New Modality Biologics (PNA, XNA, and Related Analogs): Sequence Listing Considerations

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1. Why New Modalities Strain the Framework

Sequence listing standards were designed around natural DNA, RNA, and L-amino acid proteins. New-modality therapeutics keep those familiar nucleobase or amino acid “letters” but change what is underneath them:

• Peptide nucleic acids (PNAs) carry nucleobases on a peptide-like backbone.
• Xeno nucleic acids (XNAs) replace the sugar-phosphate backbone. Examples include glycol nucleic acids (GNA), threose nucleic acids (TNA), morpholinos, hexitol (HNA), and cyclohexenyl (CeNA) nucleic acids.
• Chemically modified oligonucleotides include 2′-O-methyl, 2′-fluoro, locked (LNA), and phosphorothioate variants, often in gapmer or chimeric layouts.
• D-peptides, macrocycles, stapled peptides, and conjugates join amino acid chains to nucleic acids, lipids, or other payloads.

A single drug candidate can combine several of these. The drafting question is how much of that chemistry the sequence listing must capture, and what happens to claim support if it captures too little or too much.

ST.26 anticipates these molecules to a degree that surprises many drafters. Its definition of “nucleotide analogue” expressly names backbone types such as the amino acid backbone of PNAs, the glycol molecules of GNAs, the threofuranosyl sugars of TNAs, the morpholine rings and phosphorodiamidate groups of morpholinos, and cyclohexenyl backbones. Because the standard already covers them, the work is in applying the representation rules correctly.

2. Which Version and Which Rules Apply

Applicable rules depend on the application’s filing date, not the date the listing is submitted. Three points matter:

• Current version. ST.26 version 1.7 is the version in force. It was adopted in December 2023, and the EPO accepted sequence listings complying with version 1.6 or 1.7 from July 1, 2024.
• Version 2.0 is coming. The Committee on WIPO Standards approved version 2.0 in November 2025, with entry into force on July 1, 2027 for patent applications filed on or after that date. WIPO documents describe it as allowing optional inclusion of short nucleotide and amino acid sequences and as requiring specifically defined symbols for modified nucleotide and peptide analogs. Earlier Task Force papers described the second change as requiring a subset of analogs to be represented by the corresponding unmodified residue symbol. I could not confirm which analogs fall within that subset, so review the version 2.0 text itself before filing anything in this area on or after that date.
• No grandfathering across formats. The USPTO’s position on the earlier ST.25-to-ST.26 change shows the principle: a continuation filed after the cutoff needs a listing in the new format even if the parent used the old one. Expect the same logic to apply at future version boundaries, subject to each office’s implementing rules.

For a portfolio with a priority filing before July 2027 and follow-on filings after, plan the sequence listing conversion early.

3. What Must Be Listed

Thresholds

Under ST.26, a nucleotide sequence disclosed by enumeration of its residues is listed if it has 10 or more specifically defined nucleotides. An amino acid sequence is listed if it has 4 or more specifically defined amino acids. Sequences with nucleotide analogs such as PNAs and GNAs are included, and so are sequences with D-amino acids. Linear regions of branched sequences must also be listed.

Two classification rules matter most for new modalities:

• PNA residues count as nucleotides, not amino acids. Despite the peptide-like backbone, a PNA belongs in the nucleotide part of the standard. A PNA-peptide conjugate therefore produces different sequence types that are handled separately.
• “Specifically defined” excludes the wildcards. A nucleotide is specifically defined if it is anything other than “n”, and an amino acid if it is anything other than “X”. Only specifically defined residues count toward the minimum length.

The threshold trap

The choice of symbol for a modified residue can decide whether a sequence has to be listed at all. The USPTO’s FAQ gives the example: a 2′-O-methyl adenosine represented as “a” is specifically defined, while norleucine represented as “X” is not.

That leads to two practical consequences:

1. An oligomer built largely from residues you represent as “n” or “X” may fall below the minimum length, and short sequences cannot currently be included at all (this is what version 2.0 relaxes).
2. The representation choice affects searchability and how examiners and third parties read the disclosure, so it should be deliberate rather than defaulted by the software.

