---
title: "Nucleic Acid Builder Add-on: DNA, RNA and Aptamers Step by Step | MolDraw Blog"
url: https://www.moldraw.com/blog/nucleic-acid-builder-dna-rna-oligo-aptamer-guide.html
description: "How to use the free MolDraw Nucleic acid builder add-on: type a DNA or RNA sequence, add FAM, biotin and other modifications, fold it, find G-quadruplexes, draw the full structure or a schematic, view a B-form helix in 3D and read mass, Tm and ε260. Annotated screenshots for every step."
lang: en
publisher: Scidart Academy
generated: 2026-11-07
---
# Nucleic Acid Builder Add-on: DNA, RNA and Aptamers Step by Step

Published: 7 Nov 2026 · Author: Scidart Academy · Reading time: ~9 min

![The MolDraw Nucleic acid builder: a theophylline RNA aptamer fold diagram, a FAM and biotin labelled aptamer schematic and a B-form DNA duplex in 3D](https://www.moldraw.com/blog/thumbs/nucleic-acid-builder-guide.webp)

Three outputs of the Nucleic acid builder: a fold diagram, a labelled schematic and a 3D duplex.

**Short answer:** Open the 3D viewer, press **+** and install **Nucleic acid builder**. In the DNA/RNA tab, type or paste a sequence 5′→3′, add dyes, linkers or modified nucleotides in **Modify**, then use **Fold** for the secondary structure and G-quadruplexes, **Structure** for the full chemical drawing or a schematic, **3D** for an A- or B-form helix, and **Properties** for mass, Tm and ε260.

How to read the screenshots: each orange number in a picture matches the numbered note under it. Dashed boxes with a magnified panel are zoomed-in details.

## Step 1: Install the Nucleic acid builder add-on

![The add-on menu that opens from the plus button next to the 3D viewer tabs, with Nucleic acid builder highlighted](https://www.moldraw.com/blog/images/sequence-builders/addon-menu-nucleic.webp)

The **+** next to the 3D viewer tabs lists every add-on. Click **Install** next to Nucleic acid builder.

1. The **+** button at the end of the tab row (Structure, Protein, …) opens the add-on menu.
2. **Nucleic acid builder**: click **Install** and a **DNA/RNA** tab appears.

1. Open the [MolDraw editor](https://www.moldraw.com/) and sign in. A free account is enough to use add-ons.
2. Open the 3D viewer on the right (the **3D** button at the bottom of the atom bar) and press **+** next to the tabs.
3. Click **Install** next to **Nucleic acid builder** (callout 2). The **DNA/RNA** tab opens, and the button changes to **Open**.

Add-ons stay installed on your account. To remove one, hover its tab and click the small **×**. You can also manage them under **Settings** › **Plugins**.

## Step 2: Get to know the DNA/RNA panel

The tab opens with the thrombin-binding aptamer (TBA, `GGTTGGTGTGGTTGG`) already loaded, so every part of the panel has something to show.

![The Nucleic acid builder panel with the TBA sequence: Examples menu, DNA/RNA, Single/Duplex and Linear/Circular switches, sequence box, the Modify, Fold, Structure, 3D and Properties tabs, the strand as clickable nucleotide chips and the list of modifications with 5 prime and 3 prime buttons](https://www.moldraw.com/blog/images/sequence-builders/nucleic-panel.webp)

The top of the panel holds the sequence; the five tabs below do the work.

1. **Examples**: TBA, AS1411, sgc8c, the ATP DNA aptamer, the theophylline RNA aptamer and pegaptanib, each with its reference.
2. **DNA / RNA** sets the default sugar (deoxyribose or ribose).
3. **Single / Duplex**: one strand, or the strand with its Watson-Crick complement.
4. **Linear / Circular**: circular joins the 3′ end to the 5′ end.
5. **Sequence box**, always written 5′→3′. Spaces, line breaks, numbers, FASTA headers and 5′-/-3′ marks are ignored.
6. **The five tabs**: Modify, Fold, Structure, 3D and Properties.
7. **The strand** as chips, numbered every 10. Click one to edit that nucleotide.
8. **Modifications**: dyes, conjugation groups, linkers, phosphate and spacers, each with its mass change and **5′** / **3′** buttons.
9. **Attach any molecule…** joins your own structure (from the canvas, PubChem or a SMILES) to the 5′ or 3′ end.

