Category Archives: DNA

KXAN.com

APD releases new stats on cases impacted by DNA lab freezer break KXAN.com The Austin Police DNA lab has been shut down since June, due to a lack of properly trained staff, but a memo obtained by KXAN shows problems with the lab also extend to equipment failure from March 2016. During that time, the maintenance manager ...

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APD releases new stats on cases impacted by DNA lab freezer break - KXAN.com

Picture the scene. A detective is addressing her team:

The DNA test results are in. Were looking for a white male suspect, 3437 years old, born in the summer in a temperate climate. Hes used cocaine in the past. His mother smoked, but he doesnt. He drinks heavily, like his Dad. Were seeing high stress levels, and looking at the air pollution markers, lets start looking downtown, probably near a major intersection.

Science fiction? Yes, for now. But advances in epigenetics the study of reversible chemical modifications to chromosomes that play a role in determining which genes are activated in which cells might soon start making their way out of research labs and into criminal forensics facilities.

Take the idea of the epigenetic clock, one of the ways in which our cells and DNA can betray our age. Epigenetic patterns change throughout our lives, along broadly predictable paths, making it possible to infer age from DNA samples.

Steve Horvath at UCLA has developed a statistical model based on 350 potential epigenetic modification positions in the human genome that can estimate your age to within three and a half years. The rate of epigenetic aging seems to depend somewhat on race, and can be affected by some health conditions, but this kind of test is already at the stage when forensics labs are validating it for use in criminal investigations.

The things we get up to while our epigenetic clocks are ticking can also leave their mark on our DNA. Cigarette smoking correlates with characteristic and persistent epigenetic changes. The same goes for cocaine, opioids and other illicit substances. Theres also some evidence for epigenetic signatures of obesity, traumatic childhood experiences, exposure to tobacco in the womb, season of birth, exposure to environmental pollution, exercise, and possibly even the things our parents and grandparents did before we were born.

There are also ways to detect non-epigenetic evidence of environmental exposures that we all experience For example, international travel or exposure to certain chemicals or experiences can change the composition of the microbiome (the collection of bacteria, viruses and fungi found in and on our bodies). Tests based on these observations might also eventually find their way into forensic science.

Unless theres an urgent need to tell the difference between a pair of identical twins for example if one is suspected of murder none of these tests are likely to appear in court in the immediate future. There needs to be extensive validation before we know if these findings are specific and sensitive enough to be useful. Existing epigenetic analysis methods also use impracticably large samples of blood or tissue, much more than is usually available at a crime scene.

However, these technical challenges will hopefully soon be overcome, and its not too early to start thinking about the legal implications of this type of information. Do we want law enforcement agencies and governments to know the details of our personal and family histories, our vices and habits? Can epigenetic evidence be presented accurately by lawyers, and interpreted appropriately by jurors? Even intelligent people without statistical training can struggle with the concepts of, for example, probabilities in the context of DNA fingerprinting.

And if as a juror youre supposed to decide somebodys guilt or innocence based on evidence of the crime, what bias might be introduced by knowing their epigenetic history or that of the victim?

There are no easy answers, and there is the potential to do great harm if these shiny new technologies are applied inappropriately. Epigenetics is an exciting and fast-moving science; lets hope that the legal and ethical fields can keep up with it.

Cath Ennis book Introducing Epigenetics: A Graphic Guide (with Oliver Pugh) is out now in the UK, and can be pre-ordered for March release elsewhere

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Forensic DNA profiling might be about to take a big leap forward. Are we ready? - The Guardian

New York Post

Police catch suspect after DNA is linked to slain jogger scene New York Post They asked him for a DNA sample, which he gave voluntarily thereby potentially sealing his own fate, sources said. He had no prior record, so until he agreed to a cheek swab, his DNA profile had been unknown to law enforcement, sources told The Post.

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Police catch suspect after DNA is linked to slain jogger scene - New York Post

Alan Shearer feels this Arsenal team is unrecognisable from the ones Arsene Wenger used to produce.

Wenger's first 10 years in north London saw Arsenal win three Premier League titles, four FA Cups and reach the Champions League final. The second decade, however, has brought just two FA Cups.

The Gunners finished second in the table last season and were billed as potential challengers in 2016/17, but their 3-1 hammering at the hands of Chelsea on Saturday means they are now 12 points behind the league leaders.

Their defeat at Stamford Bridge was characterised by a lack of fight they seemed to give up after conceding the first goal and Shearer feels this current crop is the one of Arsenal's "softest" ever sides.

