1. Antisense therapy
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Antisense therapy is a form of treatment for genetic disorders or infections. When the
genetic sequence of a particular gene is known to be causative of a particular disease, it is
possible to synthesize a strand of nucleic acid (DNA, RNA or a chemical analogue) that will
bind to the messenger RNA (mRNA) produced by that gene and inactivate it, effectively
turning that gene "off". This is because mRNA has to be single stranded for it to be
translated. Alternatively, the strand might be targeted to bind a splicing site on pre-mRNA
and modify the exon content of an mRNA.[1]
This synthesized nucleic acid is termed an "anti-sense" oligonucleotide because its base
sequence is complementary to the gene's messenger RNA (mRNA), which is called the
"sense" sequence (so that a sense segment of mRNA " 5'-AAGGUC-3' " would be blocked by
the anti-sense mRNA segment " 3'-UUCCAG-5' ").
Antisense drugs are being researched to treat cancers (including lung cancer, colorectal
carcinoma, pancreatic carcinoma, malignant glioma and malignant melanoma), diabetes,
Amyotrophic lateral sclerosis (ALS), Duchenne muscular dystrophy and diseases such as
asthma, arthritis and pouchitis with an inflammatory component. Most potential therapies
have not yet produced significant clinical results[citation needed], though two antisense drugs have
been approved by the U.S. Food and Drug Administration (FDA), fomivirsen (marketed as
Vitravene) as a treatment for cytomegalovirus retinitis and mipomersen (marketed as
Kynamro] for homozygous familial hypercholesterolemia.
Example antisense therapies
Some 40 antisense oligonucleotides and siRNAs are in clinical trials, including over 20 in
advanced clinical trials (Phase II or III).[2][3]
Cytomegalovirus retinitis
Fomivirsen (marketed as Vitravene), was approved by the U.S. FDA in Aug 1998 as a
treatment for cytomegalovirus retinitis.
Hemorrhagic fever viruses
In early 2006, scientists studying the Ebola hemorrhagic fever virus at USAMRIID
announced a 75% recovery rate after infecting four rhesus monkeys and then treating them
with an antisense Morpholino drug developed by Sarepta Therapeutics (formerly named AVI
BioPharma), a U.S. biotechnology firm.[4] The usual mortality rate for monkeys infected with
Ebola virus is 100%. In late 2008, AVI BioPharma successfully filed Investigational New
Drug (IND) applications with the FDA for its two lead products for Marburg and Ebola
viruses. These drugs, AVI-6002 [5] and AVI-6003 are novel analogs based on AVI's PMO
antisense chemistry in which anti-viral potency is enhanced by the addition of positively-
charged components to the morpholino oligomer chain. Preclinical results of AVI-6002 and

2. AVI-6003 demonstrated reproducible and high rates of survival in non-human primates
challenged with a lethal infection of the Ebola and Marburg viruses, respectively.[6]
Cancer
Also in 2006, German physicians reported on a dose-escalation study for the compound AP
12009 (a phosphorothioate antisense oligodeoxynucleotide specific for the mRNA of human
transforming growth factor TGF-beta2) in patients with high grade gliomas. At the time of
the report, the median overall survival had not been obtained and the authors hinted at a
potential cure.[7]
HIV/AIDS
Starting in 2004, researchers in the US have been conducting research on using antisense
technology to combat HIV.[8]
In February 2010 researchers reported success in reducing HIV viral load using patient T-
cells which had been harvested, modified with an RNA antisense strand to the HIV viral
envelope protein, and re-infused into the patient during a planned lapse in retroviral drug
therapy.[9]
Familial Hypercholesterolemia
In January 2013 mipomersen (marketed as Kynamro] was approved by the FDA for the
treatment of homozygous familial hypercholesterolemia.[
Oligonucleotide synthesis
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Oligonucleotide synthesis is the chemical synthesis of relatively short fragments of nucleic
acids with defined chemical structure (sequence). The technique is extremely useful in
current laboratory practice because it provides a rapid and inexpensive access to custom-
made oligonucleotides of the desired sequence. Whereas enzymes synthesize DNA and RNA
in a 5' to 3' direction, chemical oligonucleotide synthesis is carried out in the opposite, 3' to 5'
direction. Currently, the process is implemented as solid-phase synthesis using
phosphoramidite method and phosphoramidite building blocks derived from protected 2'-
deoxynucleosides (dA, dC, dG, and T), ribonucleosides (A, C, G, and U), or chemically
modified nucleosides, e.g. LNA.
To obtain the desired oligonucleotide, the building blocks are sequentially coupled to the
growing oligonucleotide chain in the order required by the sequence of the product (see
Synthetic cycle below). The process has been fully automated since the late 1970s. Upon the
completion of the chain assembly, the product is released from the solid phase to solution,
deprotected, and collected. The occurrence of side reactions sets practical limits for the length
of synthetic oligonucleotides (up to about 200 nucleotide residues) because the number of
errors accumulates with the length of the oligonucleotide being synthesized.[1] Products are
often isolated by high-performance liquid chromatography (HPLC) to obtain the desired

