This document discusses strategies for designing antisense molecules and their applications. It describes antisense technology as a method to inhibit protein production by introducing single-stranded nucleotides that bind to mRNA. It discusses various strategies for designing antisense oligonucleotides including modifying phosphodiester linkages, targeting protein-binding sites, avoiding sequences that could form structures, and delivering the oligonucleotides into cells. The document also notes limitations of antisense oligonucleotides such as an inability to activate RNase H cleavage and challenges with delivery and dosage.

1. Pandit Ravishankar Shukla University
S.O.S In Biotechnology
Topic :- Strategies For Designing of Antisense Molecules And Its Application
Guided by :-
Dr. Nagendra Chandrawanshi
Submitted by :-
P. Sujata
Msc II sem
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2. Content
 Antisense technology
 Mechanism of antisense oligonucleotides
 Anti mRNA strategy
 Designing of antisense oligonucleotide
 Delivery of AS-ONs into the cells
 Limitation of antisense oligonucleotides
 Application of antisense oligonucleotides
 Conclusion
 Reference
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3. ANTISENSE TECHNOLOGY
Diseases are often connected to the insufficient or
excess production of certain “Proteins”.
If the production of these proteins is disputed many
diseases can be treated or cured.
Antisense technology is a method that can dispute
protein production. It may be used to design new
therapeutics for diseases in whose pathology the
production of a specific protein plays a crucial role.

4.  Antisense technology is a method to
inhibit translation of mRNA into
protein by introducing single stranded
nucleotides (oligo deoxy
nucleotides).
 The potential of
oligodeoxynucleotides to act as
antisense agents that inhibit viral
replication in cell culture was
discovered by Zamecnik and
Stephenson in 1978.
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5. What is Antisense
Oligonucleotide ?
 “Sense” refers to the original
sequence of the DNA or RNA
molecule. “Antisense” refers to the
complementary sequence of the DNA
or RNA molecules.
 Antisense oligonucleotides (As-ODNs)
are single stranded, synthetically
prepared strands of deoxynucleotide
sequences, usually 18–21 nucleotides
in length, complementary to the
mRNA sequence of the target gene.
 As-ODNs are able to selectively bind
cognate mRNA sequences by
sequence - specific hybridization.
 This results in cleavage or
disablement of the mRNA and, thus,
inhibits the expression of the target
gene.
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6. Mechanism of antisense nucleotides
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7. Anti mRNA - Strategy
 Antisense agents are valuable tools to inhibit the
expression of a target gene in a sequence-
specific manner.
 Three types of Anti-mRNA strategies can be
distinguished.
 The use of single stranded antisense
oligonucleotides
The triggering of RNA cleavage through catalytically
active oligonucleotides referred to as ribozymes.
 RNA interference induced by small interfering RNA
molecules. (si RNA)
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8. Designing of antisense molecules
 Modification of phospho oligonucleotide
 Ribonuclease H–Mediated Antisense Activity
 Oligo length
 Targeting protein-binding sites.
 Sequence Checks
 CG-containing sequences
 Tetraplexes formation
 Other motifs
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9. Antisense oligonucleotides modification
 One of the major challenges for antisense approaches is
the stabilization of ONs, as unmodified
oligodeoxynucleotides are rapidly degraded in biological
fluids by nucleases.
 These antisense oligonucleotides are based on two
mechanism:- Rnase –H dependent oligonucleotides and
Steric blocker oligonucleotide.
 In general, three types of modifications of
ribonucleotides can be distinguished .
 ‘First generation’ antisense- oligonucleotide
 ‘Second generation’ antisense- oligonucleotides
 ‘Third generation’ antisense-oligonucleotides
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10. First generation antisense
oligonucleotides
The first generation ODNs are
synthesized by replacing one
of the non-bridging oxygen
atoms in the phosphate group
with either a sulfur group
(phosphorothioates), methyl
group (methyl phosphonates)
or amines
(phosphoramidates).
They use RNaseH for
degradation of mRNA by
blocking translation.10

11. Advantages of 1st
generation AN-ODN’s
Disadvantages of 1st
generation AN-ODN’s
 The first generation
ODNs have more
resistance to nucleases .
 They have longer plasma
half life as compared with
phosphodiester
oligonucleotides.
 They are easy to
synthesize, carry negative
charges that ease their
cell delivery, are capable
of activating RNAse H.
 It was used for the
inhibition of HIV
replication.
 The major disadvantage of
PS oligodeoxynucleotides
is their binding to certain
proteins, such as heparin-
binding proteins.
 After PS DNA treatment of
primates, serious acute
toxicity was observed as a
result of a transient
activation of the
complement cascade that
has led to cardiovascular
collapse and death.
 In addition, the clotting
cascade was altered after
the administration of PS11

