Leaders in Pharmaceutical Business Intelligence (LPBI) Group

A Primer on DNA and DNA Replication

Reporter and Curator: Larry H. Bernstein, MD, FCAP 

 

 

This is the FIRST discussion of a several part series leading from the genome, to protein synthesis (1), posttranslational modification of proteins (2), examples of protein effects on metabolism and signaling pathways (3), and leading to disruption of signaling pathways in disease (4), and effects leading to mutagenesis.

1.  A Primer on DNAand DNA Replication

• http://pharmaceuticalintelligence.com/2014-28-07/A_Primer_on_DNA_and_DNA_Replication

 

 

 

 

 

 

 

 

 

 

 

 

 

 

2. Overview of translational medicine

• http://pharmaceuticalintelligence.com/2014-07-28/larryhbern/overview-of-posttranslational-medicine

3. Genes, proteomes, and their interaction

•  http://pharmaceuticalintelligence.com/7/17/2014/Genes, proteomes, and their interaction

4. Regulation of somatic stem cell Function

•  http://pharmaceuticalintelligence.com/2013-01-23/larryhbern/Regulation-of-somatic-stem-cell-function/

5.  Proteomics – The Pathway to Understanding and Decision-making in Medicine

• http://pharmaceuticalintelligence.com/2014/06/24/proteomics-the-pathway-to-understanding-and-decision-making-in-medicine/

6.  Genomics, Proteomics and standards

• http://pharmaceuticalintelligence.com/2014/07/06/genomics-proteomics-and-standards/

7.  Long Non-coding RNAs Can Encode Proteins After All

• http://pharmaceuticalintelligence.com/2014/06/29/long-non-coding-rnas-can-encode-proteins-after-all/
• 3:15 – 3:45, 2014, Laurie Boyer “Long non-coding RNAs: molecular regulators of cell fate”; http://pharmaceuticalintelligence.com/2014/06/04/koch-institute-for-integrative-cancer-research-mit-summer-symposium-2014-rna-biology-cancer-and-therapeutic-implications-june-13-2014-830am-430pm-kresge-auditorium-mit/

8.  Proteins and cellular adaptation to stress

• http://pharmaceuticalintelligence.com/2014/07/08/proteins-and-cellular-adaptation-to-stress/

9.  Loss of normal growth regulation

• http://pharmaceuticalintelligence.com/2014/07/06/loss-of-normal-growth-regulation/

 

 

A Primer on DNA and DNA Replication

 

DNA Replication

DNA carries the information for making all of the cell’s proteins. These pro­teins implement all of the functions of a living organism and determine the organism’­s characteristics. When the cell reproduces, it has to pass all of this information on to the daughter cells.

Before a cell can reproduce, it must first replicate, or make a copy of, its DNA. Where DNA replication occurs depends upon whether the cells is a prokaryote or a eukaryote (see the RNA sidebar on the previous page for more about the types of cells). DNA replication occurs in the cytoplasm of prokaryotes and in the nucleus of eukaryotes. Regardless of where DNA replication occurs, the basic process is the same.

The structure of DNA lends itself easily to DNA replication. Each side of the double helix runs in opposite (anti-parallel) directions. The beauty of this structure is that it can unzip down the middle and each side can serve as a pattern or template for the other side (called semi-conservative replication). However, DNA does not unzip entirely. It unzips in a small area called a replication fork, which then moves down the entire length of the molecule.

Eukaryotic DNA replication (Wikipedia), is a conserved mechanism that restricts DNA replication to only once per cell cycle. Eukaryotic DNA replication of chromosomal DNA is central for the duplication of a cell and is necessary for the maintenance of the eukaryotic genome.

DNA replication is the action of DNA polymerases synthesizing a DNA strand complementary to the original template strand. To synthesize DNA, the double-stranded DNA is unwound by DNA helicases ahead of polymerases, forming a replication fork containing two single-stranded templates.

Replication processes permit the copying of a single DNA double helix into two DNA helices, which are divided into the daughter cells at mitosis. The major enzymatic functions carried out at the replication fork are well conserved from prokaryotes to eukaryotes, but the replication machinery in eukaryotic DNA replication is a much larger complex, coordinating many proteins at the site of replication, forming the replisome.^[1]

The replisome is responsible for copying the entirety of genomic DNA in each proliferative cell. This process allows for the high-fidelity passage of hereditary/genetic information from parental cell to daughter cell and is thus essential to all organisms. Much of the cell cycle is built around ensuring that DNA replication occurs without errors.^[1]

In G₁ phase of the cell cycle, many of the DNA replication regulatory processes are initiated. In eukaryotes, the vast majority of DNA synthesis occurs during S phase of the cell cycle, and the entire genome must be unwound and duplicated to form two daughter copies. During G₂, any damaged DNA or replication errors are corrected. Finally, one copy of the genomes is segregated to each daughter cell at mitosis or M phase.^[2] These daughter copies each contain one strand from the parental duplex DNA and one nascent antiparallel strand.