3. oligonucleotides in high purity. Typically, synthetic oligonucleotides are single-stranded
DNA or RNA molecules around 15–25 bases in length.
Oligonucleotides find a variety of applications in molecular biology and medicine. They are
most commonly used as antisense oligonucleotides, small interfering RNA, primers for DNA
sequencing and amplification, probes for detecting complementary DNA or RNA via
molecular hybridization, tools for the targeted introduction of mutations and restriction sites,
and for the synthesis of artificial genes.
DNA sense
Schematic showing how antisense DNA strands can interfere with protein translation.
Molecular biologists call a single strand of DNA sense (or positive (+) ) if an RNA version
of the same sequence is translated or translatable into protein. Its complementary strand is
called antisense (or negative (-) sense). Sometimes the phrase coding strand is encountered;
however, protein coding and non-coding RNA's can be transcribed similarly from both
strands, in some cases being transcribed in both directions from a common promoter region,
or being transcribed from within introns, on both strands (see "ambisense" below).[1][2][3]
Antisense DNA
The two complementary strands of double-stranded DNA (dsDNA) are usually differentiated
as the "sense" strand and the "antisense" strand. The DNA sense strand looks like the
messenger RNA (mRNA) and can be used to read the expected protein code by human eyes
(e.g. ATG codon = Methionine amino acid). However, the DNA sense strand itself is not
used to make protein by the cell. It is the DNA antisense strand which serves as the source for
the protein code, because, with bases complementary to the DNA sense strand, it is used as a
template for the mRNA. Since transcription results in an RNA product complementary to the
DNA template strand, the mRNA is complementary to the DNA antisense strand. The mRNA
is what is used for translation (protein synthesis).
Hence, a base triplet 3'-TAC-5' in the DNA antisense strand can be used as a template which
will result in an 5'-AUG-3' base triplet in mRNA (AUG is the codon for Methionine, the start
codon). The DNA sense strand will have the triplet ATG which looks just like AUG but will
not be used to make Methionine because it will not be used to make mRNA. The DNA sense
strand is called a "sense" strand not because it will be used to make protein (it won't be), but
because it has a sequence that looks like the protein codon sequence.
Students may find this confusing if they misunderstand the meaning of "sense" and if they
misunderstand complementation. To make things more confusing, before the convention was

4. set, very early textbooks disagreed on the DNA strands called "sense" and "antisense."[citation
needed]
In biology and research, short antisense molecules can interact with complementary strands
of nucleic acids, modifying expression of genes. See the section on "antisense
oligonucleotides" below.
Example with double-stranded DNA
DNA strand 1: antisense strand (copied to)→ RNA strand (sense)
DNA strand 2: sense strand
Some regions within a double strand of DNA code for genes, which are usually instructions
specifying the order of amino acids in a protein along with regulatory sequences, splicing
sites, noncoding introns, and other complicating details. For a cell to use this information, one
strand of the DNA serves as a template for the synthesis of a complementary strand of RNA.
The template DNA strand is called the transcribed strand with antisense sequence and the
mRNA transcript is said to be sense sequence (the complement of antisense). Because the
DNA is double-stranded, the strand complementary to the antisense sequence is called non-
transcribed strand and has the same sense sequence as the mRNA transcript (though T bases
in DNA are substituted with U bases in RNA).
DNA antisense strand
5'CGCTATAGCGTTTCAT 3' (template/noncoding), Used as a template for transcription.
Watson strand
DNA sense strand
3'GCGATATCGCAAAGTA 5' (nontemplate/coding), Complementary to the template strand.
Crick strand
RNA strand that is transcribed from the
noncoding (template/antisense) strand.
Note1: Except for the fact that all thymines
are now uracils (T-->U), it is complementary
3'GCGAUAUCGCAAAGUA 5' mRNA Sense transcript to the noncoding (template/antisense) DNA
strand (identical to the coding
(nontemplate/sense) DNA strand). Note2
There is an AUG start codon at the 5' end
(although written backwards here).
RNA strand that is transcribed from the
mRNA Antisense coding (nontemplate/sense) strand. Note:
5'CGCUAUAGCGUUUCAU 3' Except for the fact that all thymines are now
transcript
uracils (T-->U), it is complementary to the
coding (nontemplate/sense) DNA strand