Enumeration matters

The requirement is triggered by enumerating residues in order. Shorthand is treated as if written out in full: the standard treats “His6Gln” as “HHHHHHQ”. A repeat notation such as a PNA trinucleotide repeat written “(CAG)10” is treated as 30 enumerated residues, and it is listed as a full 30-residue sequence. Every enumerated qualifying sequence gets its own identifier, even if it is a fragment of another listed sequence.

Sequences that are described only by structure or name, without enumerating residues, are outside this requirement. They are still part of the disclosure, so structural formulae become important (see Section 8).

4. Representing Nucleotide Analogs (PNA, GNA, TNA, Morpholino, and Others)

Core representation rules

Rule	What it means in practice
Single strand, one direction	Write each sequence as a single strand from left to right in the 5′-to-3′ direction, or in the left-to-right direction that mimics it. The designations 5′ and 3′ must not appear in the sequence.
Lowercase symbols only	Every residue is a single lowercase symbol, and each symbol equals exactly one residue.
Prefer the unmodified counterpart	Modified nucleotides should be represented as a, c, g, or t whenever possible. This is a “should,” not a “must.”
Otherwise use “n”	A modified nucleotide that no other symbol can represent, such as a non-naturally occurring nucleotide, is represented by “n”.
Annotate	A modified nucleotide is described in the feature table using the feature key “modified_base” with the mandatory “mod_base” qualifier.
Use a “note” for anything not on the abbreviation list	If the abbreviation is “OTHER,” the full unabbreviated chemical name goes in a “note” qualifier.

The standard’s own text adds that the abbreviations from its modified-nucleotide table must not be used inside the sequence itself. They belong only in the feature table.

Describing whole regions

PNA, GNA, and other backbone-defined XNAs often modify every residue in a run. The standard allows that region to be described jointly. A region of consecutive modified nucleotides sharing the same backbone moiety can be covered by one feature. The “note” value should be the most restrictive unabbreviated chemical name encompassing all the modified nucleotides in the range, or a list of the individual chemical names. The MPEP gives a glycol nucleic acid example, describing the nucleobase-containing residues as “2,3-dihydroxypropyl nucleosides”. If an individual residue carries an additional modification, that residue is also described separately.

Locations use the “x..y” syntax for a region. For a single linkage between two adjacent residues, such as one phosphorothioate bond, the USPTO FAQ describes the “x^y” format. Phosphorothioate-linked residues are annotated with “modified_base”, “mod_base” set to OTHER, and a note describing the bond.

Molecule type and organism

• The 2016 revision of ST.26 stated that for nucleotide sequences, including nucleotide analogue sequences, the sequence’s molecule type element must indicate DNA or RNA. Confirm this against the current text.
• For the organism qualifier, non-natural sequences use “synthetic construct”, and the USPTO FAQ confirms that no further description is required for that value. It nonetheless recommends supplying as much information as possible.

Chimeras and hybrids

Most therapeutic candidates are chimeric, such as gapmers with modified wings and a DNA gap, or PNA-DNA or DNA-XNA constructs. The FAQ shows the closest explicit rule: for a DNA/RNA hybrid, each DNA and RNA segment must be described with a “misc_feature” key and a note saying which it is. Extending the same discipline to XNA chimeras (one described segment for each chemically distinct region, with every residue covered) is a sensible way to draft, though I have not found rule text requiring it for non-DNA/RNA hybrids.

Also keep in mind that residues joined by a non-nucleotide spacer are handled differently from a continuous strand. ST.26 Annex VI includes worked examples on this point: nucleotide sequences interrupted by a C3 spacer (Example 3(d)-1) and nucleic acid analogues (Example 3(d)-4). Those examples are the closest official guidance for constructs with linkers, and one of them treats each segment as a separate nucleotide sequence when it meets the minimum length.

Double-stranded constructs

A double-stranded sequence disclosed by enumerating both strands is represented as a single sequence or as two sequences when the strands are fully complementary. When the strands are not fully complementary, as with most siRNA-type designs with overhangs or mismatches, each strand needs its own identifier.