This mechanism is conserved from prokaryotes to eukaryotes and is known as semiconservative DNA replication. The process of semiconservative replication for the site of DNA replication is a fork-like DNA structure, the replication fork, where the DNA helix is open, or unwound, exposing unpaired DNA nucleotides for recognition and base pairing for the incorporation of free nucleotides into double-stranded DNA.^[3]

 

Let’s look at the details:

1. An enzyme called DNA gyrase makes a nick in the double helix and each side separates
2. An enzyme called helicase unwinds the double-stranded DNA
3. Several small proteins called single strand binding proteins(SSB) temporarily bind to each side and keep them separated
4. An enzyme complex called DNA polymerase“walks” down the DNA strands and adds new nucleotides to each strand. The nucleotides pair with the complementary nucleotides on the existing stand (A with T, G with C).
5. A subunit of the DNA polymerase proofreads the new DNA
6. An enzyme called DNA ligaseseals up the fragments into one long continuous strand
7. The new copies automatically wind up again

Different types of cells replicated their DNA at different rates. Some cells constantly divide, like those in your hair and fingernails and bone marrow cells. Other cells go through several rounds of cell division and stop (including specialized cells, like those in your brain, muscle and heart). Finally, some cells stop dividing, but can be induced to divide to repair injury (such as skin cells and liver cells). In cells that do not constantly divide, the cues for DNA replication/cell division come in the form of chemicals. These chemicals can come from other parts of the body (hormones) or from the environment.

 

 

 

 

 

 

Diagram of the formation of the pre-replicative complex transforming into an active replisome. Mcm 2-7 complex loads onto DNA at replication origins during G1 and unwinds DNA ahead of replicative polymerases.Cdc6 and Cdt1 bring Mcm complexes to replication origins. CDK/DDK-dependent phosphorylation of pre-replicative proteins leads toreplisome assembly and origin firing. Cdc6 and Cdt1 are no longer required and are removed from the nucleus or degraded. Mcms and associated proteins, GINS and Cdc45, unwind DNA to expose template DNA. At this point replisome assembly is completed and replication is initiated. “P” represents phosphorylation.

 

Minichromosome Maintenance Protein Complex[edit]

Main article: Minichromosome maintenance

The assembly of the minichromosome maintenance (Mcm) proteins function together as a complex in the cell. The assembly of the Mcm proteins onto chromatin requires the coordinated function of the Origin Recognition Complex (ORC), Cdc6, and Cdt1.^[18] Once the Mcm proteins have been loaded onto the chromatin, ORC and Cdc6 can be removed from the chromatin without preventing subsequent DNA replication. This suggests that the primary role of the pre-replication complex is to correctly load the Mcm proteins.^[19]

The Mcm proteins support roles both in the initiation and elongation steps of DNA synthesis.^[20] Each Mcm protein is highly related to all others, but unique sequences distinguishing each of the subunit types are conserved across eukaryotes. All eukaryotes have exactly six Mcm protein analogs that each fall into one of the existing classes (Mcm2-7), which suggests that each Mcm protein has a unique and important function.^[21]

Minichromosome maintenance proteins have been found to be required for DNA helicase activity and inactivation of any of the six Mcm proteins prevents further progression of the replication fork. This is consistent with the requirement of ORC, Cdc6, and Cdt1 function to assemble the Mcm proteins at the origin of replication.^[22] The complex containing all six Mcm proteins creates a hexameric, doughnut like structure with a central cavity.^[23] The helicase activity of the Mcm protein complex raises the question of how the ring-like complex is loaded onto the single-stranded DNA. One possibility is that the helicase activity of the Mcm protein complex can oscillate between an open and a closed ring formation to allow single-stranded DNA loading.^[6]

Along with the minichromosome maintenance protein complex helicase activity, the complex also has associated ATPase activity.^[24] A mutation in any one of the six Mcm proteins reduces the conserved ATP binding sites, which indicates that ATP hydrolysis is a coordinated event involving all six subunits of the Mcm complex.^[25] Studies have shown that within the Mcm protein complex are specific catalytic pairs of Mcm proteins that function together to coordinate ATP hydrolysis. For example, Mcm3 but not Mcm6 can activate Mcm6 activity. These studies suggest that the structure for the Mcm complex is a hexamer with Mcm3 next to Mcm7, Mcm2 next to Mcm6, and Mcm4 next to Mcm5. Both members of the catalytic pair contribute to the conformation that allows ATP binding and hydrolysis and the mixture of active and inactive subunits create a coordinated ATPase activity that allows the Mcm protein complex to complete ATP binding and hydrolysis as a whole.^[26]

The nuclear localization of the minichromosome maintenance proteins is regulated in budding yeast cells. The Mcm proteins are present in the nucleus in G₁ stage and S phase of the cell cycle, but are exported to the cytoplasm during the G₂ stage and M phase. A complete and intact six subunit Mcm complex is required to enter into the cell nucleus.^[27] InS. cerevisiae, nuclear export is promoted by cyclin-dependent kinase (CDK) activity. Mcm proteins that are associated with chromatin are protected from CDK export machinery due to the lack of accessibility to CDK.^[28]

 

Initiation Complex[edit]

