Peptide Nucleic Acid (PNA)

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Please kindly note that our products and services can only be used to support research purposes (Not for clinical use).

What is the PNA?

The nucleobase oligomer known as peptide nucleic acid (PNA) has had its complete backbone replaced with units of N-(2-aminoethyl)glycine. So, instead of a negatively charged sugar-phosphate backbone, PNA has a neutral peptide backbone, making it similar to DNA. Although it is difficult to move into the cell, its chemical stability and resistance to hydrolytic (enzymatic) cleavage mean that it will not be degraded while inside a live cell. Using the Watson-Crick hydrogen bonding strategy, PNA can recognize particular DNA and RNA sequences. The hybrid complexes show remarkable temperature stability and unusual ionic strength effects. A stable PNA/DNA/PNA triplex with a looped-out DNA strand may also be formed when it attaches to duplex homopurine regions of DNA by strand invasion. PNA has a lot of uses in medicine and diagnostics since it is more stable chemically and enzymatically and has better hybridization properties than nucleic acids. A novel tool for antigene and antisense treatment, PNA has the ability to impede transcription and translation.

Structures of DNA and PNA.Fig.1 Structures of DNA and PNA. (MacLelland V., et al., 2023)

Peptide Nucleic Acid (PNA) Products

  • Fmoc-PNA-A(Bhoc)-OH

    CAS: 186046-82-2

    Chemical Formula: C40H35N7O7

    Molecular Weight: 725.76

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  • Fmoc-PNA-A(Boc)-OH

    CAS: 511534-99-9

    Chemical Formula: C31H33N7O7

    Molecular Weight: 615.65

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  • Boc-PNA-A(Z)-OH

    CAS: 149376-69-2

    Chemical Formula: C24H29N7O7

    Molecular Weight: 527.54’

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  • Fmoc-PNA-C(Bhoc)-OH

    CAS: 186046-81-1

    Chemical Formula: C39H35N5O8

    Molecular Weight: 701.74

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  • Fmoc-PNA-C(Boc)-OH

    CAS: 172405-61-7

    Chemical Formula: C30H33N5O8

    Molecular Weight: 591.62

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  • Boc-PNA-C(Z)-OH

    CAS: 144564-94-3

    Chemical Formula: C23H29N5O8

    Molecular Weight: 503.51

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  • Fmoc-PNA-G(Bhoc)-OH

    CAS: 186046-83-3

    Chemical Formula: C40H35N7O8

    Molecular Weight: 741.76

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  • Fmoc-PNA-G(Boc)-OH

    CAS: 1052677-90-3

    Chemical Formula: C31H33N7O8

    Molecular Weight: 631.65

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  • Boc-PNA-G(Z)-OH

    CAS: 169287-77-8

    Chemical Formula: C24H29N7O8

    Molecular Weight: 543.54

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  • Fmoc-PNA-T-OH

    CAS: 169396-92-3

    Chemical Formula: C26H26N4O7

    Molecular Weight: 506.52

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  • Boc-PNA-T-OH

    CAS: 139166-80-6

    Chemical Formula: C16H24N4O7

    Molecular Weight: 384.39

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  • Fmoc-PNA-U-OH

    CAS: 959151-70-3

    Chemical Formula: C25H24N4O7

    Molecular Weight: 492.49

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  • Boc-PNA-U-OH

    CAS: 149500-74-3

    Chemical Formula: C15H22N4O7

    Molecular Weight: 370.36

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  • Boc-PNA-thioU(PMB)-OH

    CAS: 253438-99-2

    Chemical Formula: C23H30N4O7S

    Molecular Weight: 506.57

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  • Fmoc-PNA-M(Bhoc)-OH

    CAS: NA

    Chemical Formula: C40H36N4O7

    Molecular Weight: 684.75

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  • Fmoc-PNA-M(Boc)-OH

    CAS: 1417611-27-8

    Chemical Formula: C31H34N4O7

    Molecular Weight: 574.63

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  • Fmoc-PNA-D(tetraBhoc)-OH

    CAS: NA

    Chemical Formula: C82H66N8O13

    Molecular Weight: 1371.47

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  • Fmoc-PNA-D(tetraBoc)-OH

    CAS: 2101661-88-3

    Chemical Formula: C46H58N8O13

    Molecular Weight: 931.01

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  • Boc-PNA-D(tetraZ)-OH

    CAS: NA

    Chemical Formula: C48H48N8O13

    Molecular Weight: 944.96

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Customized Peptide Nucleic Acid (PNA) Products

Creative Peptides offers high-quality Peptide Nucleic Acid (PNA) products, designed for precise gene recognition and binding. With enhanced stability, PNA provides superior binding affinity and resistance to nucleases compared to conventional DNA/RNA. Our PNAs are ideal for applications in gene regulation, diagnostics, and antisense technology. Whether you need customized synthesis or standard PNA sequences, Creative Peptides ensures reliable, efficient solutions tailored to your research needs.