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"Arsene Wenger remains, yet the Arsenal DNA he had between 1997 and 2005 has been totally lost over the last decade," Shearer wrote in his column for The Sun.

"That is what frustrates the fans, that a manager who gave them so much and put out such great teams can now be in charge of one of the softest sides in the clubs history.

"One that rolls over when the going gets tough.

"One that raises hopes one week and shatters them the next. A side that cant compete over a season. Players who simply dont work hard enough to match Watford and more starkly Chelsea, who simply bullied them off the park."

Speaking after the game, Wenger said: Im not subdued. Im disappointed and angry because we lost a very big game. But Im not subdued. The result is there and we certainly have a big wait in the race for the championship.

We have shown in the past that we can recover from that. That defeat against Watford had bigger consequences, maybe, than expected.

We lacked a little bit what makes our game efficient. In the final third we didnt look dangerous enough. That was difficult to watch from upstairs.

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Alan Shearer: Arsenal's DNA has changed - they roll over when the going gets tough - Mirror.co.uk

In a remote corner of eastern Russia, where long winters bring temperatures that rarely flicker above freezing, the genetic legacy of ancient hunter-gatherers endures.

DNA from the 7,700-year-old remains of two women is surprisingly similar to that of people living in that area today, researchers report February 1 in Science Advances. That finding suggests that at least some people in East Asia havent changed much over the last 8,000 years or so a time when other parts of the world saw waves of migrants settle in.

The continuity is remarkable, says paleogeneticist Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona, who was not involved with the work. Its a big contrast to what has been found in Europe.

In Western Europe especially, scientists studying ancient DNA have put together a picture of flux, says study coauthor Andrea Manica. Every few thousand years, there are major turnovers of people. Around 8,000 years ago, he says, migrating farmers replaced hunter-gatherers in the area. And a few thousand years after that, Bronze Age migrants from Central Asia swept in.

In DNA collected from the bones and teeth of these ancient peoples, scientists can spot genetic signatures of different populations. When a population of farmers balloons Lalueza-Fox says, the signatures of hunter-gatherers are mostly erased.

But whether thats true across the globe is unclear, says Manica, of the University of Cambridge. We wanted to see what happened in other places. Asia is huge compared to Europe, and its been neglected.

Story continues after graphic

A genetic analysis of 561 people living in populations across Asia today (colors represent different regions) reveals that two ancient women (black triangles, left) from Devils Gate Cave in Russia (see black triangle on map, right) had genomes similar to the Ulchi, a modern group of hunter-fishers.

Manicas team collected DNA from the skeletons of five ancient people found in a cave called Devils Gate. The cave rests in a far east finger of Russia, tucked along the border of China and North Korea, and holds human remains, scraps of textiles and bits of broken pottery.

Researchers gathered enough DNA from two of the people to piece together about 6 percent of the genome, the complete set of genetic instructions inside a cells nucleus. Thats not much, Manica says, but its enough to compare the Devils Gate denizens with other people. The researchers analyzed the genomes of people strewn across the far reaches of the continent from the Dolgan in Siberia to the Thai thousands of kilometers south.

Genetically, the 7,700-year-old women closely resembled the Ulchi, a small group of hunter-fishers who still live off the land today. Manica cant say whether the Ulchi are direct descendants of the two Devils Gate women, or just closely related. But the find suggests a pocket of stability in East Asia a place where hunter-gatherers werent swept out by, or folded into, booming groups of farmers.

Perhaps farming didnt take off there because the cold climate wasnt good for growing crops, Manica says. Or maybe the ideas and technologies from farmers and other migrants made it to the Ulchi without an accompanying influx of people. (The Ulchi arent like primitive hunter-gatherers of the past. They farm a bit, and have adopted new ways to fish, hunt and store food, he points out.)

This shows that ideas can travel without people moving with them, Manica says.

That makes sense, Lalueza-Fox says. But scientists now need more data additional samples from East Asia, and Southeast Asia, too, he says. I have a feeling the whole story will be much more complicated.

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DNA points to millennia of stability in East Asian hunter-fisher population - Science News

Judy Rybak is a 48 Hours producer. She investigated the questionable convictions of Darryl Pinkins and Roosevelt Glenn for the episode, Guilty Until Proven Innocent. Watch the full episode online.