During the G₁ stage of the cell cycle, the replication initiation factors, origin recognition complex (ORC), Cdc6, Cdt1, and minichromosome maintenance (Mcm) protein complex, bind sequentially to DNA to form the pre-replication complex (pre-RC). At the transition of the G₁ stage to the S phase of the cell cycle, S phase–specific cyclin-dependent protein kinase (CDK) and Cdc7/Dbf4 kinase (DDK) transform the pre-RC into an active replication fork. During this transformation, the pre-RC is disassembled with the loss of Cdc6, creating the initiation complex. In addition to the binding of the Mcm proteins, cell division cycle 45 (Cdc45) protein is also essential for initiating DNA replication.^[29][30] Studies have shown that Mcm is critical for the loading of Cdc45 onto chromatin and this complex containing both Mcm and Cdc45 is formed at the onset of the S phase of the cell cycle.^[31][32] Cdc45 targets the Mcm protein complex, which has been loaded onto the chromatin, as a component of the pre-RC at the origin of replication during the G₁ stage of the cell cycle.^[20]

GINS[edit]

The six minichromosome maintenance proteins and Cdc45 are essential during initiation and elongation for the movement of replication forks and for unwinding of the DNA. GINS are essential for the interaction of Mcm and Cdc45 at the origins of replication during initiation and then at DNA replication forks as the replisome progresses.^[37][38] The GINS complex is composed of four small proteins Sld5 (Cdc105), Psf1 (Cdc101), Psf2 (Cdc102) and Psf3 (Cdc103), GINS represents ‘go, ichi, ni, san’ which means ‘5, 1, 2, 3’ in Japanese.^[39]

Mcm10[edit]

Main article: MCM10

Mcm10 is essential for chromosome replication and interacts with the minichromosome maintenance 2-7 helicase that is loaded in an inactive form at origins of DNA replication. Mcm10 chaperones the catalytic DNA polymerase α and helps stabilize the polymerase.^[40]

DDK and CDK Kinases[edit]

Main article: Cyclin-dependent kinase

At the onset of S phase, the pre-replicative complex must be activated by two S phase-specific kinases in order to form an initiation complex at an origin of replication. One kinase is the Cdc7-Dbf4 kinase called Dbf4-dependent kinase (DDK) and the other is cyclin-dependent kinase (CDK).^[41] Chromatin-binding assays of Cdc45 in yeast and Xenopus have shown that a downstream event of CDK action is loading of Cdc45 onto chromatin.^[30][31] Cdc6 has been speculated to be a target of CDK action, because of the association between Cdc6 and CDK, and the CDK-dependent phosphorylation of Cdc6. The CDK-dependent phosphorylation of Cdc6 has been considered to be required for entry into the S phase.^[42]

Elongation[edit]

 

 

 

 

Eukaryotic replisome complex and associated proteins.

The formation of the pre-replicative complex (pre-RC) marks the potential sites for the initiation of DNA replication. Consistent with the minichromosome maintenance complex encircling double stranded DNA, formation of the pre-RC does not lead to the immediate unwinding of origin DNA or the recruitment of DNA polymerases. Instead, the pre-RC that is formed during the G₁ of the cell cycle is only activated to unwind the DNA and initiate replication after the cells pass from the G₁ to the S phase of the cell cycle.^[2]

Once the initiation complex is formed and the cells pass into the S phase, the complex then becomes a replisome. The eukaryotic replisome complex is responsible for coordinating DNA replication. Replication on the leading and lagging strands is performed by DNA polymerase ε and DNA polymerase δ. Many replisome factors including Claspin, And1, replication factor C clamp loader and the fork protection complex are responsible for regulating polymerase functions and coordinating DNA synthesis with the unwinding of the template strand by Cdc45-Mcm-GINS complex. As the DNA is unwound the twist number decreases. To compensate for this the writhe number increases, introducing positive supercoils in the DNA. These supercoils would cause DNA replication to halt if they were not removed. Topoisomerases are responsible for removing these supercoils ahead of the replication fork.

Replication Fork[edit]

The replication fork is the junction the between the newly separated template strands, known as the leading and lagging strands, and the double stranded DNA. Since duplex DNA is antiparallel, DNA replication occurs in opposite directions between the two new strands at the replication fork, but all DNA polymerases synthesize DNA in the 5′ to 3′ direction with respect to the newly synthesized strand. Further coordination is required during DNA replication. Two replicative polymerases synthesize DNA in opposite orientations. Polymerase ε synthesizes DNA on the “leading” DNA strand continuously as it is pointing in the same direction as DNA unwinding by the replisome. In contrast, polymerase δ synthesizes DNA on the “lagging” strand, which is the opposite DNA template strand, in a fragmented or discontinuous manner.