CUSTOM PEPTIDE SYNTHESIS

Peptide Nucleic Acid synthesis

By utilizing Fmoc-protected PNA monomers, a conventional solid-phase technique may be employed to effortlessly synthesize PNA oligomers. Purification via reverse-phase high-performance liquid chromatography (HPLC) follows the usual steps of deprotecting and cleaving the PNA oligomers from the resin using 4-trifluoromethylsalicylic acid (TFMSA)/trifluoroacetic acid (TFA). The matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry method describes PNA oligomers. Using conventional peptide conjugation methods such thioester condensation or maleimide cysteine coupling, PNA-peptide conjugates may be continuously produced. Many PNA analogs, including a wide range of synthetic nucleobases, have been created as a result of the success of PNA synthesis. It is common practice to employ either the Fmoc (9-fluorenylmethoxycarbonyl group) or the Bhoc (benzhydryloxycarbonyl group) to preserve the amino groups of PNA monomers. Merrifield resin (methylbenzhydrylamine) was initially used to link PNA monomers in a fritted vial. Following the resin capping of the unreacted groups, a piperidine solution (20% piperidine in dimethylformamide) was added to deprotect the Fmoc group. Reacting with the appropriate coupling chemicals, the following PNA monomers were successively linked to the resin. By the time the synthesis was complete, a piperidine solution had eliminated the Fmoc group. Using trifluoroacetic acid, the Bhoc group—which serves to protect the A, C, G, and T monomers—was eliminated.

 

Peptide Nucleic Acid structure

Repetitive units of N-(2-aminoethyl) glycine are used to replace the phosphodiester backbone in synthetic DNA analogs known as PNAs. The purine and pyrimidine bases are connected to these units via a methyl carbonyl linker. Synthesizing PNA follows the same steps as synthesizing peptides, whether by human or automated means, employing the conventional solid-phase extraction method. Fluorophores and biotin are common ways to label PNA molecules. For the next generation of PNAs, scientists may decide to alter the N-(2-aminoethyl) glycine backbone (PNA analogs) or create a chimeric structure (PNA-peptide chimeras or PNA-DNA chimeras) to enhance the solubility and cellular uptake of PNAs, or to add new biological features

Chemical structures of PNA as compared to DNA and protein.Fig.2 Chemical structures of PNA as compared to DNA and protein. (Wu J., et al., 2017)

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Peptide Nucleic Acid Properties

(1) High binding affinity: When combined with complementary DNA or RNA sequences, PNA forms extremely stable duplexes. The lack of electrostatic repulsion and the bases' planar structure, which allows for effective stacking interactions, contribute to this great binding affinity. Mutation detection and gene targeting are two examples of applications that benefit greatly from the high specificity and sensitivity offered by PNAs, as they bind to target sequences more firmly than natural oligonucleotides.

(2) Sequence specificity: Because of their extreme specificity, PNA probes may detect differences as small as a single base in their target sequences. Mutations and single nucleotide polymorphisms (SNPs) in particular can be located with the use of this function. The stability of a PNA-DNA duplex may be greatly reduced by even a single mismatch, which greatly improves the accuracy of mutation detection and diagnosis.

(3) Resistance to enzymatic degradation: Protein-degrading enzymes known as nucleases and proteases do not recognize PNAs. This makes PNAs very advantageous in biological settings, since they are not easily broken down.

(4) No charge-dependent interactions: Due to their neutral backbone, PNAs do not require salt to stabilize hybridization with DNA/RNA, in contrast to interactions between DNA and DNA or DNA and RNA, which depend on ionic circumstances. PNAs have the ability to hybridize well in environments with low salt content, which might be advantageous in some experimental settings and biological systems. More accurate targeting of nucleic acid sequences is achieved by reducing nonspecific binding to other negatively charged biomolecules, such proteins, caused by PNA's neutral charge.

