hi,

Antisense Nucleotides

Antisense nucleotides are strings of RNA or DNA that are complementary to "sense" strands of nucleotides. They bind to and inactivate these sense strands. They have been used in research, and may become useful for therapy of certain diseases.
Antisense RNA

Messenger RNA (mRNA) is a single-stranded molecule used for protein production at the ribosome . Because its sequence is used for translation , mRNA is called a "sense" strand or sense sequence. A complementary sequence to that mRNA is an "antisense" sequence. For instance, if the mRNA sequence was AUGAAACCCGUG, the antisense strand would be UACUUUGGGCAC. Complementary sequences will pair up in RNA just as they do in DNA. When this happens to an mRNA, however, it can no longer be translated at the ribosome, no protein synthesis occurs, and the "duplex" RNA is degraded.

This phenomenon has been used experimentally and commercially to block the synthesis of specific proteins in transgenic organisms (ones to which a foreign gene has been added). The strategy is to add a synthetic gene that, when transcribed, will make the antisense RNA sequence for the target protein's mRNA.

This technique was first used commercially in 1988 for the FlavrSavr tomato. The gene chosen for inactivation was polygalacturonase (PG ), whose enzyme unlinks pectins in the plant cell wall, thereby softening it. The intent was to increase the time the fruit could be left to ripen without softening, thus increasing flavor of commercial tomatoes. The Calgene company created a transgenic tomato plant expressing the antisense RNA for PG mRNA, and reduced PG production by up to 90 percent. Although the tomato was not a commercial success, it demonstrated the potential for this strategy.

Antisense RNA is currently being investigated as a human therapy for certain forms of cancer. The goal is to use gene therapy techniques to insert an antisense gene into tumor cells. Many cancers are due to overexpression of the genes that promote cell proliferation, called tumor suppressor genes. Antisense RNA might be able to inhibit this overexpression. Another target is the BCL-2 gene, whose protein prevents apoptosis, or programmed cell death. In certain cancers, the BCL-2 gene is overactive, preventing death of cells and leading to their proliferation. Antisense therapy against BCL-2 is currently being tested under the trade name Genazyme.
Antisense DNA

Antisense DNA strands can also be made (note that in the double helix, the side of the DNA that is transcribed is itself antisense). Short antisense strands of DNA can be introduced into cells, which then bind with target mRNA. Antisense DNA is currently an approved therapy for cytomegalovirus infections of the eye, under the trade name Vitravene. Vitravene targets two different viral proteins. Antisense DNA is also being explored for therapy of HIV, some cancers, and other diseases.

One advantage of using antisense therapy in treating infectious diseases such as virus infections is that it can be tailored to the particular strain in circulation, and then modified as the virus mutates. One difficulty in applying this therapy is successfully delivering the antisense DNA or RNA to all target tissues (for instance, making sure the antisense strands reach infected blood cells for HIV). Another problem is maintaining prolonged suppression of target protein expression, since the antisense molecule will eventually be degraded by the cell's nuclease enzymes. One strategy to prevent degradation is to chemically modify the DNA to interfere with nuclease action.
RNA Interference

Investigation of the mechanism of action of antisense RNA led to the surprising discovery that naturally occurring double-stranded RNA molecules (dsRNA) suppress gene expression as well as or better than antisense sequences. This suppression by dsRNA of expression of the related gene is called RNA interference. dsRNA molecules are cut into short segments by nucleases; the antisense strand of such a segment then peels off and binds with its complementary mRNA. This new, double-stranded RNA is then subject to further nuclease attack. RNA interference is believed to be an ancient means of protecting against double-stranded RNA viruses. Further understanding of RNA interference may lead to improvements in or replacement of antisense therapies.

see also Gene Therapy; Nucleases; Nucleotide; RNA Interference; Transgenic Plants.

Richard Robinson
Bibliography

Smith C. J. S., et al. "Antisense RNA Inhibition of Polygalacturonase Gene Expression in Transgenic Tomatoes." Nature 334 (1988): 724-726.