The discontinuous stretches of DNA replication products on the lagging strand are known as Okazaki fragments and are about 100 to 200 bases in length at eukaryotic replication forks. The lagging strand usually contains longer stretches of single-stranded DNA that is coated with single-stranded binding proteins, which help stabilize the single-stranded templates by preventing a secondary structure formation. In eukaryotes, these single-stranded binding proteins are a heterotrimeric complex known as replication protein A(RPA).^[56]

Each Okazaki fragment is preceded by an RNA primer, which is displaced by the procession of the next Okazaki fragment during synthesis. RNAse H recognizes the DNA:RNA hybrids that are created by the use of RNA primers and is responsible for removing these from the replicated strand, leaving behind a primer:template junction. DNA polymerase α, recognizes these sites and elongates the breaks left by primer removal. In eukaryotic cells,

 

 

Depiction of DNA replication at replication fork. a: template strands, b: leading strand, c: lagging strand, d: replication fork, e: RNA primer, f: Okazaki fragment

Leading Strand

Lagging Strand

Replicative DNA Polymerases

 

After the replicative helicase has unwound the parental DNA duplex, exposing two single-stranded DNA templates, replicative polymerases are needed to generate two copies of the parental genome. DNA polymerase function is highly specialized and accomplish replication on specific templates and in narrow localizations. At the eukaryotic replication fork, there are three distinct replicative polymerase complexes that contribute to DNA replication: Polymerase α, Polymerase δ, and Polymerase ε. These three polymerases are essential for viability of the cell.^[66]

Because DNA polymerases require a primer on which to begin DNA synthesis, polymerase α (Pol α) acts as a replicative primase. Pol α is associated with an RNA primase and this complex accomplishes the priming task by synthesizing a primer that contains a short 10 nucleotide stretch of RNA followed by 10 to 20 DNA bases.^[3] Importantly, this priming action occurs at replication initiation at origins to begin leading-strand synthesis and also at the 5′ end of each Okazaki fragment on the lagging strand.

However, Pol α is not able to continue DNA replication and must be replaced with another polymerase to continue DNA synthesis.^[67] Polymerase switching requires clamp loaders and it has been proven that normal DNA replication requires the coordinated actions of all three DNA polymerases: Pol α for priming synthesis, Pol ε for leading-strand replication, and the Pol δ, which is constantly loaded, for generating Okazaki fragments during lagging-strand synthesis.^[68]

Cdc45–Mcm–GINS Helicase Complex[edit]

The DNA helicases and polymerases must remain in close contact at the replication fork. If unwinding occurs too far in advance of synthesis, large tracts of single-stranded DNA are exposed. This can activate DNA damage signaling or induce DNA repair processes. To thwart these problems, the eukaryotic replisome contains specialized proteins that are designed to regulate the helicase activity ahead of the replication fork. These proteins also provide docking sites for physical interaction between helicases and polymerases, thereby ensuring that duplex unwinding is coupled with DNA synthesis.^[73]

Proliferating Cell Nuclear Antigen[edit]

Main article: proliferating cell nuclear antigen

To strengthen the interaction between the polymerase and the template DNA, DNA sliding clamps associate with the polymerase to promote the processivity of the replicative polymerase. In eukaryotes, the sliding clamp is a homotrimer ring structure known as the proliferating cell nuclear antigen (PCNA). The PCNA ring has polarity with surfaces that interact with DNA polymerases and tethers them securely to the DNA template. PCNA-dependent stabilization of DNA polymerases has a significant effect on DNA replication because PCNAs are able to enhance the polymerase processivity up to 1,000-fold.^[85][86] PCNA is an essential cofactor and has the distinction of being one of the most common interaction platforms in the replisome to accommodate multiple processes at the replication fork, and so PCNA is also viewed as a regulatory cofactor for DNA polymerases.^[87)

PCNA loading is accomplished by the replication factor C (RFC) complex. The RFC complex is composed of five ATPases: Rfc1, Rfc2, Rfc3, Rfc4 and Rfc5.^[88] RFC recognizes primer-template junctions and loads PCNA at these sites.^[89][90] The PCNA homotrimer is opened by RFC by ATP hydrolysis and is then loaded onto DNA in the proper orientation to facilitate its association with the polymerase.^[91][92] Clamp loaders can also unload PNCA from DNA; a mechanism needed when replication must be terminated.^[92]

Termination

The end replication problem is handled in eukaryotic cells by telomere regions and telomerase. Telomeres extend the 3′ end of the parental chromosome beyond the 5′ end of the daughter strand. This single-stranded DNA structure can act as an origin of replication that recruits telomerase. Telomerase is a specialized DNA polymerase that consists of multiple protein subunits and an RNA component. The RNA component of telomerase anneals to the single stranded 3′ end of the template DNA and contains 1.5 copies of the telomeric sequence.^[60] Telomerase contains a protein subunit that is a reverse transcriptase called telomerase reverse transcriptase or TERT. TERT synthesizes DNA until the end of the template telomerase RNA and then disengages.^[60] This process can be repeated as many times as needed with the extension of the 3′ end of the parental DNA molecule. This 3′ addition provides a template for extension of the 5′ end of the daughter strand by lagging strand DNA synthesis. Regulation of telomerase activity is handled by telomere-binding proteins.

 

A depiction of telomerase progressively elongating telomeric DNA.

 

DNA replication is a tightly orchestrated process that is controlled within the context of the cell cycle. Progress through the cell cycle and in turn DNA replication is tightly regulated by the formation and activation of pre-replicative complexs (pre-RCs) which is achieved through the activation and inactivation of cyclin-dependent kinases (Cdks). Specifically it is the interactions of cyclins and cyclin dependent kinases that are responsible for the transition from G₁ into S-phase.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

– G-quadruplex

It will be exactly 60 years ago in February that James Watson and Francis Crick famously burst into the pub next to their Cambridge laboratory to announce the discovery of the “secret of life”.

