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(α,α-dimethyl)glycyl (dmg) PNAs: achiral PNA analogs that form stronger hybrids with cDNA relative to isosequential RNA.

Gourishankar A, Ganesh KN - Artif DNA PNA XNA (2012 Jan-Mar)

Bottom Line: They show a higher binding to DNA relative to that with isosequential RNA.The results complement our previous work that had demonstrated that cyclohexanyl-PNAs favor binding with cRNA compared with cDNA and imply that the biophysical and structural properties of PNAs can be directed by introduction of the right rigidity in PNA backbone devoid of chirality.This approach of tweaking selectivity in binding of PNA constructs by installing gem-dimethyl substitution in PNA backbone can be extended to further fine-tuning by similar substitution in the aminoethyl segment as well either individually or in conjunction with present substitution.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research, Division of Organic Chemistry, National Chemical Laboratory, Pune, India.

ABSTRACT
The design and facile synthesis of sterically constrained new analogs of PNA having gem-dimethyl substitutions on glycine (dmg-PNA-T) is presented. The PNA oligomers [aminoethyl dimethylglycyl (aedmg) and aminopropyl dimethylglycyl (apdmg)] synthesized from the monomers 6 and 12) effected remarkable stabilization of homothyminePNA(2):homoadenine DNA/RNA triplexes and mixed base sequence duplexes with target cDNA or RNA. They show a higher binding to DNA relative to that with isosequential RNA. This may be a structural consequence of the sterically rigid gem-dimethyl group, imposing a pre-organized conformation favorable for complex formation with cDNA. The results complement our previous work that had demonstrated that cyclohexanyl-PNAs favor binding with cRNA compared with cDNA and imply that the biophysical and structural properties of PNAs can be directed by introduction of the right rigidity in PNA backbone devoid of chirality. This approach of tweaking selectivity in binding of PNA constructs by installing gem-dimethyl substitution in PNA backbone can be extended to further fine-tuning by similar substitution in the aminoethyl segment as well either individually or in conjunction with present substitution.

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Figure 3. Synthesis of dmg-PNA monomers (A) aedmg-PNA-T 6 and (B) apdmg-PNA-T monomer 12. Values in brackets indicate yields. In Scheme B reagents a–e are same as in Scheme A.
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Figure 3: Figure 3. Synthesis of dmg-PNA monomers (A) aedmg-PNA-T 6 and (B) apdmg-PNA-T monomer 12. Values in brackets indicate yields. In Scheme B reagents a–e are same as in Scheme A.

Mentions: A straightforward route to obtain the desired dmg-PNA monomers 6 and 12 would be to directly N-alkylate the easily accessible ethyl α-aminoisobutyrate (H2N-CMe2-COOEt, aib). However, N-alkylation of aib with Boc-HNCH2CH2Cl or by reductive alkylation of Schiff base obtained by condensation with BocHN-CH2-CHO was not successful (Supplemental Material). Since this may be due to the steric problems imposed by the gem-dimethyl group, it was thought to reverse the N-alkylation strategy by using the gem-dimethyl component as the alkylating agent to react with N-protected dialkylamine (Fig. 3A). The synthesis of aedmg-PNA-T target monomer 6 was performed starting from 1,2-diaminoethane 1 which was treated with Boc-anhydride to give the N1-Boc-1,2-diaminoethane 2 that was alkylated at N2 with ethyl-2-bromoisobutyrate to obtain aminoethyl (α,α-dimethyl)glycine ethyl ester 3 in moderate yields. This was reacted with chloroacetyl chloride to yield the corresponding N-(chloroacetyl) derivative 4 which was used for alkylation to obtain N-(Boc-aminoethyl-α,α-dimethylglycyl)-thymine ethyl ester 5. It was hydrolyzed by methanolic sodium hydroxide to yield the desired aedmg-PNA monomer acid 6 for use in PNA synthesis (Fig. 3).


