PNA Backbone Modification

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What is Peptide Nucleic Acid (PNA)?

Peptide nucleic acid (PNA) is an artificial oligonucleotide mimetic with a peptidic backbone in lieu of a phosphoribosyl backbone. As such, it combines the properties of both peptides and nucleic acids. Remarkably, it forms more stable duplexes with DNA or RNA than either of the DNA or RNA homoduplexes and is metabolically stable. These advantageous features instigated tremendous interest in PNAs as antisense and antigene agents. However, unmodified PNAs have poor cellular permeability.

Despite the advantageous features of classic PNA, its low water solubility, poor cellular uptake, propensity to self-aggregate, and orientational ambiguity in recognizing nucleic acid targets, limits the effectiveness of PNA in its applications. Furthermore, high salt concentrations encountered in the cellular environments increase the stability of the DNA/DNA duplexes, making it challenging for PNA to invade duplex DNA under physiological conditions. However, these issues can be overcome by the chemical flexibility of PNA that allows for the insertion of modifications on its backbone and nucleobases.

Advantages of Backbone Modified PNA

  • Backbone modification and Hybridization properties: Hence the enhancement of binding affinity and sequence specificity of PNA for DNA and RNA complement via chemical modification of PNA backbone is highly desirable and will have significant contribution for potential application in therapeutics and diagnostics.
  • Backbone modifications for enhanced cellular uptake: For enhanced cellular delivery, PNA has been conjugated with cell penetrating peptide (CPP), cationic peptides, and basic amino acid stretches such as Lysine and Arginine.
  • Backbone modification and strand invasion in recognition of double-stranded nucleic acid

Application of Backbone Modified PNA

Recently PNAs, because of their excellent affinity to DNA/RNA and the scope to be modified as per the application, have attracted a wide range of researchers for the development of new PNA molecules by a simple backbone or nucleobase modifications.

A randomly folded peptide nucleic acid has been transformed into a right-handed helix by simple modification at the γ-position of the backbone. The conformationally preorganized helical PNA has an excellent affinity and high sequence selectivity to bind the DNA and RNA.

Because of its antigene, antisense, anti-miR, and the scope to be labeled with various fluorophores, PNA finds application in gene expression modulation in-vivo, and development of nucleic acid-based biosensors which are useful in biotechnology researches and clinical diagnostics.

It is also used as tools for genome mapping, hybridization technologies in genetic detection, FISH technology, PCR analysis, and many more.

Examples of various strategies for backbone modifications of PNAExamples of various strategies for backbone modifications of PNA (Das A, et at. 2021)

Our Backbone modifications Services in PNAs

Acyclic Backbone modifications: Aminoethyl glycine PNA; N-(3-aminopropyl)glycine PNA; N-(2-aminoethyl)-β-alanine PNA; Arginine- derived PNA; Aminopropyldimethyl glycyl PNA; Aminopropyl glycinyl PNA; Amino methylene PNA; Diaminobutyryl PNA; Guanidine- based PNA; D- Lysine α- PNA; (R)- MiniPEG γ- PNA; L- Serine γ- PNA; Amino ethyl dimethyl glycyl PNA

Cyclic PNA Analogues: Amino ethyl prolyl PNA; Aminoethylpyrrolidinone PNA; Amino prolyl PNA; Aminoethyl glycine -Amino ethyl pipecolyl PNA; 2- Amino cyclobutane carboxylic PNA; Amino cyclopentane carboxylic PNA; Aminomethyl thiazolidine PNA; Backbone extended pyrrolidine PNA; Cyclohexyl PNA; Cyclopentyl PNA; 1- Amino pyrrolidine carboxylic acid PNA; Prolyl glycyl PNA; Pipecolyl PNA; Pyrrolidine PNA; 2- Amino cyclohexane carboxylic PNA; Aromatic PNA; Ferrocene labeled PNA

Backbone modifications of PNA (B = nucleobase)Backbone modifications of PNA (B = nucleobase) (Perera JDR, et al. 2021)

Our PNA Backbone Modification

  • Backbone extended PNA
  • Chiral PNA Backbone: Chiral PNA backbones with modifications at the α-, β-, and γ-positions have been developed, each possessing unique oligomer binding and conformational properties.
  • Conformationally constrained cyclic PNA Backbone
  • Acyclic PNA Backbone modification
  • Aromatic PNA Backbone modification
ModificationName
Acyclic BackboneAminoethyl glycine PNA
N-(3-aminopropyl)glycine PNA
N-(2-aminoethyl)-β-alanine PNA
Arginine- derived PNA
Aminopropyldimethyl glycyl PNA
Aminopropyl glycinyl PNA
Amino methylene PNA
Diaminobutyryl PNA
Guanidine- based PNA
D- Lysine α- PNA
(R)- MiniPEG γ- PNA
L- Serine γ- PNA
Amino ethyl dimethyl glycyl PNA
Cyclic PNA AnaloguesAmino ethyl prolyl PNA
Aminoethylpyrrolidinone PNA
Amino prolyl PNA
Aminoethyl glycine -Amino ethyl pipecolyl PNA
2- Amino cyclobutane carboxylic PNA
Amino cyclopentane carboxylic PNA
Aminomethyl thiazolidine PNA
Backbone extended pyrrolidine PNA
Cyclohexyl PNA
Cyclopentyl PNA
1- Amino pyrrolidine carboxylic acid PNA
Prolyl glycyl PNA
Pipecolyl PNA
Pyrrolidine PNA
2- Amino cyclohexane carboxylic PNA
Aromatic PNAAromatic PNA
Ferrocene labeled PNA

References

  1. Das A, Pradhan B. Evolution of peptide nucleic acid with modifications of its backbone and application in biotechnology. Chem Biol Drug Des. 2021 Apr;97(4):865-892. doi: 10.1111/cbdd.13815. Epub 2020 Dec 25. PMID: 33314595.
  2. Perera JDR, Carufe KEW, Glazer PM. Peptide nucleic acids and their role in gene regulation and editing. Biopolymers. 2021 Dec;112(12):e23460. doi: 10.1002/bip.23460. Epub 2021 Jun 15. PMID: 34129732.
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