## Step 3: Add a label and edit single nucleotides

Click **5′** next to FAM to add a fluorescein label, then click nucleotide 3 and change its 3′ linkage to a phosphorothioate.

![The Modify tab after adding 5 prime FAM and selecting nucleotide 3: the sequence now reads [FAM]GGT*TGGTGTGGTTGG, a FAM chip leads the strand, nucleotide 3 is outlined and an editor shows Sugar, Base and 3 prime link options with P=S selected](https://www.moldraw.com/blog/images/sequence-builders/nucleic-modify.webp)

Palette clicks rewrite the sequence text, so the text is always the full record of the oligo.

1. The text now reads `[FAM]GGT*TGGTGTGGTTGG`: `[FAM]` first means 5′, and `*` marks the phosphorothioate after T3.
2. The FAM chip at the 5′ end of the strand.
3. Nucleotide 3, selected (outlined in blue).
4. **Sugar**: dN (deoxy), rN (ribo), 2′-OMe, 2′-F or LNA for this nucleotide only.
5. **Base**: A, C, G, T, U, 5-methyl-C or inosine.
6. **3′ link**: P=O (phosphate) or P=S (phosphorothioate).
7. FAM now shows only the **3′** button, because the 5′ end is taken. Each dye row lists its mass change (+537.45 for FAM).

You can also type modifications. `mA fC +T rU dA` give 2′-OMe, 2′-F, LNA, ribo and deoxy sugars; `[5mC]` and `[I]` give 5-methyl-C and inosine; IDT codes such as `/56-FAM/` or `/3InvdT/` work too.

## Step 4: Fold the strand (secondary structure)

Open **Fold**. Here the theophylline RNA aptamer was picked from Examples because it forms a clear hairpin.

![The Fold tab for the theophylline RNA aptamer: temperature 37 °C and 150 mM Na+, MFE ΔG −8.31 kcal/mol, 10 base pairs, the dot-bracket string, the click mode switch, the colour-by-base toggle and a fold diagram above the Add to canvas button](https://www.moldraw.com/blog/images/sequence-builders/nucleic-fold.webp)

The minimum free energy (MFE) fold with its energy, pair count and diagram.

1. **Temperature and Na⁺** used for the fold, and the energy set (Turner 2004 for RNA, Mathews 2004 for DNA).
2. **MFE ΔG**: −8.31 kcal/mol for this aptamer at 37 °C.
3. **Base pairs**: 10.
4. **Dot-bracket**: brackets are pairs, dots are unpaired bases. It is editable: type your own structure to draw it.
5. **Click bases to** pair or unpair them, force a base unpaired, or force a pair; the fold is recalculated with your constraints.
6. **Colour by base** on or off.
7. **Add to canvas** puts the diagram on your drawing.

![The theophylline aptamer fold diagram on the MolDraw canvas: two stems and loops with coloured bases, numbering at 10, 20 and 30, a G·U wobble pair drawn as a dot, 5 prime and 3 prime labels and the title with ΔG −8.31 kcal/mol at 37 °C](https://www.moldraw.com/blog/images/sequence-builders/nucleic-fold-canvas.webp)

The diagram on the canvas. It moves as one group; Alt-click edits a single label.

1. Numbering every 10 nucleotides.
2. A G·U wobble pair, drawn as a dot. Watson-Crick pairs are lines.
3. The title with the name, ΔG and temperature, as editable canvas text.

The fold engine reproduces RNAfold (ViennaRNA 2.8): 40 out of 40 test sequences gave the same energy and the same structure. Modified nucleotides fold as their parent bases, and the panel lists what it left out.

## Step 5: Check for a G-quadruplex

Guanine-rich aptamers often fold into G-quadruplexes, which the base-pair fold cannot show. Scroll down the Fold tab to the **G-quadruplex** card. TBA is the classic example.

