Piperidinyl peptide nucleic acids: Synthesis and DNA-complementation studies

Article abstract of DOI:10.1081/NCN-120022747

Synthesis of a new six membered PNA analogue by introducing a methylene bridge between β carbon atom of ethylene diamine and β′ carbon atom of linker to nucleobase.

Full text of DOI:10.1081/NCN-120022747

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Piperidinyl Peptide Nucleic Acids: Synthesis and DNA-
Complementation Studies
Pallavi Lonkar a & Vaijayanti A. Kumar a b
a Division of Organic Chemistry , National Chemical Laboratory , Pune, India
b Division of Organic Chemistry , National Chemical Laboratory , Synthesis, Dr. Homi Bhabha
Road, Pune, 411008, India
Published online: 31 Aug 2006.
To cite this article: Pallavi Lonkar & Vaijayanti A. Kumar (2003) Piperidinyl Peptide Nucleic Acids: Synthesis and DNA-
Complementation Studies, Nucleosides, Nucleotides and Nucleic Acids, 22:5-8, 1105-1108, DOI: 10.1081/NCN-120022747
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 22, Nos. 5–8, pp. 1105–1108, 2003
Piperidinyl Peptide Nucleic Acids: Synthesis and
DNA-Complementation Studies
*
Pallavi Lonkar and Vaijayanti A. Kumar
Division of Organic Chemistry, National Chemical Laboratory,
Pune, India
ABSTRACT
Synthesis of a new six membered PNA analogue by introducing a methylene
bridge between b carbon atom of ethylene diamine and b0 carbon atom of linker
to nucleobase.
INTRODUCTION
Peptide Nucleic Acids have emerged as potential antisense agents.[1] They bind
to DNA in both parallel as well as antiparallel orientation. To discriminate between
this binding property one can introduce chirality in PNA. In earlier work from our
laboratory a built-in chirality was achieved by introducing a methylene bridge[2]
between the a-C atom of the glycyl unit and the b-C atom of the ethylene segment
of aegPNA(I) which gave prPNA(II). The homooligomers derived from these
aminoprolyl PNA monomer do not bind to the complementary DNA sequence,
*Correspondence: Vaijayanti A. Kumar, Division of Organic Chemistry, National Chemical
Laboratory, Synthesis, Dr. Homi Bhabha Road, Pune 411008, India; Fax: þ91 20 5893355;
E-mail: vkumar@dna.ncl.res.in.
1105
DOI: 10.1081/NCN-120022747
Copyright # 2003 by Marcel Dekker, Inc.
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com

1106
Lonkar and Kumar
probably due to conformational rigidity in the oligomer. To release this conforma-
tional rigidity, aminoethyl backbone in aminoprolyl PNA was replaced by amino-
propyl backbone still retaining the two chiral centers to obtain pipecolylPNA
(III)[3] which too was found to significantly impair the complexation of PNA with
complementary DNA.
Herein, we report synthesis of a new six membered PNA analogue by introdu-
cing a methylene bridge between b carbon atom of ethylene diamine and b0 carbon
atom of linker to nucleobase. (pip PNA molecules with a methylene bridge inserted
between a carbon atom of ethylenediamine and b0 carbon atom of linker to nucleo-
base and simultaneously removing rigid carbonyl group. Their DNA=RNA binding
preferences may be dictated by the geometry of the backbone as well as the orienta-
tion of the nucleobase.
RESULTS AND DISCUSSION
The suitably protected trans-4-hydroxy proline 1 was converted to the trans-
2S,4R pyrrolidine-2-methanol 2 by reduction of ester function. Treatment with tri-
fluoracetic anhydride followed by triethylamine gives the six membered rearranged
product 3 with retension of configuration. Mesylation of the resulting unprotected
hydroxy group and reaction with sodium azide gave 5 with inversion at C3. Com-
pound 5 was then selectively hydrogenated using Ra-Ni and Boc-protected to get
amino piperidine derivative 6 as shown in Scheme 1. Compound 6 was then
Scheme 1.

Piperidinyl Peptide Nucleic Acids
Table 1. UV TM studies of PNA2:DNA complexes.
1107
Sequences
UV TmꢀC
PNA10
PNA11
PNA12
PNA13
PNA14
DNA
H-TTTTTTTT-b-ala-OH
H-TTTTTTTt-b-ala-OH
H-TTTtTTTt-b-ala-OH
H-TTTtTTTT-b-ala-OH
H-tTTTTTTT-b-ala-OH
50-GC(A)10CG-30
43
50.7
54.4
41.4
–
t indicates modified PNA unit.
subjected to hydrogenation, alkylation of ring nitrogen using ethylbromoacetate
followed by removal of silyl protection using TBAF to get 7. Trans-5S-N3-benzoyl-
Thymin-1-yl-3S-Bocaminomethyl pyrrolidine derivative 8 was synthesized under
Mitsunobu conditions. This was then hydrolyzed using aqueous methanolic sodium
hydroxide to get the thymine monomer 9 that could be used for solid phase syn-
thesis of PNA-PyrrolidinePNA oligomer=mixmers. All the new compounds were
characterized using suitable spectroscopic analysis.
PNA oligomers containing the aegPNA and piperidine-PNA backbone units
were synthesized by SPPS using the BOC- protection strategy. DNA oligomers
were synthesized on Pharmacia GA plus synthesizer employing phosphoramidite
chemistry.
The PNA10 is the unmodified PNA10 with aminoethylglycyl backbone. PNA11-
PNA14 are the modified PNA oligomers with the modified PNA units incorporated
at the predefined sites as represented in Table 1. The UV-Tm studies of these mono-
mers indicate that the modified PNA unit at the C-terminus in PNA 11 stabilizes the
complex with complementary DNA by about 7ꢀC. The synergistic effect is observed
with one more unit in the center of the sequence PNA12 as the PNA2:DNA complex
is further stabilized by about 47ꢀC. Modified unit only in the center of the sequence
PNA13 causes 2ꢀC destabilization. These preliminary results are very encouraging
and need to be further investigated.
CONCLUSIONS
A high yielding stereospecific ring expansion of protected hydroxy prolinol gives
suitably substituted piperidine ring. The ring nitrogen is protonated at physiological
pH and oligomers are highly water-soluble. DNA complementation studies by UV-
Tm measurements indicate that the six membered monomer is capable of stabilizing
the PNA2:DNA complexes.
ACKNOWLEDGMENTS
VAK thanks Department of Science and Technology, New Delhi, and National
Chemical Laboratory, Pune, for financial support. Meena thanks CSIR, New Delhi,
for research fellowship.

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Lonkar and Kumar
REFERENCES
1. Nielsen, P.E.; Egholm, M.; Berg, R.H.; Buchardt, O. Science 1991, 254, 1497.
2. Gangamani, B.P.; Kumar, V.A.; Ganesh, K.N. Tetrahedron 1999, 55, 177.
3. Lonkar, P.S.; Kumar, V.A.; Ganesh, K.N. Nucleosides Nucleotides Nucleic
Acids 2001, 20, 1197.
4. Kumar, V.A.; Pallan, P.S.; Meena; Ganesh, K.N. Org. Lett. 2001, 3, 1269–1272.