12. Second generation antisense
oligonucleotodes
 The problems associated with
phosphorothioate
oligodeoxynucleotides are to
some degree solved in second
generation ONs containing
nucleotides with alkyl
modifications at the 2¢ position of
the ribose.
 2¢-O-methyl and 2¢-O-methoxy-
ethyl are the most important
members of this class.
 They are RNase H independent
mechanism.
 Their mechanism depends on
translation arrest by blocking 80s
ribosome complex formation as
well as with splicing interference.12

13. Advantages of Second generation
antisense oligonucleotodes
• They show high binding affinity to target mRNA.
• Best stability to nucleases.
• Less toxic than first generation AS-ON.
• Higher lipophilicity compared to first generation AS-Ons.
• Gapmers were used in these drugs which solved irrelevent cleavage.
• Gapmers consist of a central stretch of DNA or phosphorothioate
DNA monomers and modified nucleotides such as 2’-O-methyl
RNA at each end.
• The end blocks prevent nucleolytic degradation of the AS-ON .
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14. THIRD GENERATION’ ANTISENSE-
OLIGONUCLEOTIDES
 In recent years a variety of
modified nucleotides have been
developed to improve
properties such as target
affinity, nuclease resistance
and pharmacokinetics.
 The concept of conformational
restriction has been used
widely to enhance binding
affinity and biostability.
 DNA and RNA analogs with
modified phosphate linkages or
riboses as well as nucleotides
with a completely different
chemical moiety substituting
the furanose ring have been
developed. 14

15. Peptide nucleic acids (PNAs).
 In PNAs the deoxyribose phosphate backbone is
replaced by polyamide linkages.
 PNA was first introduced by Nielsen and coworkers
in 1991 .
 PNAs have favorable hybridization properties and
high biological stability, but do not elicit target RNA
cleavage by RNase H.
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16. N3¢-P5¢ phosphoroamidates (NPs).
 N3¢-P5¢ phosphoroamidates (NPs) are another
example of a modified phosphate backbone, in which
the 3¢-hydroxyl group of the2¢-
deoxyriboseringisreplacedbya3¢-aminogroup.
 NPs exhibit both a high affinity towards a
complementary RNA strand and nuclease resistance
.
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17. Locked nucleic acid (LNA).
 A ribonucleotide containing a methylene bridge that
connects the 2’-oxygen of the ribose with the 4’-
carbon.
 Introduction of LNA into a DNA ON induces a
conformational change of the DNA-RNA duplex
towards the A-type helix and therefore prevents
RNase H cleavage of the target RNA.
 2’-O-methyl–LNA ONs that do not activate RNase H
could, however, be used as steric blocks to inhibit
intracellular HIV-1 Tat-dependent trans activation
and hence suppress gene expression .
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18. Cyclohexene nucleic acids (CeNA)
 Cyclohexene nucleic acids (CeNA). Replacement of
the five-membered furanose ring by a six-membered
ring is the basis for cyclohexene nucleic acids
(CeNAs), which are characterized by a high degree of
conformational rigidity of the oligomers.
 They form stable duplexes with complementary DNA
or RNA and protect ONs against nucleolytic
degradation .
 Therefore, the design of ONs with CeNA has a long
way to go in order to obtain highly efficient AS
agents.
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19. Tricyclo-DNA (tcDNA).
 Tricyclo-DNA (tcDNA) is another nucleotide with
enhanced binding to complementary sequences,
which was first synthesized by Leumann and
coworkers.
 Tricyclo-DNA tcDNA does not activate RNase H
cleavage of the target mRNA.
 It was, however, successfully used to correct aberrant
splicing of a mutated beta -globin mRNA.
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20. 20