5. (identical to the noncoding
(template/antisense) DNA strand.)
A note on the confusion between "sense" and "antisense" strands: The strand names actually
depend on which direction you are writing the sequence that contains the information for
proteins (the "sense" information), not on which strand is on the top or bottom (that is
arbitrary). The only real biological information that is important for labeling strands is the
location of the 5' phosphate group and the 3' hydroxyl group because these ends determine
the direction of transcription and translation. A sequence 5' CGCTAT 3' is equivalent to a
sequence written 3' TATCGC 5' as long as the 5' and 3' ends are noted. If the ends are not
labeled, convention is to assume that the sequence is written in the 5' to 3' direction. Good
rule of thumb for figuring out the "sense" strand: Look for the start codon ATG (AUG in
mRNA). In the table example, the sense mRNA has the AUG codon at the end (remember
that translation proceeds in the 5' to 3' direction).
Ambisense
A single-stranded genome that contains both positive-sense and negative-sense is said to be
ambisense. Bunya viruses have 3 single-stranded RNA (ssRNA) fragments containing both
positive-sense and negative-sense sections; arenaviruses are also ssRNA viruses with an
ambisense genome, as they have 2 fragments that are mainly negative-sense except for part of
the 5' ends of the large and small segments of their genome.
Antisense RNA
Main article: Antisense RNA
Antisense RNA is an RNA transcript that is complementary to endogenous mRNA. In other
words, it is a non-coding strand complementary to the coding sequence of RNA; this is
similar to negative-sense viral RNA. Introducing a transgene coding for antisense RNA is a
technique used to block expression of a gene of interest. Radioactively-labelled antisense
RNA can be used to show the level of transcription of genes in various cell types. Some
alternative antisense structural types are being experimentally applied as antisense therapy,
with at least one antisense therapy approved for use in humans.
When mRNA forms a duplex with a complementary antisense RNA sequence, translation is
blocked. This process is related to RNA interference.
Antisense nucleic acid molecules have been used experimentally to bind to mRNA and
prevent expression of specific genes. Antisense therapies are also in development; in the
USA, the Food and Drug Administration (FDA) has approved phosphorothioate antisense
oligos fomivirsen (Vitravene) and mipomersen (Kynamro)[4] for human therapeutic use.
Cells can produce antisense RNA molecules naturally, which interact with complementary
mRNA molecules and inhibit their expression.

