identical websites inside human cell traces to see in the event that they flip cancerous, she mentioned. But even when the bacterial LGT can provoke over-proliferation, it might be laborious to stop such transfers with antibiotics. “You don’t know when these transfers happen, and you’ll’t give individuals antibiotics their complete life,” stated Dunning Hotopp. “A vaccine could be good, however that’s assuming these are causative.”
“LGT is extremely essential in evolution however many claims of particular instances of LGT have been significantly flawed,” mentioned Eisen. “I got here into this as a severe skeptic. It simply appeared so unbelievable.”
But the workforce received him over. They ran an in depth set of checks to ensure that these bacterial sequences weren’t laboratory artifacts and had not come from contaminating microbes.
For instance, they confirmed that LGT was extra frequent in most cancers cells than wholesome tissue, and two out of ten most cancers varieties had been notably exhausting hit. If the bacterial integrations have been artifacts of the methodology, it must be equally frequent in any tissue pattern. The staff additionally centered on sequences with excessive protection—that’s, these which had been learn many occasions over. When the group discovered proof of LGT, it was constant throughout all of those reads. “In the tip, the authors addressed each single query that I and the reviewers raised,” mentioned Eisen.
Hank Seifert from Northwestern University, who was not concerned within the research, stays cautious. “This paper could be very attention-grabbing and doubtlessly essential,” he mentioned. “However, till the direct evaluation of particular tumor cells will be carried out to validate that these are actual occasions, this work [is] nonetheless speculative.”
But Dunning Hotopp’s group can’t do these validation research herself. For privateness causes, they can’t entry the unique tumor samples that their knowledge got here from. “People with entry to the samples must validate that the integrations are appropriate,” she mentioned.
Danchin agrees that the outcomes must be validated however mentioned, “I am personally satisfied what they’ve discovered by screening the totally different databases is true. I suppose LGT occurs far more continuously than we think about however, more often than not, is simply not detectable.”
admin May 27th, 2014
Posted In: Uncategorized
Personal drug test: Tumor Exome
An algorithm can pick out biologically and clinically meaningful variants from whole-exome sequences of tumors.
In the march of personal drug test, genotyping cancers has change into increasingly advanced. Panels that decide up variations in a whole bunch of doubtless vital genes can assist physicians decide how a specific tumor operates and the perfect course of remedy.
Whole-exome sequencing—the evaluation of all of the coding areas of the genome—has been considerably of a pipe dream for medical oncology, however a examine revealed right this moment (May 19) in Nature Medicine introduces a platform for analyzing your entire exome of most cancers sufferers’ tumors. “It’s improbable,” stated Sameek Roychowdhury, an oncology genomics researcher at Ohio State University who didn’t take part within the research. “It’s what all people must see occurring for this discipline.”
The new complete-exome platform extracts DNA from a preserved tumor pattern, sequences all the coding areas within the genome, and runs the information by way of an algorithm that may make sense of the variations uncovered and select these for which an accessible remedy is perhaps applicable. Importantly, the protocol makes use of tumor samples fastened in formalin and embedded in paraffin, which is a regular methodology for storing tumor tissue, however one which tends to make sequencing a headache.
“This skill to make use of the sequencing know-how for these sorts of [preserved] supplies provides us entry to an unlimited quantity of samples,” stated Michal-Ruth Schweiger, who leads the most cancers biology group on the Max Planck Institute for Molecular Genetics in Munich, Germany. Schweiger, who was not concerned within the present examine, has had success sequencing formalin-mounted, paraffin-embedded samples, however on a a lot smaller scale than what the authors achieved. Eliezer Van Allen, the lead creator of the research and an teacher in medication at Harvard Medical School and the Dana-Farber Cancer Institute, mentioned that as an increasing number of genetic data is available in, it is smart to seize the entire exome, reasonably than redesign panels that focus on a restricted variety of genes. “It’s changing into extra logical to say, ‘Let’s get the entire info up entrance and use what we will,’ particularly as the quantity of knowledge begins to develop,” he instructed The Scientist.
The algorithm Van Allen and his colleagues designed, referred to as precision heuristics for deciphering the alteration panorama (PHIAL), types the genetic variations in a affected person’s tumor sequence based mostly on what’s already identified concerning the organic exercise and scientific relevance of such alterations. For occasion, in a pattern of 511 sufferers, PHIAL picked out M,842 alterations—out of 250,000 variants in complete—for which there exist medicine that may act upon the genes possessing these alterations. To reveal how PHIAL could be utilized in making medical choices, the analysis staff chosen one affected person with metastatic lung most cancers. “It turned out this affected person had a really uncommon mutation in [the oncogene] KRAS, which we don’t usually take a look at for” within the clinic, however that PHIAL had chosen as being necessary to the tumor, Van Allen stated. Fortuitously, there was a medical trial ongoing for a cyclin-dependent kinase A (CDK4) inhibitor that’s thought to cease the expansion of lung cells expressing KRAS. The affected person enrolled within the trial and responded to the remedy; it was the one remedy he’d had any success with.