About three years ago, I was on Twitter when I spotted a cry for help from DNA expert and director of the Idaho Innocence Project, Greg Hampikian. He tweeted that his Innocence Project had more cases of wrongful conviction than the money he needed to investigate them. Wondering if he had any cases that might be appropriate for 48 Hours, I called immediately.

There was one case, said Hampikian, but it was not in Idaho. It was in Indiana and was, according to him, one of the most egregious cases he had ever come across. Hampikian is a highly respected scientist who has worked on many high-profile wrongful convictions, including Amanda Knox.

Darryl Pinkins, left, and Roosevelt Glenn

He had my attention.

Darryl Pinkins and Roosevelt Glenn were serving time for a brutal 1989 gang rape in Hammond, Indiana. This despite the fact that long before their trials, both men were excluded from the DNA. The state had successfully argued that because the DNA in this case was a mixture of five rapists, the test results could be not trusted.

Outrageous, said Hampikian, who had been working for years to help convince the authorities that science does not lie. It is a complicated case, said Hampikian, so convoluted that the media had stayed away.

Complicated and convoluted is what we at 48 Hours do best, I told him.

A month later, I was in a rental car on a long stretch of Indiana highway, in the middle of a blizzard, heading to the Miami Correctional Facility to meet Darryl Pinkins for the first time. I had already read several key documents in the case and met with the defense team: Indiana University Law Professor, Fran Watson and some of the law students who had participated in her wrongful conviction clinic.

Believing I was prepared to meet Darryl and discuss his case, I emptied my pockets and went through the metal detectors, as I had dozens of times in dozens of prisons. It took me just moments to realize that this time was different. I was actually not fully prepared. I had not anticipated how much Darryl Pinkins would move and impress me.

Despite his clear and seething anger, and deep sadness, he was gentle and kind. He wanted me to know all that he had accomplished while in prison for over two decades: Earning a Bachelors Degree, studying Native American Spirituality, becoming a certified Suicide Prevention Companion, learning Tae Kwon Do and becoming fluent in braille.

From the prison, I drove several hours to Gary, Indiana, where I met Roosevelt Glenn and his family. After fighting for 16 years to have his conviction overturned, the state paroled Glenn in 2007 for good behavior and forced him to register as a sex offender.

Our meeting took place in his mothers home, where several of his supporters joined us. Among them were Roosevelts sister, Renitta, and their pastor, who both desperately wanted me to know that Roosevelt is a good man.

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Darryl Pinkins was convicted of a 1989 brutal rape. Correspondent Maureen Maher speaks with his mother and sisters who say he's been wrongfully i...

Like Darryl, Roosevelt was warm, welcoming, kind, gentle and open. He told me how he had survived all those years behind bars, and explained how he was able to forgive those who he claimed wrongly convicted him.

I did not see a rapistbut I wasnt sure what to think. I left Indiana that night committed to digging in to this case. If what I was hearing was true and, more importantly, there was DNA evidence that substantiated their claims, two innocent men were paying a steep price for a serious injustice.

Three years later, there was a break in the case and 48 Hours was there to cover it. A new DNA technology called True Allele-developed specifically to test DNA mixtures-was used in this case, and the explosive findings were about to be presented in a court hearing.

Just weeks before the hearing, Maureen Maher was interviewing Darryl Pinkins mother and sisters for our report, when they all declared that for the first time in a long time they were hopeful that Darryl would soon be free.

Why this time? asked Maureen.

Judy, said Tracy Pinkins.

I was standing behind the cameras when I heard my name, and felt my face heat up.

I went and Googled Judy. Printed everything out, called my family, I was like, Theyre listening. This is the media. They are actually listening, Tracy Pinkins said. Thats when I got my hope.

No one was sure what would happen next. The District Attorneys office had been fighting to keep Darryl behind bars for nearly a quarter century. Professor Watson was worried the prosecutor would challenge the results of the True Allele tests, and keep Darryl in prison while they argued their validity.

Then, just days before the hearing, Lake County D.A. Bernard Carter shocked everyone.

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Family and friends fought and waited almost 25 years to see Pinkins walk out of a prison a free man. After groundbreaking DNA technology helped c...

It was Thursday night and I was sitting at my desk preparing for the hearing on Monday, when I got the call from Professor Watson that Carter had decided there was no need for a hearing. Carter told the judge that the new DNA evidence is clear, and Darryl Pinkins is an innocent man.