5. Representing Peptide Analogs and Constrained Peptides

• D-amino acids are included in the listing. ST.26 says modified amino acids, including D-amino acids, should be represented as the corresponding unmodified amino acid where possible, with an annotation indicating the modification. If no symbol fits, use “X”.
• Annotation keys. Modified amino acids are annotated with the feature keys MOD_RES (post-translational modifications), SITE (other modifications), CARBOHYD, or LIPID, together with a note. The note must be an abbreviation from the standard’s modification table or the full unabbreviated name.
• Non-natural amino acids (for example norleucine) that cannot be treated as an unmodified residue plus a modification are recommended to be represented by “X”. Since “X” is not specifically defined, a peptidomimetic with many such residues may not reach 4 specifically defined amino acids.
• Cyclic peptides. If the ring closes through ordinary peptide bonds, no annotation is required, but if cyclization creates a modified residue, that residue must be annotated. Annotating the cyclic nature is recommended either way.
• Branched and side-chain-linked constructs. Linear regions with 4 or more specifically defined amino acids are listed. A branch with fewer than 4 cannot be listed separately, and the residue where it attaches is described using SITE with a note. Side-chain linkages make the residue a modified residue that must be annotated. This is directly relevant to stapled peptides and lipidated or conjugated peptides.
• Terminal modifications. Whether an end cap must be annotated depends on whether it changes the chemical structure of the residue. The FAQ says an N-terminal biotin joined by an amide bond does not require annotation, while C-terminal methylation that replaces the hydroxyl of the carboxyl group does.

A software caution

The USPTO FAQ warns that the WIPO Sequence validator does not know a residue is modified until you add the feature. Its example is a D-alanine: entered as “A” without a feature, the tool treats it as L-alanine and raises no error. Likewise, “n” and “X” without a description raise no error, because they have default values. A listing can pass validation and still misdescribe the molecule.

6. Summary Table by Modality

Modality	Sequence type under ST.26	Symbols in the sequence	Annotation
PNA	Nucleotide (not amino acid)	a, c, g, t (or n where no nucleobase symbol fits)	modified_base with note giving the backbone chemistry, region form x..y
GNA	Nucleotide analog	a, c, g, t	Joint region annotation; the MPEP example uses the dihydroxypropyl nucleoside name
TNA, HNA, CeNA, morpholino	Nucleotide analog	Nucleobase symbols where possible, otherwise n	modified_base, mod_base OTHER, note with full name
2′-O-methyl and similar	Modified nucleotide	Corresponding a, c, g, t	mod_base abbreviation from the standard’s table (for example um) or OTHER plus note
Phosphorothioate linkages	Modified linkage	Unchanged	modified_base, OTHER, note; x^y for single linkages, x..y for runs
D-peptides	Amino acid	Corresponding L-symbol or X	Feature key plus note describing the D-configuration
Macrocycles, stapled, branched peptides	Amino acid (linear regions listed)	Residue letters	Annotation where cyclization or crosslinks create modified residues
PNA-peptide or oligonucleotide-peptide conjugates	Separate nucleotide and amino acid sequences	Each segment in its own sequence	Note or SITE describing the linkage

For LNA and other analogs that add a bridge to the sugar, the standard leaves the choice between the unmodified symbol and “n” to the applicant’s discretion, with guidance that unchanged core structures point toward the unmodified symbol and structurally different residues point toward “n”. Expect version 2.0 to narrow this discretion for at least some analogs.

7. The Sequence Listing as Part of the Disclosure

A sequence listing submitted with a new application in compliance with the US rules is considered part of the specification, and so it contributes to the disclosure for written description and enablement purposes. Compliance is not required to obtain a filing date, and compliance is not itself a new-matter issue. For drafting, this means:

• Consistency is a legal issue, not only a formality. Claims, description, drawings, and listing must agree on sequences, identifiers, and modification descriptions.
• Referencing. Sequences in the listing are referred to in the description, claims, or drawings by “SEQ ID NO:” plus the identifier, even where the sequence is also written out in the text.
• Claim scope follows the annotation. If the claims recite an XNA backbone, the annotation and the chemical name in the note should support that backbone. If the claims are broader (any backbone-modified analog), the description should carry generic language and structural formulae.
• Variants and consensus sequences. Use the VARIANT feature and notes for alternatives, and consider listing separately every variant important to the invention, even where the standard does not require it. For a sequence disclosed once with variable length, the longest embodiment is the one listed.
• Placeholders. Sequences below the current minimum length that you deleted or chose not to list can be handled with intentionally skipped (empty) sequences to preserve numbering.