What they had actually done was describe the way in which two long chemical chains wound up around each other to encode the information cells need to build and maintain our bodies.

Today, the pair’s modern counterparts in the university city continue to work on DNA’s complexities.

Balasubramanian’s group has been pursuing a four-stranded version of the molecule that scientists have produced in the test tube now for a number of years.

It is called the G-quadruplex. The “G” refers to guanine, one of the four chemical groups, or “bases”, that hold DNA together and which encode our genetic information (the others being adenine, cytosine, and thymine).

The G-quadruplex seems to form in DNA where guanine exists in substantial quantities.

And although ciliates, relatively simple microscopic organisms, have displayed evidence for the incidence of such DNA, the new research is said to be the first to firmly pinpoint the quadruple helix in human cells.

‘Funny target’

The team, led by Giulia Biffi, a researcher in Balasubramaninan’s lab, produced antibody proteins that were designed specifically to track down and bind to regions of human DNA that were rich in the quadruplex structure. The antibodies were tagged with a fluorescence marker so that the time and place of the structures’ emergence in the cell cycle could be noted and imaged.

This revealed the four-stranded DNA arose most frequently during the so-called “s-phase” when a cell copies its DNA just prior to dividing.

Prof Balasubramaninan said that was of key interest in the study of cancers, which were usually driven by genes, or oncogenes, that had mutated to increase DNA replication.

If the G-quadruplex could be implicated in the development of some cancers, it might be possible, he said, to make synthetic molecules that contained the structure and blocked the runaway cell proliferation at the root of tumours.

 

 

John Berger

Founder at Novagon DNA

If the first and core mission of the genetic code is to faithfully replicate the “genetic material” encoded in the DNA and RNA nucleic acids, then every metabolic process must be functioning in a synchronous 24/7 manner. The only way to do this is to use all the purine and pyrmidine nucleotide, nucleoside and bases (ATUIXGC) =7 necessary and sufficient to make RNA first and then with the assistance of Thioredoxin i.e. ferredoxin purple sulphur bacteria to oxidize rna to dna.

In regards to purine metabolism which is my major area of focus. The two purine nucleotides left out of the current genetic code i.e. IMP and XMP have the following functions through their enzymes.1. Begin purine nucleotide synthesis de novo by IMPDH cyclodehydrogenase the last step in closing the purine ring and the current foundation molecular structure for DNA and RNA; 2. HPRT is the main enzyme is purine salvage for IMP and GMP; APRT provides same service for AMP; 3. Finally the last step in purine metabolism is by xanthine oxidase with the assistance of FES and molybendum. In essence the IMP and XMP families were the first to build the nucleic acid molecular structure; design a process to recycle functional side groups while keeping the purine ring intact and finally developing the biochemical pathway to eliminate toxic ammonia NH3 from the CNS and liver/kidneys.

I believe the 7 nucleotide Novagon DNA triplex genetic code should be called the epigenetic code since it works not only in protein metabolism which is 2% of the genome but noncoding intronic regions ie. rna editing, RNAi, piRNA, snMRN, long noncoding RNA and many other small rnas which operate above the level of the dna and rna base pair i.e. epigenesis suppressing or enhancing whole genes and networks of genes which control protein,lipid,carbohydrate and nucleic acid metabolism.

I am in the process of deveoping a 7 code epigenetic primer to control the gene switches which in turn allows the genetic material to be inherited from generation to generation as the species constantly adapts to external and internal stressors and competitive antagonist.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Agents that Damage DNA

• Certain wavelengths of radiation
  • ionizing radiation such as gamma rays and X-rays
  • ultraviolet rays, especially the UV-C rays (~260 nm) that are absorbed strongly by DNA but also the longer-wavelength UV-B that penetrates the ozone shield [Link].
• Highly-reactive oxygen radicals produced during normal cellular respiration as well as by other biochemical pathways. [Link to further discussion.]
• Chemicals in the environment
  • many hydrocarbons, including some found in cigarette smoke

 

 

 

 

 

Link to description of a test measuring the mutations caused by the hydrocarbon benzopyrene.

• some plant and microbial products, e.g. the aflatoxins produced in moldy peanuts
• Chemicals used in chemotherapy, especially chemotherapy of cancers

Types of DNA Damage

1. All four of the bases in DNA(A, T, C, G)can be covalently modified at various positions.
   • One of the most frequent is the loss of an amino group(“deamination”) — resulting, for example, in a C being converted to a U.
2. Mismatchesof the normal bases because of a failure of proofreading during DNA replication.
   • Common example: incorporation of the pyrimidineU (normally found only in RNA) instead of T.
3. Breaksin the backbone.
   • Can be limited to one of the two strands (a single-stranded break, SSB) or
   • on both strands(a double-stranded break (DSB).
   • Ionizing radiation is a frequent cause, but some chemicals produce breaks as well.
4. CrosslinksCovalent linkagescan be formed between bases
   • on the same DNA strand (“intrastrand”) or
   • on the opposite strand (“interstrand”).