6. RNA sense in viruses
In virology, the genome of an RNA virus can be said to be either positive-sense, also known
as a "plus-strand", or negative-sense, also known as a "minus-strand". In most cases, the
terms sense and strand are used interchangeably, making such terms as positive-strand
equivalent to positive-sense, and plus-strand equivalent to plus-sense. Whether a virus
genome is positive-sense or negative-sense can be used as a basis for classifying viruses.
Positive-sense
Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may be
directly translated into the desired viral proteins. Therefore, in positive-sense RNA viruses,
the viral RNA genome can be considered viral mRNA, and can be immediately translated by
the host cell. Unlike negative-sense RNA, positive-sense RNA is of the same sense as
mRNA. Some viruses (e.g., Coronaviridae) have positive-sense genomes that can act as
mRNA and be used directly to synthesize proteins without the help of a complementary RNA
intermediate. Because of this, these viruses do not need to have an RNA polymerase
packaged into the virion.
Negative-sense
Negative-sense (3' to 5') viral RNA is complementary to the viral mRNA and thus must be
converted to positive-sense RNA by an RNA polymerase prior to translation. Negative-sense
RNA (like DNA) has a nucleotide sequence complementary to the mRNA that it encodes.
Like DNA, this RNA cannot be translated into protein directly. Instead, it must first be
transcribed into a positive-sense RNA that acts as an mRNA. Some viruses (Influenza, for
example) have negative-sense genomes and so must carry an RNA polymerase inside the
virion.
Antisense oligonucleotides
Gene silencing can be achieved by introducing into cells a short "antisense oligonucleotide"
that is complementary to an RNA target. This experiment was first done by Zamecnik and
Stephenson in 1978[5] and continues to be a useful approach, both for laboratory experiments
and potentially for clinical applications (antisense therapy).[6]
If the antisense oligonucleotide contains a stretch of DNA or a DNA mimic
(phosphorothioate DNA, 2'F-ANA, or others) it can recruit RNase H to degrade the target
RNA. This makes the mechanism of gene silencing catalytic. Double-stranded RNA can also
act as a catalytic, enzyme-dependent antisense agent through the RNAi/siRNA pathway,
involving target mRNA recognition through sense-antisense strand pairing followed by target
mRNA degradation by the RNA-induced silencing complex (RISC). The R1 plasmid hok/sok
system provides yet another example of an enzyme-dependent antisense regulation process,
through enzymatic degradation of the resulting RNA duplex.
Other antisense mechanisms are not enzyme-dependent, but involve steric blocking of their
target RNA (e.g. to prevent translation or induce alternative splicing). Steric blocking
antisense mechanisms often use oligonucleotides that are heavily modified. Since there is no

7. need for RNase H recognition, this can include chemistries such as 2'-O-alkyl, peptide
nucleic acid (PNA), locked nucleic acid (LNA), and Morpholino oligomers.
Antisense RNA
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(Redirected from Antisense mRNA)
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Antisense RNA (asRNA) is a single-stranded RNA that is complementary to a messenger
RNA (mRNA) strand transcribed within a cell. Antisense RNA may be introduced into a cell
to inhibit translation of a complementary mRNA by base pairing to it and physically
obstructing the translation machinery.[1] This effect is therefore stoichiometric. An example
of naturally occurring mRNA antisense mechanism is the hok/sok system of the E. coli R1
plasmid. Antisense RNA has long been thought of as a promising technique for disease
therapy; the only such case to have reached the market is the drug fomivirsen. One
commentator has characterized antisense RNA as one of "dozens of technologies that are
gorgeous in concept, but exasperating in [commercialization]".[2] Generally, antisense RNA
still lack effective design, biological activity, and efficient route of administration.[3]
Historically, the effects of antisense RNA have often been confused with the effects of RNA
interference (RNAi), a related process in which double-stranded RNA fragments called small
interfering RNAs trigger catalytically mediated gene silencing, most typically by targeting
the RNA-induced silencing complex (RISC) to bind to and degrade the mRNA. Attempts to
genetically engineer transgenic plants to express antisense RNA instead activate the RNAi
pathway, although the processes result in differing magnitudes of the same downstream
effect, gene silencing. Well-known examples include the Flavr Savr tomato and two cultivars
of ringspot-resistant papaya.[4][5]
Transcription of longer cis-antisense transcripts is a common phenomenon in the mammalian
transcriptome.[6] Although the function of some cases have been described, such as the
Zeb2/Sip1 antisense RNA, no general function has been elucidated. In the case of
Zeb2/Sip1,[7] the antisense noncoding RNA is opposite the 5' splice site of an intron in the
5'UTR of the Zeb2 mRNA. Expression of the antisense ncRNA prevents splicing of an intron
that contains a ribosome entry site necessary for efficient expression of the Zeb2 protein.
Transcription of long antisense ncRNAs is often concordant with the associated protein-
coding gene,[8] but more detailed studies have revealed that the relative expression patterns of
the mRNA and antisense ncRNA are complex.[9