The very next morning, Darryl was scheduled to be released. While my team scrambled to change our flight reservations and find a local camera crew in Indiana to cover us until we arrived, I was given the gift of a lifetime.

With Fran Watsons very kind and generous permission, I called Darryls family and Roosevelt Glenn to deliver the news. Being a great producer, Maureen Maher made sure I had someone on the other end videotape the calls for our report.

Its over, I said, and told them that Darryl would soon be free.

The sounds I heard next will forever echo in my head: A sister shouting with joy a mother releasing 25 years of anguish and a strong, proud man (soon to be declared innocent himself) openly weeping.

One tweet and three years later, a man walked free and 48 Hours was there to see it. We were also there when Lake County Prosecutor, Bernard Carter, shook Darryl Pinkins hand, and admitted that mistakes had been made in this caseand thanks to True Allele, justice was served.

The cases of Darryl Pinkins and Roosevelt Glenn were the first wrongful convictions overturned by a new DNA technology, and 48 Hours was there to witness it.

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Could DNA unlock answers in questionable conviction case? - CBS News

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living things.

All known cellular life and some viruses contain DNA.

The main role of DNA in the cell is the long-term storage of information.

It is often compared to a blueprint, since it contains the instructions to construct other components of the cell, such as proteins and RNA molecules.

The DNA segments that carry genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the expression of genetic information.

In eukaryotes such as animals and plants, DNA is stored inside the cell nucleus, while in prokaryotes such as bacteria and archaea, the DNA is in the cell's cytoplasm.

Unlike enzymes, DNA does not act directly on other molecules; rather, various enzymes act on DNA and copy its information into either more DNA, in DNA replication, or transcribe it into protein.

Other proteins such as histones are involved in the packaging of DNA or repairing the damage to DNA that causes mutations.

DNA is a long polymer of simple units called nucleotides, which are held together by a backbone made of sugars and phosphate groups.

This backbone carries four types of molecules called bases and it is the sequence of these four bases that encodes information.

The major function of DNA is to encode the sequence of amino acid residues in proteins, using the genetic code.

To read the genetic code, cells make a copy of a stretch of DNA in the nucleic acid RNA.

These RNA copies can then used to direct protein synthesis, but they can also be used directly as parts of ribosomes or spliceosomes.

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DNA - ScienceDaily

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance. DNA is made up of a double helix of two complementary strands. During replication, these strands are separated. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.[1][2]

In a cell, DNA replication begins at specific locations, or origins of replication, in the genome.[3] Unwinding of DNA at the origin and synthesis of new strands results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. DNA replication occurs during the S-stage of interphase.

DNA replication can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. The polymerase chain reaction (PCR), a common laboratory technique, cyclically applies such artificial synthesis to amplify a specific target DNA fragment from a pool of DNA.

DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides. Nucleotides in DNA contain a deoxyribose sugar, a phosphate, and a nucleobase. The four types of nucleotide correspond to the four nucleobases adenine, cytosine, guanine, and thymine, commonly abbreviated as A,C, G and T. Adenine and guanine are purine bases, while cytosine and thymine are pyrimidines. These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the nuclei bases pointing inward (i.e., toward the opposing strand). Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine (two hydrogen bonds), and guanine pairs with cytosine (stronger: three hydrogen bonds).

DNA strands have a directionality, and the different ends of a single strand are called the "3' (three-prime) end" and the "5' (five-prime) end". By convention, if the base sequence of a single strand of DNA is given, the left end of the sequence is the 5' end, while the right end of the sequence is the 3' end. The strands of the double helix are anti-parallel with one being 5' to 3', and the opposite strand 3' to 5'. These terms refer to the carbon atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3' end of a DNA strand.

The pairing of complementary bases in DNA (through hydrogen bonding) means that the information contained within each strand is redundant. Phosphodiester (intra-strand) bonds are stronger than hydrogen (inter-strand) bonds. This allows the strands to be separated from one another. The nucleotides on a single strand can therefore be used to reconstruct nucleotides on a newly synthesized partner strand.[4]

DNA polymerases are a family of enzymes that carry out all forms of DNA replication.[6] DNA polymerases in general cannot initiate synthesis of new strands, but can only extend an existing DNA or RNA strand paired with a template strand. To begin synthesis, a short fragment of RNA, called a primer, must be created and paired with the template DNA strand.