Several chemotherapeutic drugs used against cancers crosslink DNA [Link].

Repairing Damaged Bases

Damaged or inappropriate bases can be repaired by several mechanisms:

• Direct chemical reversal of the damage
• Excision Repair, in which the damaged base or bases are removed and then replaced with the correct ones in a localized burst of DNA synthesis. There are three modes of excision repair, each of which employs specialized sets of enzymes.

1. Base Excision Repair (BER)
2. Nucleotide Excision Repair (NER)
3. Mismatch Repair (MMR)

 

 

Gene expression profiles associated with acute myocardial infarction and risk of cardiovascular death

J Kim,  N Ghasemzadeh,  DJ Eapen, NC Chung, JD Storey, AA Quyyumi and G Gibson
Kim et al. Genome Medicine 2014, 6:40
http://genomemedicine.com/content/6/5/40

Background: Genetic risk scores have been developed for coronary artery disease and atherosclerosis, but are not predictive of adverse cardiovascular events. We asked whether peripheral blood expression profiles may be predictive of acute myocardial infarction (AMI) and/or cardiovascular death.

Methods: Peripheral blood samples from 338 subjects aged 62 ± 11 years with coronary artery disease (CAD) were analyzed in two phases (discovery N = 175, and replication N = 163), and followed for a mean 2.4 years for cardiovascular death. Gene expression was measured on Illumina HT-12 microarrays with two different normalization procedures to control technical and biological covariates. Whole genome genotyping was used to support comparative genome-wide association studies of gene expression. Analysis of variance was combined with receiver operating curve and survival analysis to define a transcriptional signature of cardiovascular death.

Results: In both phases, there was significant differential expression between healthy and AMI groups with overall down-regulation of genes involved in T-lymphocyte signaling and up-regulation of inflammatory genes. Expression quantitative trait loci analysis provided evidence for altered local genetic regulation of transcript abundance in AMI samples. On follow-up there were 31 cardiovascular deaths. A principal component (PC1) score capturing covariance of 238 genes that were differentially expressed between deceased and survivors in the discovery phase significantly predicted risk of cardiovascular death in the replication and combined samples (hazard ratio = 8.5, P< 0.0001) and improved the C-statistic (area under the curve 0.82 to 0.91, P= 0.03) after adjustment for traditional covariates.

Conclusions: A specific blood gene expression profile is associated with a significant risk of death in Caucasian subjects with CAD. This comprises a subset of transcripts that are also altered in expression during acute myocardial infarction.

 

Lecture Contents delivered at Koch Institute for Integrative Cancer Research, Summer Symposium 2014: RNA Biology, Cancer and Therapeutic Implications, June 13, 2014 @MIT

Curator of Lecture Contents: Aviva Lev-Ari, PhD, RN
https://pharmaceuticalintelligence.com/wp-admin/post.php?post=23174&action=edit
3:15 – 3:45, 6/13/2014, Laurie Boyer “Long non-coding RNAs: molecular regulators of cell fate”     http://pharmaceuticalintelligence.com/2014/06/13/315-345-2014-laurie-boyer-long-non-coding-rnas-molecular-regulators-of-cell-fate/

 

TAR DNA-binding protein 43

TDP-43 is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. In particular, TDP-43 is a splicing factor binding to the intron8/exon9 junction of the CFTR gene and to the intron2/exon3 region of the apoA-II gene.^[2] A similar pseudogene is present on chromosome 20.^[3]

TDP-43 has been shown to bind both DNA and RNA and have multiple functions in transcriptional repression, pre-mRNA splicing and translational regulation.

TDP-43 was originally identified as a transcriptional repressor that binds to chromosomally integrated trans-activation response element (TAR) DNA and represses HIV-1 transcription.^[1] It was also reported to regulate alternate splicing of theCFTR gene and the apoA-II gene.

In spinal motor neurons TDP-43 has also been shown in humans to be a low molecular weight microfilament (hNFL) mRNA-binding protein.^[4] It has also shown to be a neuronal activity response factor in the dendrites of hippocampal neurons suggesting possible roles in regulating mRNA stability, transport and local translation in neurons.^[5]

Clinical significance[edit]

Hyper-phosphorylated, ubiquitinated and cleaved form of TDP-43, known as pathologic TDP43, is the major disease protein in ubiquitin-positive, tau-, and alpha-synuclein-negative frontotemporal dementia (FTLD-TDP, previously referred to as FTLD-U^[6]) and in Amyotrophic lateral sclerosis (ALS).^[7] Elevated levels of the TDP-43 protein have also been identified in individuals diagnosed with chronic traumatic encephalopathy, a condition that often mimics ALS and that has been associated with athletes who have experienced multiple concussions and other types of head injury.^[8]

HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator “Tat” is dependent on an RNA regulatory element (TAR) located “downstream” (i.e. to-be transcribed at a later point in time) of the transcription initiation site.

