A brief introduction on structures of PNA (peptide nucleic acid) and LNA (locked nucleic acid).

1. NUCLEIC ACID MIMETICS
(PNA & LNA)
By
Amit Patro

2. NNuucclleeiicc AAcciidd MMiimmeettiiccss
It is the phenomenon of imitating the
behavior or function of natural occurring
nucleic acids (i.e.- DNA and RNA) by some
chemical compounds or oligo-nucleotides.
PNA LNA

3. PNA – A DNA Mimic with Unique Properties
DNA
N
N
NH2
N
N
N
NH2
Peptide Nucleic Acid carries the same bases as DNA (orange), but
has a totally different protein-like backbone (blue) i.e. N-amino-ethyl
glycine based polyamide structure.
N
N
O
NH2
O
O
O
P
O
O O
O
O
O P O
N
O
NH
O NH
N
N
O
NH2
N
O
O
N
N
N
PNA
Nielsen et al. 1991

4. PPNNAA ffeeaattuurreess
¨ Neutral backbone
¨ Stronger and faster binding to nucleic acids
¨ High sequence-specificity
¨ No nucleic acid Þ no degradation by nucleases
¨ No peptide Þ no degradation by protease
¨ Strand invasion into duplex DNA

6. PNA/DNA chimera

7. bbaassee ttrriiaaddss
Hoogsteen
pairing
Watson-Crick pairing
Hoogsteen
pairing
Watson-Crick pairing

9. PPNNAA ooppeenneerrss
Triplex
Invasion
Double Duplex
Invasion
Pseudocomplementary
pcPNA
any base composition
Homopyrimidine
PNA

10. PPNNAA AApppplliiccaattiioonn::
•Regulating biological process:
1- antisense oligonuceotide target mRNA
2- antigene oligonucleotide target chromosomal DNA
3- antigene PNAs disrupt protein binding at transcription
factor binding site.
• PNA in gene therapy:
1- used as delivery vehicle for gene therapy
2- high affinity and specificity of binding to DNA
3- covalently link other molecules to PNA
4- used as adapter that link plasmid vector to peptides,
proteins and drugs.
• Other Application:
1- induce mutation
2- nucleic acid biosensor
3- tools for genome mapping
4- modulation of PCR analysis
5- induce gene expression

11. E.coli
B.subtilis S.mutans
AEM 2007

12. LLoocckkeedd NNuucclleeiicc AAcciiddss
The furanose ring conformation is restricted in LNA by a
methylene linker that connects the 2'-O position to the
4'-C position. By convenience, all nucleic acids
containing one or more LNA modifications are called
LNA.

13. FFeeaattuurreess ooff LLNNAA
•Affinity (Watson-Crick base pairing system )
•LNA:LNA > LNA:RNA > RNA:RNA > RNA:DNA > DNA:DNA
•Tm modulation
•LNA/DNA or LNA/RNA duplexes have increased thermal
stability compared DNA or RNA. In general, the thermal
stability of a LNA/DNA duplex is increased 3°C to 8°C per
modified base in the oligonucleotide.
•It is possible to fine-tune the placement of LNA bases to reach
the desired Tm level without losing specificity.
•Specificity
•LNA enhances hybridization performance relative to native
DNA and RNA, phosphorothiate or peptide nucleic acid (PNA)
probes.
•LNA lowers experimental error rates due to better mismatch
discrimination.
•LNA provides more robust assay conditions.
•Simplicity & Design Flexibility

16. (A) Crystal structure of an RNA:RNA
duplex (left) and an all
LNA:LNA duplex (right),
(B) space filling models,
derived from crystal structures,
of DNA:DNA duplex(left),
RNA:RNA duplex(middle) and
LNA:LNA duplex (right).

17. Application
• Hybridization probes
• Strand invasion
• In-situ hybridization
• Triple-helix forming
oligos
• Nuclease protection
assays
• Capture probes
• Sample preparation
(mRNA)
• SNP analysis
• Mutation analysis
• Allele specific PCR
• Antisense Target
Validation

18. P
N
A
L
N
A

19. References
Nielsen JT, Stein PC, Petersen M; NMR structure of an alpha-L-LNA:RNA
hybrid: structural implications for RNase H recognition, Nucleic Acids Res.
2003; 31(20):5858-67
Campbell M A. and Wengel J; Locked vs. unlocked nucleic acids (LNA vs.
UNA): contrasting structures work towards common therapeutic goals,
Chem. Soc. Rev., 2011, 40, 5680–5689.
Uhalmann E; Peptide nucleic acid (PNA) & PNA-DNA chimeras; from high
binding affinity towards biological function; Biol. Chem., 1998, 379, 1045-
1052
Nielsen P. E.; Peptide Nucleic Acid, a molecule with two identities;
Accounts of chemical Research, 1999, 32, 624-630.
Betts L, Josey JA, Veal JM, Jordan SR. A nucleic acid triple helix formed by
a peptide nucleic acid-DNA complex. Science, 1995; 270(5243): 1838-41