Tamm I., B. Dorken, and G. Hartmann. "Antisense Therapy in Oncology: New Hope for an Old Idea?" Lancet 358, no. 9280 (2001): 489-497.

hello sir,

The present study was designed to elucidate the consequences of antisense oligonucleotide-mediated knockdown of striatal dopamine reuptake transporters on 3,4-methylenedioxymethamphetamine (MDMA)-induced neurotoxicity. Antisense oligonucleotide complementary to the mRNA translational start site of the rat dopamine transporter was delivered by constant (7 days) intranigral infusion with an osmotic minipump. Delivery of the antisense oligonucleotide by this method resulted in a 70% reduction in the density of the dopamine transporter in the ipsilateral striatum, as measured by [(3)H]mazindol binding. The effect of this transporter knockdown on MDMA-induced serotonergic neurotoxicity was then examined. MDMA (2x20 mg/kg, s.c., given 12 h apart) administered to control rats produced hyperthermia following the first dose and led to a 45-50% reduction in striatal serotonin, 5-hydroxyindoleacetic acid, and serotonin reuptake transporter density 1 week after the second dose. Conversely, in antisense-, but not missense-treated rats, a significant attenuation of MDMA-induced neurotoxicity was observed only in the ipsilateral striatum. The hyperthermic response elicited by MDMA was not altered by prior administration of antisense. In vivo microdialysis revealed that the antisense treatment attenuated MDMA-induced dopamine release in the ipsilateral striatum.These results suggest that the dopamine transporter plays an essential role in the neurodegeneration induced by MDMA, and provides additional support for the hypothesis that extracellular dopamine is involved in the neurotoxic process, at least in the striatum. this was the simple example which explains the toxicity of ASO. There are various other examples but it is also true that the therapeutic benefit overweighs this toxicity.

reference

Unilateral infusion of a dopamine transporter antisense into the substantia nigra protects against MDMA-induced serotonergic deficits in the ipsilateral striatum
by
Kanthasamy A, Sprague J, Shotwell J, Nichols D.
Department of Biomedical Sciences,
School of Veterinary Medicine,
Iowa State University, 50011, Ames, IA, USA .
Neuroscience 2002 Nov 1;114(4):917

hi,
it increases the half life by increasing the thermal stability to siRNA.

hi,

yet now his technique is not useful for emergency treatment, but in future there is a hope for the same. This is so because it involve the treatment using the human genome.

hi,

1. Genetic testing "the analysis of RNA, chromosomes (DNA), proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, or karyotypes for clinical purposes."[4] It can provide information about a person's genes and chromosomes throughout life. Available types of testing include:

* Newborn screening: Newborn screening is used just after birth to identify genetic disorders that can be treated early in life. The routine testing of infants for certain disorders is the most widespread use of genetic testing—millions of babies are tested each year in the United States. All states currently test infants for phenylketonuria (a genetic disorder that causes mental illness if left untreated) and congenital hypothyroidism (a disorder of the thyroid gland).
* Diagnostic testing: Diagnostic testing is used to diagnose or rule out a specific genetic or chromosomal condition. In many cases, genetic testing is used to confirm a diagnosis when a particular condition is suspected based on physical mutations and symptoms. Diagnostic testing can be performed at any time during a person's life, but is not available for all genes or all genetic conditions. The results of a diagnostic test can influence a person's choices about health care and the management of the disease.
* Carrier testing: Carrier testing is used to identify people who carry one copy of a gene mutation that, when present in two copies, causes a genetic disorder. This type of testing is offered to individuals who have a family history of a genetic disorder and to people in ethnic groups with an increased risk of specific genetic conditions. If both parents are tested, the test can provide information about a couple's risk of having a child with a genetic condition.
* Prenatal testing: Prenatal testing is used to detect changes in a fetus's genes or chromosomes before birth. This type of testing is offered to couples with an increased risk of having a baby with a genetic or chromosomal disorder. In some cases, prenatal testing can lessen a couple's uncertainty or help them decide whether to abort the pregnancy. It cannot identify all possible inherited disorders and birth defects, however.
* Preimplantation genetic diagnosis: Genetic testing procedures that are performed on human embryos prior to the implantation as part of an in vitro fertilization procedure.
* Predictive and presymptomatic testing: Predictive and presymptomatic types of testing are used to detect gene mutations associated with disorders that appear after birth, often later in life. These tests can be helpful to people who have a family member with a genetic disorder, but who have no features of the disorder themselves at the time of testing. Predictive testing can identify mutations that increase a person's chances of developing disorders with a genetic basis, such as certain types of cancer. For example, an individual with a mutation in BRCA1 has a 65% cumulative risk of breast cancer [1]. Presymptomatic testing can determine whether a person will develop a genetic disorder, such as hemochromatosis (an iron overload disorder), before any signs or symptoms appear. The results of predictive and presymptomatic testing can provide information about a person’s risk of developing a specific disorder and help with making decisions about medical care.
* Forensic testing: Forensic testing uses DNA sequences to identify an individual for legal purposes. Unlike the tests described above, forensic testing is not used to detect gene mutations associated with disease. This type of testing can identify crime or catastrophe victims, rule out or implicate a crime suspect, or establish biological relationships between people (for example, paternity).
* Research testing: Research testing includes finding unknown genes, learning how genes work and advancing our understanding of genetic conditions. The results of testing done as part of a research study are usually not available to patients or their healthcare providers.