DNA polymerase adds a new strand of DNA by extending the 3' end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds. The energy for this process of DNA polymerization comes from hydrolysis of the high-energy phosphate (phosphoanhydride) bonds between the three phosphates attached to each unincorporated base. Free bases with their attached phosphate groups are called nucleotides; in particular, bases with three attached phosphate groups are called nucleoside triphosphates. When a nucleotide is being added to a growing DNA strand, the formation of a phosphodiester bond between the proximal phosphate of the nucleotide to the growing chain is accompanied by hydrolysis of a high-energy phosphate bond with release of the two distal phosphates as a pyrophosphate. Enzymatic hydrolysis of the resulting pyrophosphate into inorganic phosphate consumes a second high-energy phosphate bond and renders the reaction effectively irreversible.[Note 1]

In general, DNA polymerases are highly accurate, with an intrinsic error rate of less than one mistake for every 107 nucleotides added.[7] In addition, some DNA polymerases also have proofreading ability; they can remove nucleotides from the end of a growing strand in order to correct mismatched bases. Finally, post-replication mismatch repair mechanisms monitor the DNA for errors, being capable of distinguishing mismatches in the newly synthesized DNA strand from the original strand sequence. Together, these three discrimination steps enable replication fidelity of less than one mistake for every 109 nucleotides added.[7]

The rate of DNA replication in a living cell was first measured as the rate of phage T4 DNA elongation in phage-infected E. coli.[8] During the period of exponential DNA increase at 37C, the rate was 749 nucleotides per second. The mutation rate per base pair per replication during phage T4 DNA synthesis is 1.7 per 108.[9]

DNA replication, like all biological polymerization processes, proceeds in three enzymatically catalyzed and coordinated steps: initiation, elongation and termination.

For a cell to divide, it must first replicate its DNA.[10] This process is initiated at particular points in the DNA, known as "origins", which are targeted by initiator proteins.[3] In E. coli this protein is DnaA; in yeast, this is the origin recognition complex.[11] Sequences used by initiator proteins tend to be "AT-rich" (rich in adenine and thymine bases), because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair) and thus are easier to strand separate.[12] Once the origin has been located, these initiators recruit other proteins and form the pre-replication complex, which unzips the double-stranded DNA.

DNA polymerase has 5'-3' activity. All known DNA replication systems require a free 3' hydroxyl group before synthesis can be initiated (note: the DNA template is read in 3' to 5' direction whereas a new strand is synthesized in the 5' to 3' directionthis is often confused). Four distinct mechanisms for DNA synthesis are recognized:

The first is the best known of these mechanisms and is used by the cellular organisms. In this mechanism, once the two strands are separated, primase adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand is continuously extended from the primer by a DNA polymerase with high processivity, while the lagging strand is extended discontinuously from each primer forming Okazaki fragments. RNase removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on the lagging strand can be found. Ligase works to fill these nicks in, thus completing the newly replicated DNA molecule.

The primase used in this process differs significantly between bacteria and archaea/eukaryotes. Bacteria use a primase belonging to the DnaG protein superfamily which contains a catalytic domain of the TOPRIM fold type.[13] The TOPRIM fold contains an / core with four conserved strands in a Rossmann-like topology. This structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein.

The primase used by archaea and eukaryotes, in contrast, contains a highly derived version of the RNA recognition motif (RRM). This primase is structurally similar to many viral RNA-dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of the A/B/Y families that are involved in DNA replication and repair. In eukaryotic replication, the primase forms a complex with Pol .[14]

Multiple DNA polymerases take on different roles in the DNA replication process. In E. coli, DNA Pol III is the polymerase enzyme primarily responsible for DNA replication. It assembles into a replication complex at the replication fork that exhibits extremely high processivity, remaining intact for the entire replication cycle. In contrast, DNA Pol I is the enzyme responsible for replacing RNA primers with DNA. DNA Pol I has a 5' to 3' exonuclease activity in addition to its polymerase activity, and uses its exonuclease activity to degrade the RNA primers ahead of it as it extends the DNA strand behind it, in a process called nick translation. Pol I is much less processive than Pol III because its primary function in DNA replication is to create many short DNA regions rather than a few very long regions.

In eukaryotes, the low-processivity enzyme, Pol , helps to initiate replication because it forms a complex with primase.[15] In eukaryotes, leading strand synthesis is thought to be conducted by Pol ; however, this view has recently been challenged, suggesting a role for Pol .[16] Primer removal is completed Pol [17] while repair of DNA during replication is completed by Pol .