8. What the Sequence Listing Cannot Do

A sequence listing describes residue order and per-residue annotations. It cannot show three-dimensional structure, precise linker chemistry, conjugation sites on complex payloads, or stoichiometry. For these, use:

• Structural formulae in the description or drawings, following the chemical structure and drawing conventions covered in the earlier article in this series.
• Definitions of generic terms in the text, such as what “XNA” or “nucleobase-bearing backbone” means for the claimed genus.
• Figure-level references to the relevant SEQ ID NO. Where a figure shows a qualifying sequence, identify it with “SEQ ID NO:”.

9. A Worked Illustration (Hypothetical)

Consider a construct with three components: a 16-mer PNA, a 6-residue cell-penetrating peptide with two D-amino acids attached by an amide linker, and a 12-mer GNA guide with three phosphorothioate linkages.

Component	Qualifies for listing?	Sketch of representation
16-mer PNA	Yes (10 or more specifically defined nucleotides)	Lowercase nucleobase symbols, one modified_base feature over 1..16 with a note naming the backbone chemistry
6-residue peptide with two D-residues	Yes (4 or more specifically defined amino acids)	L-symbols for the D-residues plus features describing D-configuration; separate sequence identifier
12-mer GNA with three phosphorothioates	Yes	Nucleobase symbols; one feature over the region describing the glycol backbone; separate features for each phosphorothioate location
Amide linker joining PNA and peptide	Not a sequence	Describe in the text and in a structural formula; add a note or SITE describing the attachment where a residue is affected

This is a drafting sketch, not a filing template. Exact feature keys, qualifier values, and note wording must be checked against the current ST.26 text and Annex VI examples.

10. Common Pitfalls

1. Treating PNA as a peptide. It is a nucleotide under ST.26, so listing it as an amino acid sequence is wrong.
2. Letting the tool default a modification away. The validator will not flag a missing D-configuration or an undescribed “n”.
3. Over-using “n” and “X”. It can drop a sequence below the minimum length or hide chemistry you intend to claim.
4. Forgetting to expand repeats and shorthand. Notations such as “(CAG)10” count as enumerated residues.
5. Skipping the annotation “because it is optional.” Some annotation is required where the residue’s structure changes, and the rest is strongly recommended.
6. Inconsistent numbering between the listing and the text. Every enumerated qualifying sequence has its own identifier, and fragments cannot be cited as “residues 1-10 of SEQ ID NO: 1”.
7. Assuming a passing validation means compliance. Some requirements need human review, and responsibility for accuracy stays with the applicant.
8. Ignoring the 2027 version change. Applications filed on or after July 1, 2027 fall under version 2.0’s rules for analogs and short sequences.

11. Drafting Workflow

1. Inventory every molecule in the claims and description, classify each segment (nucleotide, analog, amino acid, non-sequence linker), and mark which are disclosed by enumeration.
2. Fix the version and rules from the application’s filing date, and check the local office’s implementing notices.
3. Decide the symbol strategy for each modified residue (unmodified counterpart versus “n” or “X”), and record the reasoning, including its effect on the minimum-length test.
4. Draft the annotations with region-wise features and notes that match the claim language and the chemical names in the description.
5. Build the listing in the current WIPO Sequence tool, validate it, then have a person review every modified residue, every “n” and “X”, and every organism and molecule-type entry.
6. Reconcile identifiers across claims, description, drawings, and listing.
7. Add structural formulae for anything the listing cannot convey.
8. Re-check at each filing in the family, since version and rules may differ.

Conclusion

PNA and XNA modalities are not outside the sequence listing regime. ST.26 names them, classifies PNA as a nucleotide, requires the sequences to be listed when they meet the length thresholds, and gives a mechanism for annotating backbone chemistry. The real risk lies in the choices the standard leaves open, such as unmodified symbol versus “n”, and how much of the chemistry to encode in features versus prose. Those choices affect whether a sequence must be listed, what a searcher or examiner sees, and how well the disclosure supports the claims. With version 2.0 arriving for filings on or after July 1, 2027, drafters of new-modality applications should treat the annotation strategy as a deliberate part of claim drafting, and watch the new text closely.