Reference

Holtzman NA, Murphy PD, Watson MS, Barr PA (October 1997). "Predictive genetic testing: from basic research to clinical practice". Science (journal) 278 (5338): 602–5. PMID 9381169

2.Frozen sections of the tumor tissues were prepared followed by rapid staining. Clusters of the cancer cells were isolated from the sections by micromanipulation technique and purified for extracting intact RNA that was subsequently assayed. this is one of the simplest method.

Reference
Rapid isolation of cancer cells from tumor tissue by micromanuiplator and extraction of tiny amount of RNA.

Jiang PZ, Shen XM, Huang H, Shi YM, Yao KT.

Department of Pathology, First Military Medical University, Guangzhou 510515, China.

3. no, different genes & chromosomes are responsible for different types of cancer.

4. Transfection of cis-element double-stranded oligonucleotides, referred to as decoy ODNs, has been reported to be a powerful tool that provides a new class of antigene strategies for gene therapy. However, one of the major limitations of the decoy approach is the rapid degradation of phosphodiester oligonucleotides by intracellular nucleases. To date, several DNA analogs have been employed to overcome this issue, but insufficient efficacy and/or specificity have limited their in vivo usefulness. In this paper we have investigated the use of conformationally restricted nucleotides in the design of decoy molecules for nuclear transcription factor {kappa}B (NF-{kappa}B). Starting from a synthetic double-stranded oligonucleotide, containing the {kappa}B consensus binding sequence, we designed a panel of decoy molecules modified to various extents and at various positions with locked nucleic acids (LNAs). Our results indicate that the addition of terminal LNA bases, outside the {kappa}B sequence, to generate LNA–DNA–LNA co-polymers was sufficient to confer appreciable protection towards nuclease digestion, without interfering with transcription factor binding. Conversely, insertion of LNA substitutions in the context of the {kappa}B-binding site resulted in further increased stability, but caused a loss of affinity of NF-{kappa}B for the target sequence. However, our results also indicate that this latter effect was apparently dependent not only on the extent but also on strand positioning of the internal LNA substitutions. This observation is of great importance since it provides evidence for the possibility of tuning DNA–LNA duplexes with internal LNAs into decoy agents with improved features in terms of biological stability and inhibitory effect.

Reference
J. SHEN, R. LI, and G. LI
Inhibitory Effects of Decoy-ODN Targeting Activated STAT3 on Human Glioma Growth In Vivo
In Vivo, March 1, 2009; 23(2): 237 - 243.

hi,

The present study was designed to elucidate the consequences of antisense oligonucleotide-mediated knockdown of striatal dopamine reuptake transporters on 3,4-methylenedioxymethamphetamine (MDMA)-induced neurotoxicity. Antisense oligonucleotide complementary to the mRNA translational start site of the rat dopamine transporter was delivered by constant (7 days) intranigral infusion with an osmotic minipump. Delivery of the antisense oligonucleotide by this method resulted in a 70% reduction in the density of the dopamine transporter in the ipsilateral striatum, as measured by [(3)H]mazindol binding. The effect of this transporter knockdown on MDMA-induced serotonergic neurotoxicity was then examined. MDMA (2x20 mg/kg, s.c., given 12 h apart) administered to control rats produced hyperthermia following the first dose and led to a 45-50% reduction in striatal serotonin, 5-hydroxyindoleacetic acid, and serotonin reuptake transporter density 1 week after the second dose. Conversely, in antisense-, but not missense-treated rats, a significant attenuation of MDMA-induced neurotoxicity was observed only in the ipsilateral striatum. The hyperthermic response elicited by MDMA was not altered by prior administration of antisense. In vivo microdialysis revealed that the antisense treatment attenuated MDMA-induced dopamine release in the ipsilateral striatum.These results suggest that the dopamine transporter plays an essential role in the neurodegeneration induced by MDMA, and provides additional support for the hypothesis that extracellular dopamine is involved in the neurotoxic process, at least in the striatum. this was the single example of toxicity.

