DNA-Alanyl-PNA chimeras are oligomers combining peptide nucleic acids (PNAs) and DNA oligonucleotides for the creation of new molecules with improved properties and a potential to be beneficial in DNA diagnostics.
Roviello et al. (2010) reported the synthesis of mono-methoxy-trityl/acyl-protected nucleo alanine monomers for the preparation of DNA/alanyl-PNA chimeras. The derivatives enabled the synthesis of alanyl-PNA/DNA chimeras following the molecular beacon concept via standard phosphoramidite DNA synthesis.
Hybrid DNA-Alanyl-PNA chimeras combine a DNA oligonucleotide segment with a peptide nucleic acid (PNA) segment linked by an alanyl bridge. PNAs are oligonucleotide analogs with a pseudo peptide skeleton instead of a sugar-phosphate backbone that binds to DNA and RNA with high specificity and selectivity.
The image below shows an example of an Alanyl-PNA/DNA/alanyl-PNA-chimera composed of alanyl amino acids carrying linked nucleobase in β-position of the chain combined with a linker and a DNA segment:
Design of a DNA-PNA chimera
Select DNA Segment: The DNA segment contains natural nucleotides, allowing it to hybridize specifically with complementary DNA or RNA strands through Watson-Crick base pairing.
Select PNA Segment: The PNA segment is a sequence of synthetic nucleic acid analogs, where the sugar-phosphate backbone is a neutral peptide-like backbone. This modification makes PNAs highly stable, resistant to enzymatic degradation, and binding firmly to complementary DNA or RNA.
Select Linker: The alanine-based linker connects the DNA and PNA segments, preserving structural integrity and flexibility. The alanyl linker provides a bridge that enables the chimera to retain both DNA-like and PNA-like properties. Other linker types maybe used for the design of similar chimeric molecules.
-> Combine and synthesize.
DNA-PNA chimeras are valuable in research because of their unique hybridization properties, which make them useful in diagnostics, gene targeting, and molecular biology studies. Their stable backbone and sequence-specific affinity can improve target specificity and resistance to nucleases, making them promising tools in therapeutic and diagnostic applications.
Synthesis: Solid phase assembly enables the synthesis of DNA/alanyl-PNA chimeras, oligomers with a mixed oligonucleotide/peptide backbone. Chimeric oligomers with a mixed oligonucleotide/peptide backbone are synthesized using DNA synthesis conditions, in which the nucleotides are introduced as phosphoramidites, whereas the nucleo amino acids contained acid labile monomethoxytrityl (MMT) groups for temporary protection of the α-amino groups and acyl protecting groups for the exocyclic amino functions of the nucleobases. The resulting Boc/acyl intermediates, during deprotection, are compatible with the standard phosphoramidite DNA synthesis strategy.
The oligomerization of nucleo-amino acids results in rigid and well-defined double strands based on a linear topology-based base pair recognition, stacking, and solvation. Base pairs stacking occurs at a distance of about 3.5 A°, resulting in an extended peptide backbone. However, introducing glycines in opposite positions in a molecular beacon makes intercalation possible.
Properties: DNA/alanyl-PNA chimeras have improved aqueous solubility and cellular uptake compared to pure PNAs and bind exclusively in the antiparallel orientation under physiological conditions.
Biological functions: DNA/alanyl-PNA chimeras can assume biological functions, such as a primer for DNA polymerases. In addition, they can also stimulate the cleavage of target RNA through RNase H.
Potential use: DNA/alanyl-PNA chimeras have the potential to be beneficial in DNA diagnostics.
Reference
Roviello GN, Gröschel S, Pedone C, Diederichsen U. Synthesis of novel MMT/acyl-protected nucleo alanine monomers for the preparation of DNA/alanyl-PNA chimeras. Amino Acids. 2010 May;38(5):1301-9. doi: 10.1007/s00726-009-0324-x. Epub 2009 Jul 24. Erratum in: Amino Acids. 2010 May;38(5):1311-2. [PMC]
---...---
Bio-Synthesis provides a full spectrum of high quality custom oligonucleotide modification services including 5'-triphosphate and back-bone modifications, conjugation to fatty acids, biotinylation by direct solid-phase chemical synthesis or enzyme-assisted approaches to obtain artificially modified oligonucleotides, such as BNA antisense oligonucleotides, mRNAs or siRNAs, containing a natural or modified backbone, chimeric molecules, as well as base, sugar and inter-nucleotide linkages.
Bio-Synthesis provides custom morpholinos including Phosphorodiamidate Morpholino, and Thiomorpholino Oligonucleotides.
Bio-Synthesis also provides biotinylated mRNA and long circular oligonucleotides.
---...---