As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming a replication fork with two prongs. In bacteria, which have a single origin of replication on their circular chromosome, this process creates a "theta structure" (resembling the Greek letter theta: ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these.>[18]

The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching "prongs", each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands, which will be created as DNA polymerase matches complementary nucleotides to the templates; the templates may be properly referred to as the leading strand template and the lagging strand template.

DNA is always synthesized in the 5' to 3' direction. Since the leading and lagging strand templates are oriented in opposite directions at the replication fork, a major issue is how to achieve synthesis of nascent (new) lagging strand DNA, whose direction of synthesis is opposite to the direction of the growing replication fork.

The leading strand is the strand of nascent DNA which is being synthesized in the same direction as the growing replication fork. A polymerase "reads" the leading strand template and adds complementary nucleotides to the nascent leading strand on a continuous basis.

The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading strand. As a consequence, the DNA polymerase on this strand is seen to "lag behind" the other strand.

The lagging strand is synthesized in short, separated segments. On the lagging strand template, a primase "reads" the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined together by DNA ligase.

As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead.[19] This build-up forms a torsional resistance that would eventually halt the progress of the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix; topoisomerases (including DNA gyrase) achieve this by adding negative supercoils to the DNA helix.[20]

Bare single-stranded DNA tends to fold back on itself forming secondary structures; these structures can interfere with the movement of DNA polymerase. To prevent this, single-strand binding proteins bind to the DNA until a second strand is synthesized, preventing secondary structure formation.[21]

Clamp proteins form a sliding clamp around DNA, helping the DNA polymerase maintain contact with its template, thereby assisting with processivity. The inner face of the clamp enables DNA to be threaded through it. Once the polymerase reaches the end of the template or detects double-stranded DNA, the sliding clamp undergoes a conformational change that releases the DNA polymerase. Clamp-loading proteins are used to initially load the clamp, recognizing the junction between template and RNA primers.[2]:274-5

At the replication fork, many replication enzymes assemble on the DNA into a complex molecular machine called the replisome. The following is a list of major DNA replication enzymes that participate in the replisome:[22]

Replication machineries consist of factors involved in DNA replication and appearing on template ssDNAs. Replication machineries include primosotors are replication enzymes; DNA polymerase, DNA helicases, DNA clamps and DNA topoisomerases, and replication proteins; e.g. single-stranded DNA binding proteins (SSB). In the replication machineries these components coordinate. In most of the bacteria, all of the factors involved in DNA replication are located on replication forks and the complexes stay on the forks during DNA replication. These replication machineries are called replisomes or DNA replicase systems. These terms are generic terms for proteins located on replication forks. In eukaryotic and some bacterial cells the replisomes are not formed.

Since replication machineries do not move relatively to template DNAs such as factories, they are called a replication factory.[24] In an alternative figure, DNA factories are similar to projectors and DNAs are like as cinematic films passing constantly into the projectors. In the replication factory model, after both DNA helicases for leading strands and lagging strands are loaded on the template DNAs, the helicases run along the DNAs into each other. The helicases remain associated for the remainder of replication process. Peter Meister et al. observed directly replication sites in budding yeast by monitoring green fluorescent protein(GFP)-tagged DNA polymerases . They detected DNA replication of pairs of the tagged loci spaced apart symmetrically from a replication origin and found that the distance between the pairs decreased markedly by time.[25] This finding suggests that the mechanism of DNA replication goes with DNA factories. That is, couples of replication factories are loaded on replication origins and the factories associated with each other. Also, template DNAs move into the factories, which bring extrusion of the template ssDNAs and nascent DNAs. Meisters finding is the first direct evidence of replication factory model. Subsequent research has shown that DNA helicases form dimers in many eukaryotic cells and bacterial replication machineries stay in single intranuclear location during DNA synthesis.[24]

The replication factories perform disentanglement of sister chromatids. The disentanglement is essential for distributing the chromatids into daughter cells after DNA replication. Because sister chromatids after DNA replication hold each other by Cohesin rings, there is the only chance for the disentanglement in DNA replication. Fixing of replication machineries as replication factories can improve the success rate of DNA replication. If replication forks move freely in chromosomes, catenation of nuclei is aggravated and impedes mitotic segregation.[25]

Eukaryotes initiate DNA replication at multiple points in the chromosome, so replication forks meet and terminate at many points in the chromosome; these are not known to be regulated in any particular way. Because eukaryotes have linear chromosomes, DNA replication is unable to reach the very end of the chromosomes, but ends at the telomere region of repetitive DNA close to the ends. This shortens the telomere of the daughter DNA strand. Shortening of the telomeres is a normal process in somatic cells. As a result, cells can only divide a certain number of times before the DNA loss prevents further division. (This is known as the Hayflick limit.) Within the germ cell line, which passes DNA to the next generation, telomerase extends the repetitive sequences of the telomere region to prevent degradation. Telomerase can become mistakenly active in somatic cells, sometimes leading to cancer formation. Increased telomerase activity is one of the hallmarks of cancer.