reference
Unilateral infusion of a dopamine transporter antisense into the substantia nigra protects against MDMA-induced serotonergic deficits in the ipsilateral striatum
by
Kanthasamy A, Sprague J, Shotwell J, Nichols D.
Department of Biomedical Sciences,
School of Veterinary Medicine,
Iowa State University, 50011, Ames, IA, USA .
Neuroscience 2002 Nov 1;114(4):917

hi,

i know its not successful today bit in future it can be considered as the most accurate & triumphant technique. This is so because genetic profile is involved in the treatment. so topic is not baseless. You can see the presentation & various answers for more reasons.

hi,

thank you sir for asking such questions.

1. same can be explained by taking the following example:

Antisense oligonucleotides can block the expression of specific target genes involved in the development of human diseases. Therapeutic applications of antisense techniques are currently under investigation in many different fields. The use of antisense molecules to modify gene expression is variable in its efficacy and reliability, raising objections about their use as therapeutic agents. However, preliminary results of several clinical studies demonstrated the safety and to some extent the efficacy of antisense oligodeoxynucleotides (ODNs) in patients with malignant diseases. Clinical response was observed in some patients suffering from ovarian cancer who were treated with antisense targeted against the gene encoding for the protein kinase C-alpha. Some hematological diseases treated with antisense oligos targeted against the bcr/abl and the bcl2 mRNAs have shown promising clinical response. Antisense therapy has been useful in the treatment of cardiovascular disorders such as restenosis after angioplasty, vascular bypass graft occlusion, and transplant coronary vasculopathy. Antisense oligonucleotides also have shown promise as antiviral agents. Several investigators are performing trials with oligonucleotides targeted against the human immunodeficiency virus-1 (HIV-1) and hepatitis viruses. Phosphorothioate ODNs now have reached phase I and II in clinical trials for the treatment of cancer and viral infections, so far demonstrating an acceptable safety and pharmacokinetic profile for continuing their development. The new drug Vitravene, based on a phosphorothioate oligonucleotide designed to inhibit the human cytomegalovirus (CMV), promises that some substantial successes can be reached with the antisense technique.

Rferences

Antisense oligonucleotides as therapeutic agents
Umberto Galderisi 1 2, Antonino Cascino 1, Antonio Giordano 1 *
1Department of Pathology, Anatomy and Cell Biology, Jefferson Medical College of Thomas Jefferson University, Philadelphia, Pennsylvania
2Istituto di Farmacologia e Tossicologia, Second University of Naples, Naples, Italy

*Correspondence to Antonio Giordano, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Jefferson Alumni Hall, 1020 Locust Street, Room 226, Philadelphia, PA 19107

Funded by:
Sbarro Institute for Cancer Research and Molecular Medicine
NIH

2. It is feasible in case of some diseases (like HIV, some cancers etc)but for other diseases research is going on.

3. for success rate please refer the other answers.

hi,

please refer the other answers for success rate(as i have already given the ans for the same question)

hi,

there is a scope of pharmacogenomics in future. This is explained as follows:

Pharmacogenomics represents a radical advance in medical history. In the past, most drugs were designed to work on the population level rather than being targeted for the individual patient. By reversing that trend, pharmacogenomics helps to refine the focus of treatment and makes drugs more effective and less toxic.

Rather than relying on the outward manifestation of disease—the signs and symptoms that physicians call the phenotype—pharmacogenomic medicine examines and treats the genotype. Think of the genotype as the inward manifestation of disease—the DNA itself is addressed first and matched with the way the disease presents in the patient—the phenotypic presentation.

In one approach, researchers use computers to gain access to the sequence of genes that encode proteins that might influence drug response. They then use DNA samples obtained from a National Institutes of Health's repository. They then sequence these genes, looking for common genetic variation.

"We find genetic variations in every gene we look at," says Dr. Weinshilboum. "From this, we can determine which of the common variations is functionally important, and immediately test it in a clinical setting."

Armed with pharmacogenomic insights, Mayo Clinic researchers collaborate with physicians who treat patients to give them the "inside scoop" about the genetic involvement in their response to drug therapy. This allows Mayo researchers to take their findings out of the lab and improve patients' lives more quickly. Researchers in Dr. Weinshilboum's group are working with Mayo physicians to team pharmocogenomic approaches with improved patient care in areas as diverse as breast cancer and psychiatric disorders.