(α,α-dimethyl)glycyl (dmg) PNAs: achiral PNA analogs that form stronger hybrids with cDNA relative to isosequential RNA.

Gourishankar A, Ganesh KN - Artif DNA PNA XNA (2012 Jan-Mar)

Figure 3. Synthesis of dmg-PNA monomers (A) aedmg-PNA-T 6 and (B) apdmg-PNA-T monomer 12. Values in brackets indicate yields. In Scheme B reagents a–e are same as in Scheme A.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3368815&req=5

Figure 3: Figure 3. Synthesis of dmg-PNA monomers (A) aedmg-PNA-T 6 and (B) apdmg-PNA-T monomer 12. Values in brackets indicate yields. In Scheme B reagents a–e are same as in Scheme A.
Mentions: A straightforward route to obtain the desired dmg-PNA monomers 6 and 12 would be to directly N-alkylate the easily accessible ethyl α-aminoisobutyrate (H2N-CMe2-COOEt, aib). However, N-alkylation of aib with Boc-HNCH2CH2Cl or by reductive alkylation of Schiff base obtained by condensation with BocHN-CH2-CHO was not successful (Supplemental Material). Since this may be due to the steric problems imposed by the gem-dimethyl group, it was thought to reverse the N-alkylation strategy by using the gem-dimethyl component as the alkylating agent to react with N-protected dialkylamine (Fig. 3A). The synthesis of aedmg-PNA-T target monomer 6 was performed starting from 1,2-diaminoethane 1 which was treated with Boc-anhydride to give the N1-Boc-1,2-diaminoethane 2 that was alkylated at N2 with ethyl-2-bromoisobutyrate to obtain aminoethyl (α,α-dimethyl)glycine ethyl ester 3 in moderate yields. This was reacted with chloroacetyl chloride to yield the corresponding N-(chloroacetyl) derivative 4 which was used for alkylation to obtain N-(Boc-aminoethyl-α,α-dimethylglycyl)-thymine ethyl ester 5. It was hydrolyzed by methanolic sodium hydroxide to yield the desired aedmg-PNA monomer acid 6 for use in PNA synthesis (Fig. 3).

Bottom Line: They show a higher binding to DNA relative to that with isosequential RNA.The results complement our previous work that had demonstrated that cyclohexanyl-PNAs favor binding with cRNA compared with cDNA and imply that the biophysical and structural properties of PNAs can be directed by introduction of the right rigidity in PNA backbone devoid of chirality.This approach of tweaking selectivity in binding of PNA constructs by installing gem-dimethyl substitution in PNA backbone can be extended to further fine-tuning by similar substitution in the aminoethyl segment as well either individually or in conjunction with present substitution.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research, Division of Organic Chemistry, National Chemical Laboratory, Pune, India.

ABSTRACT
The design and facile synthesis of sterically constrained new analogs of PNA having gem-dimethyl substitutions on glycine (dmg-PNA-T) is presented. The PNA oligomers [aminoethyl dimethylglycyl (aedmg) and aminopropyl dimethylglycyl (apdmg)] synthesized from the monomers 6 and 12) effected remarkable stabilization of homothyminePNA(2):homoadenine DNA/RNA triplexes and mixed base sequence duplexes with target cDNA or RNA. They show a higher binding to DNA relative to that with isosequential RNA. This may be a structural consequence of the sterically rigid gem-dimethyl group, imposing a pre-organized conformation favorable for complex formation with cDNA. The results complement our previous work that had demonstrated that cyclohexanyl-PNAs favor binding with cRNA compared with cDNA and imply that the biophysical and structural properties of PNAs can be directed by introduction of the right rigidity in PNA backbone devoid of chirality. This approach of tweaking selectivity in binding of PNA constructs by installing gem-dimethyl substitution in PNA backbone can be extended to further fine-tuning by similar substitution in the aminoethyl segment as well either individually or in conjunction with present substitution.

Show MeSH
Related in: MedlinePlus