“It was a compelling occasion of why we’d like to do that extra broadly,” Van Allen mentioned. The workforce has made a database of clinically actionable genes (together with one hundred thirty to this point) available online, and Van Allen stated his group intends to make the PHIAL program freely accessible as properly. Roychowdhury stated the platform is an efficient mannequin for different teams to comply with in increasing the utility of most cancers genomics. “I suppose subsequent step shall be to determine that this can be a medical-grade assay,” he informed The Scientist. Schweiger agreed that the methodological and bioinformatics headway made within the examine are “highly effective” and will advance efforts towards customized medication.
One means to enhance upon the method, she famous, can be to automate the choice of a medical trial or experimental remedy as soon as PHIAL has chosen the alterations that may profit from intervention. “They had so as to add plenty of handbook work in there,” she advised The Scientist. Schweiger mentioned there are already databases in growth that might complement complete-exome analyses. Stacey Gabriel, the director of the Genomics Platform on the Broad Institute and one of many senior authors of the examine, mentioned her facility expenses $P,500 for complete-exome sequencing, however doesn’t supply the scientific session. Roychowdhury estimated that the full price may go as much as $10,000, together with the experience required for making remedy choices primarily based on the outcomes. “In the context of therapies we’re creating, which price $H,000 to $30,000 a month, we have to have instruments to verify we use these therapies in the correct manner,” he mentioned. “I assume it’s price it.”
admin May 27th, 2014
Posted In: innovations
Tags: cancer genomics and cancer, exome sequencing, genetics & genomics, personalized medicine
DNA: new pair of letters
We are Denis Malyshev (/u/danmalysh), Kiran Dhami (/u/kdhami), Thomas Lavergne (/u/ThomasLav), Yorke Zhang (/u/yorkezhang), Elie Diner (/u/ediner), Aaron Feldman (/u/AaronFeldman), Brian Lamb (/u/technikat), and Floyd Romesberg (/u/fromesberg), past and present members of the Romesberg Lab that recently published the paper A semi-synthetic organism with an expanded genetic alphabet
The Romesberg lab at The Scripps Research Institute has had a long standing interest in expanding the alphabet of life. All natural biological information is encoded within DNA as sequences of the natural letters, G, C, A, and T (also known as nucleotides). These four letters form two “base pairs:” every time there is a G in one strand, it pairs with a C in the other, and every time there is an A in one strand it pairs with a T in the other, and thus two complementary strands of DNA form the famous double stranded helix. The information encoded in the sequences of the DNA strands is ultimately retrieved as the sequences of amino acids in proteins, which directly or indirectly perform all of a cell’s functions. This way of storing information is the same in all organisms, in fact, as best we can tell, it has always been this way, all the way back to the last common ancestor of all life on earth.
Adding new letters to DNA has proven to be a challenging task: the machinery that replicates DNA, so that it may be passed on to future generations, evolved over billions of years to only recognize the four natural letters. However, over the past decade or so, we have worked to create a new pair of letters (we can call them X and Y for simplicity) that are well recognized by the replication machinery, but only in a test tube. In our recent paper, we figured out how to get X and Y into a bacterial cell, and that once they were in, the cells’ replication machinery recognized them, resulting in the first organism that stably stores increased information in its DNA.
Now that we have cells that store increased information, we are working on getting them to retrieve it in the form of proteins containing unnatural amino acids. Based on the chemical nature of the unnatural amino acids, these proteins could be tailored to have properties that are far outside the scope of natural proteins, and we hope that they might eventually find uses for society, such as new drugs for different diseases.
You can read more about our work at Nature News&Views,The Wall Street Journal, The New York Times, NPR.
admin May 22nd, 2014
Posted In: innovations
Genome project: What advances are being made in DNA sequencing
DNA sequencing refers to determining the exact order of nucleotides (Adenine, Thiamine, Guanine, Cytosine) for the DNA in a cell. The major scientific advancement that occurred in this area was the completion of the Human Genome Project in 2003. The aim of this project was to sequence the entire DNA in a human cell and to determine which sections of DNA represent individual genes (protein-coding units).
DNA samples were collected from all over the world
and sent to the Human Genome centres where scientists performed DNA sequencing and analysis. Therefore the full sequence was published and researchers determined that within this sequence there was somewhere between 30,000 and 40,000 genes.