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Innovative Peptides provides high quality peptide nucleic acid (PNA) services, supported by a professional team. We are known for our rapid response to ensure efficient and reliable service to meet your scientific needs.

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Peptide Nucleic Acid probe

In the same way as DNA-DNA or RNA-DNA interactions use the conventional Watson-Crick base pairing, PNA probes can detect and hybridize to complementary nucleic acid sequences. The neutral backbone of PNAs makes them highly hybridizable with DNA or RNA, allowing for more accurate detection of even short sequences. The imaging of cancer cells can be greatly enhanced with the application of a well-designed PNA molecular beacon (MB). Colorectal cancer (CRC) in vitro and ex vivo detection was facilitated by the PNA MB diagnostic probe. A cell-penetrating peptide, a thiazole orange (TO) fluorescent dye, and a colon cancer-associated transcript 1 (CCAT1) specific PNA made up the molecular beacon. They saw a PNA beacon hybridizing in situ with human CRC samples that contained CCAT1. A potent diagnostic tool for CRC diagnosis, this PNA MB.

Schema of PNA probe binding modes for targeting double-stranded DNA.Fig.3 Schema of PNA probe binding modes for targeting double-stranded DNA. (Pellestor F., et al., 2004)PNA microarray for the detection of target DNA on gold electrodes.Fig.4 PNA microarray for the detection of target DNA on gold electrodes. (Wu J., et al., 2017)
 
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Peptide Nucleic Acid monomer

PNA possesses a backbone composed of 2-aminoethylglycine links, substituting the conventional phosphodiester backbone found in DNA, while the methylene carbonyl groups serve to attach the nucleotide bases to the backbone. Due to their achiral nature, PNAs can be synthesized without the necessity of a stereoselective route. The synthesis of PNA molecules/oligomers parallels that of peptides, utilizing conventional solid-phase synthesis procedures, such as employing a (methylbenzhydryl)amine polystyrene resin as the solid support. The safeguarding of amino groups in PNA monomers during synthesis relies on either Bhoc (benzhydryloxycarbonyl group) or Fmoc (9-fluorenylmethoxycarbonyl group) chemistry. The exocyclic monomers of A, G, C, and T are safeguarded by the Bhoc group, which is eliminated at the conclusion of synthesis using trifluoroacetic acid. The Fmoc group safeguards the main amino acids inside the monomer backbone. A 20% piperidine solution in dimethylformamide (DMF) effectively cleaves the Fmoc group post-synthesis. Each PNA monomer is linked to a nucleobase (adenine, cytosine, guanine, or thymine), analogous to real nucleic acids. The nucleobase facilitates Watson-Crick base pairing with compatible nucleic acid sequences (DNA or RNA). The nucleobase is linked to the PNA backbone via a methylene carbonyl bond, substituting the sugar-phosphate connection seen in natural nucleotides. This connection facilitates the correct alignment of the nucleobase for base pairing while retaining the peptide-like characteristics of the backbone.

Bhoc/Fmoc PNA monomers.Fig.5 Bhoc/Fmoc PNA monomers. (Shakeel S., et al., 2006)

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Peptide Nucleic Acid application

(1) Nucleic acid purification

Purifying target nucleic acids using PNAs is possible due to their very high binding affinity; nevertheless, this process necessitates prior knowledge of the target sequence and the production of a capture oligomer for each individual target nucleic acid. For instance, target nucleic acids may be purified by PNAs with six histidine residues using nickel affinity chromatography, as one nickel ion binds to six histidines. Additionally, biotinylated PNAs coupled with streptavidin-coated magnetic beads can be used to purify nucleic acids in place of PNAs bearing histidine residues. But there are a few issues with this nucleic acid purification method: first, you need to know the target sequence in order to synthesize the PNA. Second, you have to synthesize separate PNAs for each nucleic acid you want to remove.

(2) In situ hybridization (PNA-FISH)

Due to their neutral backbone, which offers great specificity in situ, needs less concentration, and hybridizes fast, PNA probes are extremely useful in FISH (fluorescent in situ hybridization) applications. Reduced background binding, minimal photobleaching, a gentle washing method, and an outstanding signal-to-noise ratio are further benefits of employing PNA probes in situ. A single labeled 15-mer PNA oligomer efficiently accomplishes in situ labeling. Quantitative telomere analysis was the initial motivation for developing the PNA-FISH technology. Using fluorescein-labeled PNA probes, one research was able to accurately assess telomere size. Several in situ cancer and aging investigations following that utilized telomeric PNA probes. Researchers continued to advance the field by developing PNA probes that could specifically identify human chromosomes on metaphase and interphase nuclei based on their satellite repeat sequences.