Mutations in the TARDBP gene are associated with neurodegenerative disorders including frontotemporal lobar degeneration and amyotrophic lateral sclerosis (ALS).^[9] In particular, the TDP-43 mutants M337V and Q331K are being studied for their roles in ALS.^[10][11] Cytoplasmic TDP-43 pathology is the dominant histopathological feature of multisystem proteinopathy.^[12]

 

 

General annotation (Comments)

Function	DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3′-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3′ UTR. Ref.2 Ref.12
Subunit structure	Homodimer. Interacts with BRDT By similarity. Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimun of six contiguous repeats. Interacts with ATNX2; the interaction is RNA-dependent. Ref.16
Subcellular location	Nucleus. Note: In patients with frontotemporal lobar degeneration and amyotrophic lateral sclerosis, it is absent from the nucleus of affected neurons but it is the primary component of cytoplasmic ubiquitin-positive inclusion bodies. Ref.2 Ref.11
Tissue specificity	Ubiquitously expressed. In particular, expression is high in pancreas, placenta, lung, genital tract and spleen.
Domain	The RRM domains can bind to both DNA and RNA By similarity.
Post-translational modification	Hyperphosphorylated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU. Ref.11Ubiquitinated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU. Ref.2 Ref.11  Cleaved to generate C-terminal fragments in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU.
Involvement in disease	Amyotrophic lateral sclerosis 10 (ALS10) [MIM:612069]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases.  Note: The disease is caused by mutations affecting the gene represented in this entry. 16Ref.21 Ref.22 Ref.23 Ref.24 Ref.25 Ref.26 Ref.27 Ref.28 Ref.29 Ref.30 Ref.31Ref.32
Sequence similarities	Contains 2 RRM (RNA recognition motif) domains.

 

 

How DNA is made?

Deoxyribonucleic acid (DNA) synthesis is a process by which copies of nucleic acid strands are made. In nature, DNA synthesis takes place in cells by a mechanism known as DNA replication. Using genetic engineering and enzyme chemistry, scientists have developed man-made methods for synthesizing DNA. The most important of these is poly-merase chain reaction (PCR). First developed in the early 1980s, PCR has become a multi-billion dollar industry with the original patent being sold for $300 million dollars.

History

DNA was discovered in 1951 by Francis Crick, James Watson, and Maurice Wilkins. Using x-ray crystallography data generated by Rosalind Franklin, Watson and Crick determined that the structure of DNA was that of a double helix. For this work, Watson, Crick, and Wilkins received the Nobel Prize in Physiology or Medicine in 1962. Over the years, scientists worked with DNA trying to figure out the “code of life.” They found that DNA served as the instruction code for protein sequences. They also found that every organism has a unique DNA sequence and it could be used for screening, diagnostic, and identification purposes. One thing that proved limiting in these studies was the amount of DNA available from a single source.

After the nature of DNA was determined, scientists were able to examine the composition of the cellular genes. A gene is a specific sequence of DNA base pairs that provide the code for the construction of a protein. These proteins determine the traits of an organism, such as eye color or blood type. When a certain gene was isolated, it became desirable to synthesize copies of that molecule. One of the first ways in which a large amount of a specific DNA was synthesized was though genetic engineering.

Genetic engineering begins by combining a gene of interest with a bacterial plasmid. A plasmid is a small stretch of DNA that is found in many bacteria. The resulting hybrid DNA is called recombinant DNA. This new recombinant DNA plasmid is then injected into bacterial cells. The cells are then cloned by allowing it to grow and multiply in a culture. As the cells multiply so do copies of the inserted gene. When the bacteria has multiplied enough, the multiple copies of the inserted gene can then be isolated. This method of DNA synthesis can produce billions of copies of a gene in a couple of weeks.

In 1983, the time required to produce copies of DNA was significantly reduced when Kary Mullis developed a process for synthesizing DNA called polymerase chain reaction (PCR). This method is much faster than previous known methods producing billions of copies of a DNA strand in just a few hours. It begins by putting a small section of double stranded DNA in a solution containing DNA polymerase, nucleotides and primers. The solution is heated to separate the DNA strands. When it is cooled, the polymerase creates a copy of each strand. The process is repeated every five minutes until the desired amount of DNA is produced. In 1993, Mullis’s development of PCR earned him the Nobel Prize in Chemistry.

Background

The key to understanding DNA synthesis is understanding its structure. Typically, DNA exists as two chains of chemically linked nucleotides. These links follow specific patterns dictated by the base pairing rules. Each nucleotide is made up of a deoxyribose sugar molecule, a phosphate group, and one of four nitrogen containing bases. The bases include the pyrimidines thymine (T) and cytosine (C)and the purines adenine (A) and guanine (G). In DNA, adenine generally links with thymine and guanine with cytosine. The molecule is arranged in a structure called a double helix which can be imagined by picturing a twisted ladder or spiral staircase. The bases make up the rungs of the ladder while the sugar and phosphate portions make up the ladder sides. The order in which the nucleotides are linked, called the sequence, is determined by a process known as DNA sequencing.