![The G-quadruplex card for TBA: G4Hunter score 1.13, the motif with 2 tetrads, G-tracts at 1, 5, 10 and 14 and loops TT, TGT, TT, an Antiparallel/Parallel switch and the chair-type schematic with G1, G2, G5, G6, G10, G11, G14 and G15](https://www.moldraw.com/blog/images/sequence-builders/nucleic-g4.webp)

TBA folds as a two-tetrad antiparallel (chair) quadruplex.

1. **G4Hunter** scores for the whole strand and the best 25-nt window. Above about 1.2 a quadruplex is likely.
2. The motif found: number of tetrads, where the G-tracts start and the loop sequences.
3. **Draw as** antiparallel or parallel. The default comes from the loop lengths and is labelled as an assumption, not a prediction.
4. The schematic: tetrads G1·G6·G10·G15 and G2·G5·G11·G14, with arrows for strand direction.
5. **Add to canvas** inserts the schematic as an editable drawing.

## Step 6: Draw the full chemical structure

![The Structure tab in Full-atom segment mode for nucleotides 1 to 6 of TBA: every atom of the deoxyribose phosphate backbone and the G, G, T, T, G, G bases, with Add to canvas, Copy image, Copy SMILES and whole-molecule export buttons](https://www.moldraw.com/blog/images/sequence-builders/nucleic-structure.webp)

Full-atom mode draws up to 12 nucleotides at a time with every atom and wedge.

1. Three ways to draw: **Full-atom segment**, **Block mode** (one labelled box per unit) and **Schematic**.
2. Which nucleotides to draw: here 1 to 6. Up to 12 per segment.
3. The preview, exactly as it will be inserted.
4. **Add to canvas**, copy as an image, or **Copy SMILES** for the segment.
5. **Whole molecule**: copy or download the SMILES or molfile of the full strand at any length.

![Nucleotides 1 to 6 of TBA on the canvas: a zigzag sugar-phosphate backbone with furanose rings, phosphate groups and guanine and thymine bases, with stereo bonds on the sugars](https://www.moldraw.com/blog/images/sequence-builders/nucleic-structure-canvas.webp)

The segment on the canvas: a normal, editable structure.

## Step 7: Make a publication figure with Schematic

For a labelled aptamer the full structure is too large to read. Schematic mode draws the end groups in full and the oligo as one wavy line. Here the sequence was typed as `[FAM]GGTTGGTGTGGTTGG[Biotin]`.

![Schematic mode for FAM-TBA-biotin: strand colour swatches, text under the line set to Sequence, the fluorescein label drawn in full on the left, the oligo as a red wavy line with 5 prime and 3 prime marks, the biotin drawn in full on the right and the Add to canvas button](https://www.moldraw.com/blog/images/sequence-builders/nucleic-schematic.webp)

Schematic mode: both labels drawn atom by atom, the strand as a wavy line.

1. Choose **Schematic**.
2. **Strand colour**: six presets or any colour.
3. **Text under** the line: the sequence, the name, or nothing.
4. The 5′ group in full, through its linker and phosphate to the oligo (6-FAM on a C6 amino linker).
5. The oligo as a wavy line with 5′ and 3′ marks.
6. The 3′ group in full (biotin on a C6 linker).
7. **Add to canvas**.

![The FAM-TBA-biotin schematic on the canvas with the fluorescein and biotin structures joined by a red wavy line labelled with the sequence](https://www.moldraw.com/blog/images/sequence-builders/nucleic-schematic-canvas.webp)

On the canvas the schematic is one group: drag the line to move it all. The structures stay editable.

## Step 8: View it in 3D

![The 3D tab showing an idealised B-form DNA duplex of TBA and its complement, with the duplex sequence shown above, B-form/A-form and Single/Duplex switches and Add to canvas, Download PDB and Download molfile buttons](https://www.moldraw.com/blog/images/sequence-builders/nucleic-3d.webp)

An idealised B-form duplex built from the sequence.