Termination requires that the progress of the DNA replication fork must stop or be blocked. Termination at a specific locus, when it occurs, involves the interaction between two components: (1) a termination site sequence in the DNA, and (2) a protein which binds to this sequence to physically stop DNA replication. In various bacterial species, this is named the DNA replication terminus site-binding protein, or Ter protein.

Because bacteria have circular chromosomes, termination of replication occurs when the two replication forks meet each other on the opposite end of the parental chromosome. E. coli regulates this process through the use of termination sequences that, when bound by the Tus protein, enable only one direction of replication fork to pass through. As a result, the replication forks are constrained to always meet within the termination region of the chromosome.[26]

Within eukaryotes, DNA replication is controlled within the context of the cell cycle. As the cell grows and divides, it progresses through stages in the cell cycle; DNA replication takes place during the S phase (synthesis phase). The progress of the eukaryotic cell through the cycle is controlled by cell cycle checkpoints. Progression through checkpoints is controlled through complex interactions between various proteins, including cyclins and cyclin-dependent kinases.[27] Unlike bacteria, eukaryotic DNA replicates in the confines of the nucleus.[28]

The G1/S checkpoint (or restriction checkpoint) regulates whether eukaryotic cells enter the process of DNA replication and subsequent division. Cells that do not proceed through this checkpoint remain in the G0 stage and do not replicate their DNA.

Replication of chloroplast and mitochondrial genomes occurs independently of the cell cycle, through the process of D-loop replication.

In vertebrate cells, replication sites concentrate into positions called replication foci.[25] Replication sites can be detected by immunostaining daughter strands and replication enzymes and monitoring GFP-tagged replication factors. By these methods it is found that replication foci of varying size and positions appear in S phase of cell division and their number per nucleus is far smaller than the number of genomic replication forks.

P. Heun et al.(2001) tracked GFP-tagged replication foci in budding yeast cells and revealed that replication origins move constantly in G1 and S phase and the dynamics decreased significantly in S phase.[25] Traditionally, replication sites were fixed on spatial structure of chromosomes by nuclear matrix or lamins. The Heuns results denied the traditional concepts, budding yeasts don't have lamins, and support that replication origins self-assemble and form replication foci.

By firing of replication origins, controlled spatially and temporally, the formation of replication foci is regulated. D. A. Jackson et al.(1998) revealed that neighboring origins fire simultaneously in mammalian cells.[25] Spatial juxtaposition of replication sites brings clustering of replication forks. The clustering do rescue of stalled replication forks and favors normal progress of replication forks. Progress of replication forks is inhibited by many factors; collision with proteins or with complexes binding strongly on DNA, deficiency of dNTPs, nicks on template DNAs and so on. If replication forks stall and the remaining sequences from the stalled forks are not replicated, the daughter strands have nick obtained un-replicated sites. The un-replicated sites on one parent's strand hold the other strand together but not daughter strands. Therefore, the resulting sister chromatids cannot separate from each other and cannot divide into 2 daughter cells. When neighboring origins fire and a fork from one origin is stalled, fork from other origin access on an opposite direction of the stalled fork and duplicate the un-replicated sites. As other mechanism of the rescue there is application of dormant replication origins that excess origins don't fire in normal DNA replication.

Most bacteria do not go through a well-defined cell cycle but instead continuously copy their DNA; during rapid growth, this can result in the concurrent occurrence of multiple rounds of replication.[29] In E. coli, the best-characterized bacteria, DNA replication is regulated through several mechanisms, including: the hemimethylation and sequestering of the origin sequence, the ratio of adenosine triphosphate (ATP) to adenosine diphosphate (ADP), and the levels of protein DnaA. All these control the binding of initiator proteins to the origin sequences.