Mayo Clinic researchers say the pharmacogenomic approach to improved treatment will become increasingly common. Dr. Weinshilboum believes that collaborations such as Dr. Mrazek's work in psychiatry are typical of the Mayo Clinic research-patient care continuum that is central to the success of pharmacogenomic medicine.

In addition to his collaboration with Dr. Mrazek, Dr. Weinshilboum collaborates with researchers in breast cancer as well. One such project examines the influence of genetic variations in a woman's response to tamoxifen, a drug often prescribed to prevent recurrence of breast cancer. Because the study is ongoing, results are not yet available.

But as interest in—and evidence for—pharacogenomic medicine grows, Dr. Weinshilboum fully expects to see more collaborations that scrutinize both the therapeutic and the toxic response to a given drug.

"Modern biological and medical science today is an international collaborative activity," Dr. Weinshilboum notes. "Many of our collaborations have been with investigators conducting leukemia trials in Sheffield, United Kingdom, and in Copenhagen, Denmark. In addition, we rely on extensive collaborations with investigators across the United States and, of course, here at Mayo. At Mayo Clinic we excel at collaboration—and we have the enormous clinical and research capacity to continue making significant contributions to this exciting field."

Reference

Mayo Medicine-Pharmacogenomics: Personalizing Medicine

hi,

Treatment of systemic disease with phosphorothioate antisense oligonucleotides (PS ASOs) has been accomplished using local or parenteral routes of administration to date. This report describes, for the first time, the effective oral delivery of a second generation oligonucleotide where significant milligram amounts of intact drug are absorbed in human subjects. In this study, a variety of oral solid dosage formulations were evaluated and it was determined that pulsing the delivery of sodium caprate (C10), a well-known permeation enhancer, in a novel manner may provide optimal ASO plasma bioavailability. Further, these dosage forms, containing C10 and ASO, were well tolerated in both fasted and fed volunteers. Oral absorption of the 2'-O-(2-methoxyethyl) modified antisense oligonucleotide (2'-MOE ASO), ISIS 104838, was demonstrated in healthy volunteers with an average 9.5% plasma bioavailability across four formulations tested. The greatest average performance achieved in this study for a single formulation was 12.0% bioavailability within an individual dose and subject range of 1.96-27.5%. The totality of the data suggests that formulations can be devised that allow oral administration of oligonucleotides that maintain systemic concentrations associated with inhibition of targeted human mRNA.

hello sir,

Pharmacogenomics is an extension of pharmacogenetics, a science described here in terms of five stages of development: 1) some clinical observations predicted genetic alterations of drug response; 2) additional case discoveries led to the term “pharmacogenetics,” a concept broadened by 3) many systemic case studies, and the realization of its wide applicability; 4) came the recognition of systematic pharmacogenetic differences between human populations. Then it became clear that 5) most human drug-repsonse differences were multifactorial, caused by many genetic alterations plus environmental factors. The recognition of these complexities, and the advance of genetics into genomics led to the broader science of pharmacogenomics. This led to plans to create “personalized medicine,” that is, making drug use more effective and safer by giving drugs that fit a person’s genes. Much of the science of genetics, dealing with gene structure, was changed by the realization that gene expression and thereby gene function was variable; this leads to systematic studies of drug action on genes, reversing the traditional studies of genes affecting drug action.
Finally, the realization that gene-protein variations contribute to most common diseases leads to efforts of creating new drugs that act on these variants.
yes, right now there is no universal therapy but in future there are chances of such therapy as the research is on progress.

hi,

The tissue microarray is a recently-implemented, high-throughput technology for the analysis of molecular markers in oncology. This research tool permits the rapid assessment of a biomarker in thousands of tumor samples, using commonly available laboratory assays such as immunohistochemistry and in-situ hybridization. Although introduced less than a decade ago, the TMA has proven to be invaluable in the study of tumor biology, the development of diagnostic tests, and the investigation of oncological biomarkers. This review describes the impact of TMA-based research in clinical oncology and its potential future applications. Technical aspects of TMA construction, and the advantages and disadvantages inherent to this technology are also discussed.

