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CAS 172405-16-2
Catalog BAT-008273
Molecular Weight 269.25
Molecular Formula C11H15N3O5
C(Boc) Acetic acid
CAS 186046-99-1
Catalog BAT-010863
Molecular Weight 293.28
Molecular Formula C12H15N5O4
A(Boc) Acetic acid
CAS 1028077-12-4
Catalog BAT-014361
Molecular Weight 309.28
Molecular Formula C12H15N5O5
G(Boc) Acetic acid
CAS 20924-05-4
Catalog BAT-014362
Molecular Weight 184.15
Molecular Formula C7H8N2O4
T Acetic acid
Catalog BAT-014363
Molecular Weight 336.36
Molecular Formula C15H16N2O5S
thioT(PMB) Acetic acid
CAS 4113-97-7
Catalog BAT-014364
Molecular Weight 170.12
Molecular Formula C6H6N2O4
U Acetic acid
Catalog BAT-014365
Molecular Weight 322.34
Molecular Formula C14H14N2O5S
thioU(PMB) Acetic acid
CAS 1256337-02-6
Catalog BAT-014366
Molecular Weight 252.27
Molecular Formula C12H16N2O4
M(Boc) Acetic acid
CAS 221362-48-7
Catalog BAT-014367
Molecular Weight 269.26
Molecular Formula C11H15N3O5
J(Boc) Acetic acid

BOC Sciences offers a wide variety of PNA nucleobases products, all of which are structural units for building peptide nucleic acid. We can also customize nucleobases for you.

What are Nucleobases of PNA?

The nucleotide bases of PNA (peptide nucleic acid) include Adenine, Cytosine, Guanine, Thymine or Uracil. These nucleotide bases enable PNAs to undergo specific base pairing with DNA or RNA and have a wide range of potential for bioscience research and applications. It is important to note that the nucleotide bases of PNA are not connected to the bases of DNA or RNA through a sugar-phosphate backbone, but rather are attached to the backbone of PNA through a linker group. This structural feature makes PNA highly resistant to enzymatic degradation and stability, and enables specific base pairing with DNA or RNA.

Types of nucleobases in peptide nucleic acid.Fig.1 Types of nucleobases in peptide nucleic acid.

How to use Nucleobases to Prepare PNA?

  • Synthesis of Nucleobase Units

Methods for synthesizing nucleobase units include chemical synthesis, enzymatic methods, and synthetic biology methods.

  • Protective Groups for Nucleobase Units

In order to control the reactivity and selectivity of the nucleobase unit, protective groups need to be introduced into the nucleobase. These protecting groups will protect specific positions of the nucleobase in subsequent steps.

  • Attachment of Nucleobase Units

The synthesized nucleobase units are joined to form a PNA chain. The joining is usually done by peptide bond formation rather than the traditional sugar-phosphate backbone joining of nucleic acids.

Nucleobases Modification

PNA is a kind of substance with polypeptide as the backbones without charge. Its structure is composed of repeated N-(2-aminoethyl) glycine as a unit, which is connected to the base through α-N-acyl methyl. And the nucleobases are connected with the backbones by the methylene carbonyl group.

All four bases of PNA are alkylated with amine to form base acetic acid derivatives, which are then combined with unprotected nitrogen on the backbones by common peptide synthesis method.

  • Thymine

The alkylation reaction of thymine usually does not require the use of protective groups, so thymine acetic acid can be obtained by reacting with bromoacetate, saponification or directly reacting with bromoacetic acid.

The other three bases have active groups, which need to be protected first.

  • Cytosine

The active group on cytosine is the amino group at position 4, and the optional protective groups are benzyloxycarbonyl (Cbz), 4-tert-butylbenzoyl (4-t-BuBz), Benzoyl (Bz) and 4-methoxyphenyldiphenylmethyl (Mmt). Then it is alkylated with bromoacetate, and saponify to obtain the derivatives of cytosine acetic acid.

  • Adenine

The protection process of adenine is basically the same as that of cytosine. The available protective groups are Cbz, Mmt and p-methoxyphenyl (An).

  • Guanine

The protection of guanine is relatively complex, so it is necessary to avoid the side reaction interference of N7 alkylation in the process of N9 alkylation. A common method is to use 2-amino-6-chloropurine in alkylation, and then backflow under acidic or alkaline conditions after alkylation to hydrolyze chlorine into carbonyl group or directly alkylate N2 adenine with protective group, separate N7/N9 alkylation products by chromatography, and then saponify them to obtain derivatives of guanine acetic acid.

Roles of Nucleobases in PNA

  • Base Pairing

The nucleotide bases of PNA can specifically base pair with complementary bases in DNA or RNA, allowing the PNA to form a stable double-stranded structure or triple-stranded structure with the target sequence of DNA or RNA.

  • Sequence Recognition

By designing appropriate nucleotide base sequences, PNA can selectively bind to target sequences and form stable PNA/DNA or PNA/RNA complexes, which have a wide range of potential applications in molecular diagnosis, gene regulation, and gene therapy.

  • Blocking DNA/RNA Function

PNAs can interfere with or inhibit specific gene expression, protein synthesis or RNA translation processes. This ability allows PNA to be used for gene silencing, gene knockdown, and other research and applications related to DNA or RNA function.

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