In a eukaryotic cell, DNA synthesis occurs just prior to cell division through a process called replication. When replication begins the two strands of DNA are separated by a variety of enzymes. Thus opened, each strand serves as a template for producing new strands. This whole process is catalyzed by an enzyme called DNA polymerase. This molecule brings corresponding, or complementary, nucleotides in line with each of the DNA strands. The nucleotides are then chemically linked to form new DNA strands which are exact copies of the original strand. These copies, called the daughter strands, contain half of the parent DNA molecule and half of a whole new molecule. Replication by this method is known as semiconservative replication.

Raw Materials

The primary raw materials used for DNA synthesis include DNA starting materials, taq DNA polymerase, primers, nucleotides, and the buffer solution. Each of these play an important role in the production of millions of DNA molecules.

Controlled DNA synthesis begins by identifying a small segment of DNA to copy. This is typically a specific sequence of DNA that contains the code for a desired protein. Called template DNA, this material must be highly purified.

While the process of DNA replication was known before 1980, PCR was not possible because there were no known heat stable DNA polymerases.  In the early 1980s, scientists found bacteria living around natural steam vents. It turned out that these organisms, called thermus aquaticus, had a DNA polymerase that was stable and functional at extreme levels of heat. This taq DNA polymerase became the cornerstone for modern DNA synthesis techniques. During a typical PCR process, 2-3 micrograms of taq DNA polymerase is needed.

The polymerase builds the DNA strands by combining corresponding nucleotides on each DNA strand. Chemically speaking, nucleotides are made up of three types of molecular groups including a sugar structure, a phosphate group, and a cyclic base. The sugar portion provides the primary structure for all nucleotides. In general, the sugars are composed of five carbon atoms with a number of hydroxy (-OH) groups attached. For DNA, the sugar is 2-deoxy-D-ribose. The defining part of a nucleotide is the hetero-cyclic base that is covalently bound to the sugar. These bases are either pyrimidine or purine groups, and they form the basis for the nucleic acid code. Two types of purine bases are found including adenine and guanine. In DNA, two types of pyrimidine bases are present, thymine and cytosine. A phosphate group makes up the final portion of a nucleotide. This group is derived from phosphoric acid and is covalently bonded to the sugar structure on the fifth carbon.

 

 

 

 

The first phase of polymerase chain reaction (PCR) involves the denaturation of DNA. This “opening up” of the DNA molecule provides the template for the next DNA molecule from which to be produced. With the DNA split into separate strands, the temperature is lowered—the primer annealing step. During the next phase, the DNA polymerase interacts with the strands and adds complementary nucleotides along the entire length. The time required at this phase is about one minute for every 1,000 base pairs.

To initiate DNA synthesis, short primer sections of DNA must be used. These primer sections, called oligo fragments, are about 18-25 nucleotides in length and correspond to a section on the template DNA. They typically have a C and G nucleotide concentration of about 60% with even distribution. This provides the maximum efficiency in the synthesis process.

The buffer solution provides the medium in which DNA synthesis can occur. This is an aqueous solution which contains MgCl2, HCI, EDTA, and KCI. The MgCl2 concentration is important because the Mg2+ ions interact with the DNA and the primers creating crucial complexes for DNA synthesis. The pH of this system is critical so it may also be buffered with ammonium sulfate. To energize the reaction, various energy molecules are added such as ATP, GTP, and NTP.

DNA synthesis involves three distinct processes, typically done in separate areas to avoid contamination, including sample preparation, DNA synthesis reaction cycle and DNA isolation. Following these procedures scientists are able to convert a few strands of DNA into millions and millions of exact copies.

Preparation of the samples

• 1 Typically, all of the starting solutions except the primers, polymerases and the dNTPs are put in an autoclave to kill off any contaminating organism. Two separate solutions are made. One contains the buffer, primers and the polymerase. The other contains the MgCl2 and the template DNA. These solutions are all put into small tubes to begin the reaction.

 

Kary Banks Mullis.

Kary Banks Mullis was born in Lenoir, North Carolina, in 1944. Upon graduation from Georgia Tech in 1966 with a B.S. in chemistry, Muilis entered the biochemistry doctoral program at the University of California, Berkeley. Earning his Ph.D. in 1973, he accepted a teaching position at the University of Kansas Medical School in Kansas City. In 1977, he assumed a postdoctoral fellowship at the University of California, San Francisco.

Muilis accepted a position as a research scientist in 1979 with a growing biotech firm—Cetus Corporation, in Emeryville, California—that synthesized chemicals used by other scientists in genetic cloning. While there, he designed polymerase chain reaction (PCR), a fast and effective technique for reproducing specific genes or DNA (deoxyribonucleic acid) fragments that can create billions of copies in a few hours. The most effective way to reproduce DNA was by cloning, but it was problematic. It took time to convince Mullis’s colleagues of the importance of this discovery but soon PCR became the focus of intensive research. Scientists at Cetus developed a commercial version of the process and a machine called the Thermal Cycler (with the addition of the chemical building blocks of DNA [nucleotides] and a biochemical catalyst [polymerase], the machine would perform the process automatically on a target piece of DNA).

Read more: http://www.madehow.com/Volume-6/DNA-Synthesis.html#ixzz38sovuX5n

 

 

Additional References to Leaders in Pharmaceutical Intelligence

Read Full Post »