TMAs permit the rapid assessment of individual molecular markers on large patient cohorts. This approach complements molecular screening and discovery studies by confirming results on large numbers of primary tumor cases. TMAs have been so employed, for example, in the initial papers characterizing new breast cancer oncogenes such as EMSY and alpha-basic crystallin, and the recently-identified prostate cancer fusion oncogene TMPRSS2:ERG.
TMAs are similarly useful in characterizing the immunohistochemical profile of cancer subtypes. For example, two studies have applied a large panel of antibodies to determine differences in the molecular profile of BRCA1/2 breast cancer as compared to sporadic breast cancers. They found that BRCA1 tumors were hormone receptor and HER2 negative, p53 positive, and expressed a specific set of cell cycle antigens. There have also been studies that found new molecular markers in lower incidence cancers including nasopharyngeal cancer and malignant melanoma. The discovery of new molecular markers provides some insight into the biochemical aberrations that lead to malignant progression, and in turn, this knowledge can contribute to the development of specific targeted therapies. In a prostate cancer study using TMAs, it was reported that there was co-expression of HIF, androgen receptor, and VEGF. Based on their results, the authors suggested that androgens may regulate VEGF levels (a key angiogenesis factor) through the activation of HIF, a transcription factor that regulates biological processes in response to hypoxia.
Progression TMAs are composed of cores demonstrating distinct stages of neoplasia (normal tissue, pre-invasive lesions, low and high grade invasive tumors, etc.) and they are also useful in the development of diagnostic assays. For some cancers, there is increasing evidence that screening can reduce cancer incidence and mortality, suggesting that early detection and treatment can improve patient outcomes. Screening procedures, including mammography and endoscopy, will often diagnose pre-malignant conditions. Progression TMAs are used to determine the expression of a biomarker in different stages of neoplasia, and can be used to identify markers of malignant transformation. Recent studies have reported on the expression of PCNA to distinguish esophageal adenocarcinoma from Barrett’s esophagus, and have found that the loss of ANXII for prostatic epithelium is a marker for neoplasia.

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hi,

I can give you many references but before that consider the following example:

Purpose: To better understand microRNA miR-21 function in carcinogenesis, we analyzed miR-21 expression patterns in different stages of colorectal cancer development using in situ hybridization (ISH).

Experimental Design: Locked nucleic acid (LNA)/DNA probes and a biotin-free tyramide signal amplification system were used in ISH analyses of miRNA expression. Conditions for specific detection of miR-21 were determined using human cell lines and miR-21–expressing lentiviral vectors. Expression was determined in 39 surgically excised colorectal tumors and 34 endoscopically resected colorectal polyps.

Results: In the surgical samples, miR-21 expression was much higher in colorectal cancers than in normal mucosa. Strong miR-21 expression was also observed in cancer-associated stromal fibroblasts, suggesting miR-21 induction by cancer-secreted cytokines. Protein expression of PDCD4, a miR-21 target, was inversely correlated with miR-21 expression, confirming that miR-21 is indeed a negative regulator of PDCD4 in vivo. In the endoscopic samples, miR-21 expression was very high in malignant adenocarcinomas but was not elevated in nontumorigenic polyps. Precancerous adenomas also frequently showed miR-21 up-regulation.

Conclusion: Using the LNA-ISH system for miRNA detection, miR-21 was detectable in precancerous adenomas. The frequency and extent of miR-21 expression increased during the transition from precancerous colorectal adenoma to advanced carcinoma. Expression patterns of miR-21 RNA and its target, tumor suppressor protein PDCD4, were mutually exclusive. This pattern may have clinical application as a biomarker for colorectal cancer development and might be emphasized by self-reinforcing regulatory systems integrated with the miR-21 gene, which has been previously shown in cell culture.

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hi,

answers for your questions are as follows:

1. Singh et al. (1998) and Obika et al. (1998) reported on a minimal alteration of the pentose sugar of ribo- and deoxyribonucleotides that constrained, or “locked,” the sugar in the N-type conformation seen in A-form DNA. The lock was achieved via a 2’-O, 4’-C methylene linkage in 1,2:5,6 di-O-isopropylene-
-D-allofuranose. This alteration then served as the foundation for synthesizing locked nucleotide phosphoramidite monomers. Oligonucleotides containing one or more of these monomers were given the name lock nucleic acid, LNA (Koshkin et al, 1998).