Because E. coli methylates GATC DNA sequences, DNA synthesis results in hemimethylated sequences. This hemimethylated DNA is recognized by the protein SeqA, which binds and sequesters the origin sequence; in addition, DnaA (required for initiation of replication) binds less well to hemimethylated DNA. As a result, newly replicated origins are prevented from immediately initiating another round of DNA replication.[30]

ATP builds up when the cell is in a rich medium, triggering DNA replication once the cell has reached a specific size. ATP competes with ADP to bind to DnaA, and the DnaA-ATP complex is able to initiate replication. A certain number of DnaA proteins are also required for DNA replication each time the origin is copied, the number of binding sites for DnaA doubles, requiring the synthesis of more DnaA to enable another initiation of replication.

Researchers commonly replicate DNA in vitro using the polymerase chain reaction (PCR). PCR uses a pair of primers to span a target region in template DNA, and then polymerizes partner strands in each direction from these primers using a thermostable DNA polymerase. Repeating this process through multiple cycles amplifies the targeted DNA region. At the start of each cycle, the mixture of template and primers is heated, separating the newly synthesized molecule and template. Then, as the mixture cools, both of these become templates for annealing of new primers, and the polymerase extends from these. As a result, the number of copies of the target region doubles each round, increasing exponentially.[31]

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DNA replication - Wikipedia

But don't expect it to lead to an arrest in the 20-year-old JonBenet Ramsey case in the near future.

The Colorado Bureau of investigation is opening a new DNA testing facility in 2017 and will next year use new technology in the JonBenet case -- as well as other cold cases.

Boulder County District Attorney Stan Garnett told CNN's Jean Casarez that he expects the DNA testing results will be "not significant and not a big deal."

Garnett stressed the JonBenet investigation is much more than a DNA case. Any new results will only be significant if they can be matched with other evidence authorities already have.

As he told CNN affiliate KMGH: "To ever have a prosecutable case, we have to have several different pieces of evidence come together."

Garnett told CNN that his office along with the Boulder Police Department meets periodically with the Colorado Bureau of Investigation as they continue to keep up with the changes in DNA testing.

The district attorney said he isn't sure whether they will use DNA from pieces of evidence or only re-test results they already have.

Boulder police officials said they will only have comments if there is new information to be announced.

JonBenet's body was found in on December 26, 1996, in the basement of the family's home in Boulder, hours after her mother discovered a handwritten, three-page ransom note.

JonBenet was found with a garrote fashioned out of rope embedded deep into her neck. The same rope was around one of her wrists. At the end of the garrote was a broken paintbrush that appeared to be from the art set of her mother Patsy Ramsey.

Her father, John Ramsey, said he removed duct tape from her mouth when he found his 6-year-old girl.

Two years after JonBenet's killing, with the case not close to being solved, Boulder's district attorney convened a grand jury in 1998.

At the conclusion of the proceedings 13 months later, then-Boulder County District Attorney Alex Hunter convened a press conference broadcast live nationwide.

Hunter announced there would be no charges in the death of JonBenet. In an interesting twist, the Boulder Daily Camera reported in January 2013 that the grand jury had voted to indict the Ramseys, neither of whom were ever charged.

In 2008 there were new forensic findings. Unknown male DNA had been found on the waistband of JonBenet's long johns. Earlier tests had found unknown male DNA on the crotch of her underwear. The two samples matched or "were consistent" with each other, according to testing done by forensic scientist Dr. Angela Williamson.

That DNA finding led Mary Lacy, the Boulder district attorney at the time, to make one of the most controversial decisions in the case.

She issued an apology to John and Patsy Ramsey, at the same time saying they were exonerated of any criminal wrongdoing in the death of their daughter.

Garnett, although respecting his predecessor, has told CNN, "I disagreed that an exoneration on the state of that evidence at that time was appropriate."

No one has ever been charged in the case. An American teacher in Thailand who confessed in 2006 to JonBenet's killing was brought to Boulder, but John Mark Karr's DNA didn't match the unidentified male DNA he ultimately was released.

Patsy Ramsey died of cancer in 2006. John Ramsey remarried and lives in the western United States.

CNN's Elise Zeiger contributed to this report.

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JonBenet Ramsey case: New DNA testing planned - CNN.com

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a persons body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people. The order, or sequence, of these bases determines the information available for building and maintaining an organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.

DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar, and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladders rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.

An important property of DNA is that it can replicate, or make copies of itself. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. This is critical when cells divide because each new cell needs to have an exact copy of the DNA present in the old cell.

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What is DNA? - Genetics Home Reference