Some scientists still argue that the complete sequencing of the human genome is not complete because current technology has left many bases of repeat-rich heterochromatin and several small gaps unfinished. However, they seem to agree that the confirmed number of genes in the human is closer to 25,000.
Scientists are currently using this information to work on projects that compare genomes between human beings and other animals while other projects are investigating interactions between DNA sequences, gene products and environmental factors and analysing genetic variations between individuals in a population. An online system known as ENCODE (Encyclopaedia of DNA Elements) has also been invented that enables the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. In addition to the variation information catalogued by the International HapMap in 2007 and 100 Genomes project in 2012, researchers have built a reliable foundation for genetic research routed in the human genome sequence. The first genome-wide ENCODE papers were published in 2012 to help everyone in and outside the scientific community understand the meaning of these sequences.
Archiving of a lot of information on sequencing is operating under the International Nucleotide Sequence Database Collaboration (INSDC) which is currently preserving all sequences equally but it has been indicated that the rapid increase in the rate of global sequence production will soon lead to differentiated treatment of DNA sequences being submitted. This will be a major advancement in the storage and maintenance of the records. It will also contribute to easy retrieval of these sequences for different scientific purposes. Rapid advancement in sequencing technology, commonly referred to as the next generation sequencing, has contributed towards analyzing large numbers of DNA thus delivering large volumes of data over a short period of time. Sanger sequencing method which has been used for several years is no longer the only technique that can be applied for analysis of DNA.
Over the past several decades technical advances automated and refined the Sanger sequencing method. The new technologies that have been developed to further increase the efficiency of sequencing include flow cytometry, scanning microscopes, mass spectrophotometer and hybridization strategies. Next generation sequencing has been seen to be a major contributor towards
advancement of DNA sequencing and molecular biology as a whole
.
admin February 9th, 2014
Posted In: DNA sequencing
Tags: DNA sequencing
Liquid drops – genetic innovations – footage
Liquid drops – genetic innovations from gilbert pascal on Vimeo.
admin January 25th, 2014
Posted In: Resources, videos / footages
Single neuron fly through – video footage
single neuron fly through from gilbert pascal on Vimeo.
admin January 25th, 2014
Posted In: Resources, videos / footages
DNA BASES
DNA is a polymer. The monomer units of DNA are nucleotides, and the polymer is known as a “polynucleotide.” Each DNA nucleotide consists of 3 components 1) 5-carbon sugar (deoxyribose), 2) a nitrogen containing base attached to the sugar, 3) and a phosphate group.
There are four different types of nucleotides found in DNA, differing only in the nitrogenous base (Nucleobases). The nucleobases are adenine (A), guanine (G), cytosine (C), and thymine (T). The sugars and phosphates of the nucleotides bond strongly together to form a “backbone” of the double helix to which these four bases connect, forming the “rungs”.
The skeleton of adenine and guanine is purine, hence the name purine-bases. A purine has 9 atoms that make up the fused rings (5 carbon, 4 nitrogen). The skeleton of cytosine and thymine is pyrimidine, hence pyrimidine-bases. A pyrimidine has 6 atoms (4 carbon, 2 nitrogen). All ring atoms of both purines and pyrimidines lie in the same plane.
BASE PAIRING:
Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hydrogen bonds with C on the opposite strand. dA-dT and dG-dC base pairs are the same length, and occupy the same space within a DNA double helix with uniform diameter. dA-dT and dG-dC base pairs can occur in any order within DNA molecules.
This simplicity is useful when the DNA replicates. The enzyme helicase triggers the unwinding and opening up of the double helix structure. Another enzyme, DNA polymerase, matches up each newly unbonded base with its complementary base. When replication is complete, there are two identical copies of the original DNA molecule. As hydrogen bonds are not covalent, they can be broken and rejoined easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper. This process called melting forms two single-stranded DNA molecules (ssDNA) molecules. Melting occurs at high temperature, low salt and high pH (low pH also melts DNA, but DNA becomes unstable due to acid depurination, so low pH is rarely used.
The stability of the double stranded DNA form depends not only on the GC-content (% GC basepairs) but also on sequence and also length (longer molecules are more stable). Long DNA helices with a high GC-content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands. In the laboratory, the strength of this interaction can be measured by finding the temperature necessary to break the hydrogen bonds or their melting temperature (also called Tm value).
ANALOGUES: The most common application of nucleobase analogues are fluorescent probes. In medicine, they are used as anticancer and antiviral agents.
The information in DNA is stored as a genetic code made up of these four nucleobases. Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same across populations. The order, or sequences, of these bases are the building blocks of an organism.
admin January 17th, 2014
Posted In: Uncategorized
Tags: application of nucleobase, BASE PAIRING, DNA BASES, stability of the double stranded DNA