LNAs were immediately seen to display remarkably increased thermodynamic stability and enhanced nucleic acid recognition. Initial investigations of LNA melting temperatures (Tm) by Koshkin et al. (1998) revealed increased values per LNA monomer (Tm) of +3 to +5oC and +4 to +8oC against complementary DNA and RNA oligonucleotides respectively. Subsequent examination of various LNA constructs indicated that the presence of a locked nucleotide influences the conformational status of adjacent unmodified nucleotides such that the N-type conformer is favored over the S-type conformer in those bases as well (Petersen et al., 2000). Also, Kvaerno and Wengel (1999) synthesized an abasic LNA monomer, a 1-deoxy-2-O, 4-C-methylene-Dribofuranose, that was used by them to examine the thermodynamic properties of the modified sugar alone against complementary DNA oligonucleotides. Their results indicate that the conformational restriction of the pentofuranose and backbone alone will not induce an increase in Tm. Thus, they conclude, the nucleobase is essential as a
mediator of the conformational change (Kvaerno and Wengel, 1999: 658).

These early studies suggested that LNAs could potentially be important tools for a wide range of molecular applications (cf., Braasch and Corey, 2001; Petersen and Wengel, 2003). Numerous recent reports have confirmed both the utility and theversatility of LNAs (see below) and a refined thermodynamic study of LNA-DNA duplex formation by McTigue et al. (2004) has contributed even greater precision to LNA design parameters. McTigue et al. (2004) examined hybridization entropy (Ho) and enthalpy (So) as well as Tm for 100 LNA-DNA duplexes containing a single internal LNA nucleotide. Their results show that LNA pyrimidines contribute more stability than do LNA purines
with average Tm values of 4.44±1.46oC for LNA-C, 3.21±1.41oC for LNA-T,
2.83±1.75oC for LNA-G, and 2.11±1.30oC for LNA-A. Further, the observed range of Tm for each LNA nucleotide is context dependent with both 5’ and 3’ unmodified neighbors influencing stability. Interestingly, purine neighbors appear to make the more substantial difference in stability. Their observations of Ho and So in their 100 constructs provide a more accurate overall Tm estimate for LNAs than previously available.

References
1. Braasch DA, and DR Corey 2001 Locked nucleic acid (LNA): fine-tuning the
recognition of DNMA and RNA. Chem Biol 8: 1-7.
2. Braasch DA, Y Liu, and DR Corey 2002 Antisense inhibition of gene expression in cells by oligonucleotides incorporating locked nucleic acids: effect of mRNA targetsequence and chimera design. NAR 30: 5160-5167.
3. Grunweller A, E Wyszko, B Bieber, R Jahnel, VA Erdmann, and J Kurreck 2003
Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2’-O-methyl RNA, phosphorothioates and small interfering RNA. NAR 31: 3185-3193.
4. Hendrix C, H Rosemeyer, B De Bouvere, A Van Aerschot, F Seela, and P Herdewijn 1997 1',5'-Anhydrohexitol oligonucleotides: hybridisation and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Eur J Chem 3: 1513–1520.
5. Hyrup B, and PE Nielson 1996 Peptide nucleic acids (PNA): synthesis, properties and potential applications. Bioorg Med Chem 4:5-23.
6. Johnson MP, LM Haupt, and LR Griffiths 2004 Locked nucleic acids (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. NAR 32: e55.
7. Koshkin AA, SK Singh, P Nielsen, VK Rajwanshi, R Kumar, M Meldgaard, CE Olsen, and J Wengel 1998 LNA (Locked Nucelic Acid): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54: 3607-3630.
8. Kurreck J, E Wyszko, C Gillen, and VA Erdmann 2002 Design of antisense
oligonucleotides stabilized by locked nucleic acids. NAR 30: 1911-1918.
Kvaerno L, and J Wengel 1999 Investigation of restricted backbone conformation as an explanation for the exceptional thermal stabilities of duplexes involving LNA (Locked Nucleic Acid): synthesis and evaluation of abasic LNA. Chem Commun 1999, 7: 657-658.
9. Latorra D, K Campbell, A Wolter, and JM Hurley 2003a Enhanced allele-specific PCR discrimination in SNP genotyping using 3’ locked nucleic acid (LNA) primers. Hum Mut 22: 79-85.
10. Latorra D, K Arar, and JM Hurley 2003b Design considerations and effects of LNA in PCR primers. Mol Cell Probes 17: 253-9.
11. McTigue PM, RJ Peterson, and JD Kahn 2004 Sequence-dependent thermodynamic
parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43:
5388-5405.
12. Nielson PE, and G Haaima 1997 Peptide nucleic acid (PNA). A DNA mimic with a pseudopeptide backbone. Chem Soc Rev 26: 73-78.

2. they are highly stable when conjugated with nanoparticles like gold, silver etc.

Reference

Locked Nucleic Acid–Nanoparticle
Conjugates- Dwight S. Seferos, David A. Giljohann,Nathaniel L. Rosi, and Chad A. Mirkin*[a].