Applications of PNA as diagnostic agents.Fig.6 Applications of PNA as diagnostic agents. (MacLelland V., et al., 2023)

(3) PNA for diagnosis and detection

By synthesizing PNA targeting the primer binding site, the PCR approach may be used for single-nucleotide polymorphism (SNP) or single-base-pair mutation analysis. The approach is based on many PNA features, such as the fact that a PNA/DNA duplex is more stable than the comparable DNA/DNA duplex, that PNA binds to DNA with greater specificity, and that PNA is ineffective as a primer for DNA polymerases. The PNA-directed PCR clamping method essentially involves directing the PNA to a specific PCR primer site during the annealing process. In this stage, the temperature is adjusted higher than in the standard PCR primer annealing step, which involves the selective binding of PNA to the DNA molecule. A PCR product cannot be formed because the PNA binds to the primer binding site in place of the primer. PNA can tell the difference between entirely complementary and single-mismatch targets (mutations) in a mixed target PCR. This is because, when there are mismatches, the melting point of the PNA/DNA hybrid is significantly lower than the typical one. Therefore, primer binding is more likely to succeed than PNA annealing. The result is amplification of mutant sequences. Three distinct point mutations may be distinguished at a single site using this PNA clamping.

(4) Antisense therapy

By binding to complementary mRNA sequences, PNAs can impede protein translation and serve as antisense oligonucleotides. This has great promise as a treatment for cancer, genetic abnormalities, and viral infections since it blocks the production of proteins that cause illness.

(5) Gene editing

The potential of PNAs as gene editing tools is being investigated, especially in conjunction with CRISPR/Cas9. To improve the precision of genome editing for therapeutic purposes, PNA-based technologies can direct the CRISPR apparatus to target DNA regions with greater precision.

 Antibacterial Peptide Nucleic Acids (PNAs).Fig.7 Antibacterial Peptide Nucleic Acids (PNAs). (Wojciechowska M., et al., 2020)

References

  1. MacLelland V., et al., Therapeutic and diagnostic applications of antisense peptide nucleic acids, Molecular Therapy-Nucleic Acids, 2023.
  2. Shakeel S., et al., Peptide nucleic acid (PNA)—a review, Journal of Chemical Technology & Biotechnology: International Research in Process, Environmental & Clean Technology, 2006, 81(6): 892-899.
  3. Pellestor F., et al., The peptide nucleic acids (PNAs), powerful tools for molecular genetics and cytogenetics, European journal of human genetics, 2004, 12(9): 694-700.
  4. Wu J., et al., Recent advances in peptide nucleic acid for cancer bionanotechnology, Acta Pharmacologica Sinica, 2017, 38(6): 798-805.
  5. Carufe K E W., et al., Peptide Nucleic Acid-Mediated Regulation of CRISPR-Cas9 Specificity, nucleic acid therapeutics, 2024.
  6. Wojciechowska M., et al., Antibacterial peptide nucleic acids—facts and perspectives, Molecules, 2020, 25(3): 559.
Creative Peptides provides high-quality products and reliable services for antimicrobial peptides, welcoming inquiries on any aspect of peptide nucleic acids (PNA). Our team is dedicated to meeting your research needs with expertise and support.

Q: What PNA synthesis services does Creative Peptides offer?

A: We provide custom PNA synthesis tailored to specific research needs, including modifications, labeling, and high-purity products for various applications in molecular biology.

Q: Can Creative Peptides assist with PNA design?

A: Yes, our experts offer consultation and design services, guiding clients through sequence selection and modification options for optimal PNA performance in their projects.

Q: Why choose Creative Peptides for PNA solutions?

A: We deliver high-quality PNA products, custom services, and technical support, ensuring reliable, accurate results for research, diagnostics, and drug development.

Q: Does Creative Peptides offer labeled PNAs for research?

A: Yes, we provide PNAs with various labeling options, including fluorescent and biotin labels, to support detection and tracking in molecular biology experiments.

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