8. Antisense therapy in Modern medicine
Antisense therapy is one of the types of treatment for genetic disorders. The therapy aims at
working at the mRNA level and switching off the translation of the protein from the mRNA
of a mutated gene. Hence, the antisense drugs are responsible for the silencing of the gene
responsible for the disease and thereby have great potential to cure many incurable, genetic
diseases. Extensive research is going on in this field to develop antisense drugs for HIV,
Cancer, Asthma, etc.
Antisense refers to a stretch of oliognucleotides, which may be DNA or RNA, that is

9. complementary to the mRNA, produced from the target gene. The antisense, then binds to the
mRNA and stop the translation and expression of the protein from the mRNA, thereby
silencing the target gene, although the exact mechanism by which the gene silencing takes
place is not certain. It is proposed that maybe the mRNA and antisense oligonucleotides or
ASO form a duplex structure, thereby mediating the cleavage of mRNA by RNAase H. Some
other models have also been proposed like the mRNA transport to the cytoplasm being
prevented, the formation of triple helix structure by the binding of the ASO with the duplex
DNA, inhibiting DNA transcription, inhibition of the splicing of the mRNA, etc. The
construction of a proper ASO is very essential and is possible only after the proper study of
the genes responsible for the disease and the sequence of the mRNA formed from the
transcription of the gene. The site available for the hybridization of the ASO on the mRNA
must also be known as then only the ASO can bind to the mRNA and switch off the
expression of the mRNA. The in-vivo stability of the ASO is crucial as it has to reach the
target mRNA within the cell without getting degraded. The ASO drugs are developed by
proper chemical modification to their backbone structure such that they are resistant to the
degradation by nuclease and have proper tissue distribution within the body along with good
in-vivo half life.
The use of ASO drugs over other drugs is advantageous as the latter usually target the
proteins formed during the expression of the disease, while the former works at the gene
level. The ASOs being made of nucleotides are much easier to prepare as only the sequence
of the mRNA is needed. The ASO target is only of one domain, compared to multiple
domains in case of protein related drugs. Hence, the sensitivity of the ASO drugs can be
easily measured by scanning or the southern and northern blotting. The manifestation of the
diseases in case of the ASO drugs is much less as the mRNA is itself silenced, hence to
overcome this silencing the clonal expansion of the cells that is needed takes a long time. The
binding of the ASO with the mRNA is by means of hydrogen bonds, which is much more
stronger than any other types of forces like Van der Waals force, etc which occurs in case of
the binding of the drugs to proteins.
The research on the ASO therapeutics has moved from the pre-clinical models to the clinical
trials. Antisense technology has proved to be a formidable tool for the discovery and study of
the various physiological and pathological processes within the body. The research going on
will refine the drug delivery methods, specificity, and affinity of the antisense therapeutics,
which would be a better tool for the treatment of the patients considering the progress in the
use of various gene therapies for treating incurable diseases. ASOs are being researched upon
for the treatment of different types of cancer, diabetes, Duchanne muscular dystrophy,
obesity, different inflammatory diseases like Asthma, autoimmune diseases like HIV/AIDS,
different cardiovascular diseases and many other diseases.
Antisense technology has proved to be better method of treatment considering short drug
development time and lesser failure in clinical trials compared to other traditional drugs. The
approach of the antisense technology is in accord with the latest, emerging technology in the
drug development process, technologies based on genome and the integration of the
therapeutics with diagnostics. Hence, these advantages put the ASO therapy on a higher scale
than the other drugs targeting proteins, which gives scope for further research on the topic.
Antisense technology has provided a good base for the research of more new and highly
specific therapeutics.

10. Laboratory of Molecular Design
Antisense Therapy
If a particular gene has a role in disease, and the genetic code of that gene is known, one
could use this knowledge to stop that gene specifically. Genes are made of double-helical
DNA. When a gene is turned on, the genetic code in that segment of DNA is copied out as a
single strand of RNA, called messenger RNA. The messenger RNA is called a "sense"
sequence, because it can be translated into a string of amino acids to form a protein. The
opposite strand in a DNA double helix (A opposite T, T opposite A, C opposite G, G opposite C)
is called the "antisense" strand. We use the antisense coding sequence of a disease gene to
make short antisense DNAs in our laboratory. These antisense DNA drugs work by binding
to messenger RNAs from disease genes, so that the genetic code in the RNA cannot be read,
stopping the production of the disease-causing protein.
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