21. Ribonuclease H–Mediated
Antisense Activity
• The RNase H class of endonucleases acts primarily in
the nucleus, although activity can de detected in
cytoplasm . It is thought that the antisense
oligonucleotide probe binds specifically to target
mRNA, which initiates RNase H–mediate stranded
antisense probe:mRNA hybrid . RNA degradation
products corresponding to the fragments expected from
RNase H action can be detected in living cells treated
with antisense agents .
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22. Oligo length
 The stability of hybrids can depend on length, particularly for shorter
oligonucleotides. Also, as the length of an oligonucleotide increases, it
is less likely that it will encounter a complementary sequence other
than the targeted RNA.
 On the other hand, increasing the length of the oligonucleotide
increases the probability that it will bind a partially complementary
sequence in a non-target message, thereby activating RNase H, which
requires only six or seven base pairs in a heteroduplex substrate for
activation.
 The usual length for antisense oligonucleotides is around 20 bases,
which is a convenient size for synthesis and long enough, on
statistical grounds, to be unique in the human genome.
 In special cases, structural features in the target RNA may enable the
use of shorter oligomers . However, most studies find a decrease or loss
of antisense activity as length is reduced from twenty to ten bases
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23. Targeting protein-binding sites
 Sequences in RNA that interact with proteins, ribosomes,
spliceosomes, and other large entities are also likely to be
accessible to oligon assuming no unwinding activity is required.
 Early on, the cap, initiator codon, and 3’-end were selected as
targets .
 Many later studies have also found that the initiator codon is a
good target and has become something of an industry standard
despite the occasional failure.
 Antisense oligonucleotides have also been used to redirect
splicing to prevent formation of the functional mRNA .
 Successful targeting of splice sites requires that the
oligonucleotide gain access to the nucleus whereas inhibition of
translation may be accomplished by hybridization in the
cytoplasm.
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24. Sequence Checks
 Before synthesizing an antisense
oligonucleotide, the investigator should check
the sequence for various features that could
affect its activity.
 For instance, if the sequence complements
non-target RNAs, the probe may not be useful.
 In addition, the oligonucleotide should be
examined for self-complementary sequences
that might interfere with hybridization to the
target.
 Certain sequence motifs have potent biological
effects unrelated to antisense activity.
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25. CG-CONTAINING SEQUENCES
 Oligonucleotides containing CG can act as
immunostimulators by causing proliferation of B
lymphocytes; by activating macrophages, dendritic cells,
and T cells; and by inducing cytokine release .
 These CG mediated immune effects depend on the
sequences flanking the CG dimer, and are strongest
with the purine.purine, pyrimidine.pyrimidine motif .
 The easiest solution is to choose oligonucleotides that
do not contain CG, particularly those with flanking
sequences that favor immune stimulation.
 An alternative is to replace the C in CG sequences with
5-methylcytidine .
 Although it increases the expense of synthesis, this 5-
methyl cytidine substitution prevents immune stimulation
without affecting hybridization.
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26. Tetraplex Formation
 In addition to forming duplexes and hairpins by Watson–Crick base
pairing, some oligonucleotides can form structures comprising
three, four, or more strands. In particular, formation of tetraplexes
with potent biological activity has caused some problems in the
antisense field
 The most extensively studied tetraplexes are formed by
oligonucleotides containing multiple adjacent guanine residues .
These may occur in a single run of around four residues but they
can also be found in repeated GG or GGG motifs that occur in
close proximity .
 Even if they do not form tetraplexes, G-rich sequences with
multiple GG dimers may form other unusual structures depending
on sequence context .
 Tetraplex-forming runs of Gs seem to have an affinity for various
proteins and when included in synthetic oligonucleotides, they
produce a multitude of biological effects.
 The ability to form tetraplexes can be blocked by replacing
guanosine residues with 7-deazaG or 6-thioG . It should also be
noted that a phosphorothioate oligonucleotide containing only C
residues was shown to have activity similar to one containing a G-
tetraplex . 26