3. Locked nucleic acids (LNAs) are RNA derivatives that have an O-methylene linkage between the 2 and 4 positions of the ribose. This leads to exceptionally high-affinity binding to complementary sequences. LNAs are synthesized from a commercially available sugar, 1,2:5,6-di-O-isopropylidene-a-d-allofuranose. An efficient and simplified procedure is presented for synthesizing a glycol donor that can be used for synthesis of a variety of LNA monomers. Then, as an example, the synthesis of the thymidine analog of LNA from this glycol donor is presented. The protocols give high yields of the desired products and avoid the use of time-consuming column chromatography.

Reference

Locked Nucleic Acids: Synthesis and Characterization of LNA‐T Diol
Henrik M. Pfundheller1, Christian Lomholt1
1Exiqon A/S, Vedbaek, Denmark Publication Name: Current Protocols in Nucleic Acid Chemistry Unit Number: UNIT 4.12
DOI: 10.1002/0471142700.nc0412s08 Print Publication Date: March, 2002
Online Posting Date: May, 2002

hi,

first ASO came into limelight which was then replaced by LNA in some cases(not in each case). generally LNA is considered as more advanced than ASO but both are mostly interrelated.

hi,

A locked nucleic acid (LNA), often referred to as inaccessible RNA, is a modified RNA nucleotide. The ribose moiety of an LNA nucleotide is modified with an extra bridge connecting the 2' and 4' carbons. The bridge "locks" the ribose in the 3'-endo structural conformation, which is often found in the A-form of DNA or RNA. LNA nucleotides can be mixed with DNA or RNA bases in the oligonucleotide whenever desired. Such oligomers are commercially available. The locked ribose conformation enhances base stacking and backbone pre-organization. This significantly increases the thermal stability (melting temperature) of oligonucleotides.

LNA nucleotides are used to increase the sensitivity and specificity of expression in DNA microarrays, FISH probes, real-time PCR probes and other molecular biology techniques based on oligonucleotides. For the in situ detection of miRNA the use of LNA is currently (2005) the only efficient method. A triplet of LNA nucleotides surrounding a single-base mismatch site maximizes LNA probe specificity unless the probe contains the guanine base of G-T mismatch.

References

1. ^ Kaur, H; Arora, A; Wengel, J; Maiti, S (2006). "Thermodynamic, Counterion, and Hydration Effects for the Incorporation of Locked Nucleic Acid Nucleotides into DNA Duplexes". Biochemistry 45 (23): 7347–55. doi:10.1021/bi060307w. PMID 16752924.
2. ^ You Y.; Moreira B.G.; Behlke M.A. and Owczarzy R. (2006). "Design of LNA probes that improve mismatch discrimination". Nucleic Acids Res. 34 (8): e60. doi:10.1093/nar/gkl175. PMID 16670427

Benefits of the LNA™ technology

Some of the benefits of using LNA™ include:

* Ideal for the detection of short RNA and DNA targets
* Increases the thermal stability of duplexes
* Capable of single nucleotide discrimination
* Resistant to exo- and endonucleases resulting in high stability in vivo and in vitro applications
* Increased target specificity
* Facilitates T m normalization
* Strand invasion properties enables detection of “hard to access” samples
* Compatible with standard enzymatic processes

The placement of the LNA™ monomers is of great importance for the performance of the oligonucleotide. Exiqon has developed in-house algorithms that enable the design of LNA™-enhanced oligonucleotides with high melting temperatures ( T m), optimal mismatch discrimination and high binding specificity while avoiding unacceptable secondary structure and self-complementarity.

The major disadvantages in using LNAzymes in cells are
the same as for all other antisense strategies, namely the
difficulty in achieving efficient uptake and localization of
the oligonucleotide.

References
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hi,

Genomics
• Chemogenomics
• Structural genomics
• Pharmacogenetics
• Toxicogenomics
• Clinomics
• p450

references

1. ^ "Guidance for Industry Pharmacogenomic Data Submissions" (PDF). U.S. Food and Drug Administration. March 2005. http://www.fda.gov/cder/guidance/6400fnl.pdf. Retrieved 2008-08-27.

Pharmacogenomics is the study of a patient's genes to predict response to drugs and hence select the right drug and the right quantity.

FDA have Released a List of Genomic Biomarkers Predictive of Drug Interactions in August 1, 2008 http://www.fda.gov/cder/genomics/genomic_biomarkers_table.htm