1. With **Duplex** on, the complement is shown under the strand (5′-GGTTGGTGTGGTTGG-3′ / 3′-CCAACCACACCAACC-5′).
2. **B-form** (10 bp per turn) or **A-form** (11 bp per turn) helix.
3. **Single** strand in helical shape, or the Watson-Crick **Duplex**.
4. The model. Drag to rotate, scroll to zoom.
5. **Add to canvas** inserts a snapshot of the view.
6. **Download PDB** or molfile for PyMOL, Chimera or docking.

These are fibre-model helices, not predicted or energy-minimised structures: an aptamer is shown as a straight helix. Dyes and linkers are not drawn in 3D.

## Step 9: Read masses, Tm and ε260

![The Properties tab for FAM-TBA-biotin: formula, monoisotopic mass 5666.0607 Da and average mass 5668.95 g/mol, melting temperature inputs for oligo, Na+, Mg2+ and dNTP concentration, Tm 50.4 °C, ε260 143,300 L mol−1 cm−1 and the hairpin ΔG](https://www.moldraw.com/blog/images/sequence-builders/nucleic-properties.webp)

Everything you need to order, quantify and use the oligo.

1. **Formula**, monoisotopic and average mass, including the labels. Use them to check an ESI or MALDI spectrum.
2. **Buffer** for the melting temperature: oligo concentration, Na⁺, Mg²⁺ and dNTP.
3. **Tm** from the nearest-neighbour model (SantaLucia 1998 for DNA; salt correction by Owczarzy). The basic GC rule of thumb is shown below it for comparison.
4. **ε260**, the extinction coefficient at 260 nm, with nmol and µg per A260 unit for quantifying your sample.
5. Hairpin (fold) ΔG and, below it, the self-dimer ΔG, to spot primers that fold back or pair with themselves.

The Tm values match Biopython's `Tm_NN` for 210 out of 210 test cases. Labels such as FAM are not part of the Tm or ε260 models, and the panel says so under each value.

## Ways to use it

- **Aptamer papers:** draw the fold, the G-quadruplex and a labelled schematic for the same sequence.
- **Ordering oligos:** check mass, Tm and ε260 before you order, and paste IDT codes straight from the order sheet.
- **Teaching:** show A- and B-form helices, base pairing and the effect of salt on Tm.
- **Modelling:** download a PDB of the duplex as a starting geometry.

## Questions and answers

### How do I draw a DNA or RNA structure from a sequence?

Install the Nucleic acid builder add-on in MolDraw, open the DNA/RNA tab, type the sequence 5′ to 3′, open Structure and click Add to canvas. Full-atom mode draws up to 12 nucleotides with every atom; the whole strand is available as SMILES or molfile.

### Can I add FAM, Cy5 or biotin to an oligo?

Yes. In Modify, click 5′ or 3′ next to the group, or type it in brackets: [FAM]GGTTGG[Biotin]. IDT codes such as /56-FAM/ also work. Attach any molecule joins your own structure to an end.

### How is the secondary structure predicted?

With a minimum free energy fold using the ViennaRNA loop model and the Turner 2004 (RNA) or Mathews 2004 (DNA) parameters, at the temperature and Na+ concentration you set.

### Does it predict G-quadruplexes?

It scores the sequence with G4Hunter, finds G-tract motifs and draws a schematic. The strand arrangement is a rule of thumb from loop lengths and is labelled as assumed, not predicted.

### How accurate is the melting temperature?

Tm uses the nearest-neighbour model (SantaLucia 1998 for DNA, Xia 1998 for RNA) with Owczarzy salt corrections, and matches Biopython for all 210 test cases. Modifications are not included in the model.

### Is the Nucleic acid builder free?

Yes. You only need a free MolDraw account to install add-ons.

## Related guides

[Sequence to structure tool](https://www.moldraw.com/blog/peptide-dna-sequence-to-structure-guide.html) [Protein viewer](https://www.moldraw.com/blog/protein-viewer-plugin-pdb-3d.html) [All plugins](https://www.moldraw.com/docs/plugins/moldraw-plugins-overview-and-how-to-install/)

Last updated: November 7, 2026