27.  Investigators have suggested that stretches
of purines in the target might stabilize the
heteroduplex formed .
 From examining the sequences of active
antisense oligonucleotides in many published
studies, investigators have proposed that
selecting a target containing the sequence
GGGA gives a much better chance of success
.
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28. Delivery of Antisense into cells
(a) Endocytosis: One of the simplest methods to get nucleotide in
the cell, it relies on the cells natural process of receptor mediated
endocytosis. The drawbacks to this method are the long amount of
time for any accumulation to occur, the unreliable result, and the
inefficiency.
(b) Micro-Infection: As the name implies, the antisense molecule
would be injected into the cell. The yield of this method is very high,
but because of the precision needed to inject a very small cell with
smaller molecules only about 100 cells can be injected per day.
(c) Liposome–Encapsulation: This is the most effective method,
but also a very expensive one. Liposome encapsulation can be
achieved by using products such as lipofect ACE™ to create a
cationic phospholipids bilayer that will surround the nucleotide
sequence. The resulting liposome can merge with the cell
membrane allowing the antisense to enter the cell.
(d) Electroporation: The conventional method of adding a
nucleotide sequence to a cell can also be used. The antisense
molecule should transverse the cell membrane offer a shock is
applied to the cells.
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29. Limitations of antisense
oligonucleotides
 A major inherent disadvantage of nucleotides with
modifications in the ribose moiety is their inability to
activate efficient RNase H cleavage of the target RNA.
 Delivery of the treatment to the brain is challenging because
it must cross the blood – brain barrier.
 Entry of antisense oligos can’t be accomplished through
injection or a pill.
 It can cause unintended damage because it can regulate
both mutant and normal alleles.
 Challenge to determine the dosage and composition of
antisense molecule .
 Complex and high cost and causes inevitable toxic effects.
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30.  Antisense Oligonucleotides in Cancer
Therapeutics
 Antisense Oligonucleotides in Therapeutic
Intervention
 Antisense Oligonucleotides in Viral
Therapeutics
 Antisense Oligonucleotides in Allergic, Infl
ammatory and Autoimmune Diseases
 Antisense Oligonucleotides in Target Indentifi
cation/Validation.
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31. Antisense Oligonucleotides in Cancer
Therapeutics
• The main focus is on the knockdown of the genes that become
up regulated during tumorogenesis such as the genes
involved in apoptosis, cell growth and survival, angiogenesis
and metastasis.
• Of these, the most promising candidates for antisense therapy
are those molecules that have been shown to be causally
related to cancer progression or therapeutic resistance and
are not amenable to inhibition by the conventional therapy .
• Mutations in the genes encoding the Ras family of proteins
result in abnormal cell growth and malignant transformation.
• A 20 mer PS-ODN, ISIS 2503 (ISIS Pharmaceuticals),
targeted to the translation initiation region of H-ras mRNA
selectively reduced the expression of H-ras protein in vitro.
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32. Antisense Oligonucleotides in Viral
Therapeutics
• A lot of attention is currently being paid to the
treatment of viral cytopathic effects by As-
ODNs.
• Many valuable contributions have been made to
the As-ODN antiviral strategies by studies
involving various viruses, such as Herpes
Simplex virus (HSV), Human Immunodeficiency
Virus (HIV), Cytomegalovirus (CMV), Hepatitis
B virus (HBV), Hepatitis C virus (HCV),
Epstein—Barr Virus (EBV) and many more.
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33. ANTISENSE OLIGONUCLEOTIDES IN ALLERGIC, INfl
AMMATORY AND AUTOIMMUNE DISEASES
As-ODNs have been explored for their therapeutic benefits
in various allergic and infl ammatory diseases e.g. in
bronchial asthma, Crohn’s disease (CD), Ulcerative
colitis (UC), psoriasis.
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34.  The use of As-ODNs permits the study of the
effect of knockdown of the target gene on the
whole animal in a rapid manner and at different
stages of development, ranging from the
embryonic stage to the adult animal.
 The use of As-ODNs in target identifi
cation/validation is the identification of
Sphingosine Kinase-1 (SPHK-1) as a key player in
the pro-inflammatory responses triggered by
TNFα in human monocytes.
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35. Conclusion
• The past two decades have seen an increasing use of As-ODNs for the
purpose of target identification/ validation and the use of the information,
thus obtained, for the development of effective therapeutic interventions.
• Most of the structural motifs in PS-ODNs, that interfere with their
antisense effects and are responsible for toxicities, have been delineated.
Many desirable properties such as efficient uptake by the cells, stability
against nucleases, and a strong affi nity for target mRNA have been
identified.
• Effective chemical modifications are likely to avoid the non antisense
effects and further enhance the safety and efficacy of As-ODNs and thus
expand their potential clinical applications.
• However, more work needs to be done to further optimize the stability and
bioavailability of As-ODNs. Moreover, proof of principle for the biological
activity of As-ODNs is needed in the clinical samples, in order to confirm
the successful blockade of target protein expression .
• The rather disappointing results of some of the recent clinical trials indicate
a need to clearly establish the relevance of the target to the patient
population being studied, an early determination of optimal biological dose
and the rational use of combination strategies for the treatment of the
disease.
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36. Reference
• Eur. J. Biochem. 270, 1628–1644 (2003)
FEBS 2003 (Article )
• www.genelink.com
• www.slideshare.com
• www.ncbi.nlm.nih.gov
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37. Thank you
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