Molecular biology is a fundamental branch of science that focuses on biological molecules, such as DNA, RNA, and proteins, and their intricate interactions within cells. It connects MolBio mechanisms to real-world situations, such as representing cellular functions, understanding disease mechanisms, and developing therapeutics. For experienced molecular biologists tackling complex research and development challenges in these demanding fields, effective software tools are not just helpful; they are crucial for accelerating scientific progress, enabling faster discovery, more effective design and analysis, and streamlining scientific workflows.

Sapio provides a comprehensive suite of seamless Molecular Biology tools to support these efforts. This toolkit helps users create, edit, and display annotated sequences, facilitate the design of PCR primers, perform various kinds of analysis, and perform molecular cloning procedures. The molecular biology toolkit is part of the Sapio Platform. Sequence data generated with the molecular biology tools are stored in Sapio’s multi-modal registry.

Sequence Design

Sequence Editor

This editor enables users to create, edit, and annotate DNA/RNA and protein sequences, including sequence features. It supports opening sequences from various formats and importing from GenBank, Addgene, and UniProt, as well as visualizing annotated sequences alongside a graphical map. Incorporating phylogenetic alignment tools and oligonucleotide design, the Sequence Editor solution can provide computational specificity and restriction endonuclease analysis.

CRISPR Design

The Sapio toolkit features a CRISPR Wizard designed to facilitate CRISPR-related workflows. This tool is often integrated with the Genome Browser. It features capabilities for designing CRISPR gRNAs. Sapio offers off-target analysis, primer design, and identification of optimal genomic loci for future editing, as well as the construction of CRISPR expression vectors (plasmid construction).

PCR Primer Design

Sapio’s toolkit facilitates the design of PCR primers through dedicated tools and wizards. Primer Design can ensure optimal specificity and amplification efficiency when validating constructs and monitoring transgene expression.

Users can perform manual primer design or utilize the automatic scanning feature. The tool also supports editing existing PCR primers. Automatic PCR primer design running behind the scenes is fundamental for various procedures supported by the toolkit, such as Gibson Assembly, Golden Gate Assembly, and Vector Modification for site-directed mutagenesis.

Codon Optimization

Codon optimization can bridge the gap between sequence design and protein expression. Additionally, by accounting for tRNA and ribosome kinetics, Sapio can achieve high protein yields while maintaining the original amino acid sequences.

Sapio’s Codon Optimization feature intelligently reverse-translates proteins or modifies existing cDNA sequences to maximize expression yields. It automatically detects and replaces rare codons, optimizes GC content, and removes destabilizing motifs, hairpins, internal polyA signals, and repetitive sequences. This ensures your constructs are biologically efficient and expression-ready in the selected host organism.

Cloning

Restriction

Sapio’s Restriction Cloning Wizard simplifies the traditional cloning process with a step-by-step visual workflow. Users can easily select source and destination sequences, visualize restriction sites, and preview the resulting construct in real-time after the software automatically suggests suitable combinations of restriction sites for cloning. With support for precise cut-site matching and seamless construct verification, this tool accelerates cloning design while reducing error and complexity.

Golden Gate

Sapio provides a Golden Gate Assembly Wizard, enabling the representation of complex multi-fragment assemblies with Type IIS restriction enzymes, which can facilitate workflow benefits, such as directional cloning.

This tool allows users to perform Golden Gate Assembly procedures. It supports designing PCR primers for fragment joining or adding necessary overhangs and cloning sites. Updates to this wizard include support for Entry Plasmid Sets, Combinatorial Assembly, Advanced Assembly, and Split Sequence methods.

Gibson Assembly

The tool in an integrated platform can illuminate primer design through assembly validation in a unified environment while embedding thermostable 5′ exonuclease, polymerase, and ligase reactions.

This tool supports Single Set Assembly, which automatically designs primers with homology flanks based on the previous and next fragments and simulates the assembly process. It also provides Combinatorial Assembly for sets of parts grouped in bins, verifying feasibility, designing primers, generating all possible combinations, and simulating the assembly. Furthermore, the Split Sequence feature identifies suitable split points for optimal primer placement and simulates the assembly process.

Sequence Registration

Multimodal Registration

Multi-modal registration can include DNA, RNA, protein, peptides, modified peptides, modified nucleic acids, non-natural amino acids, and combinations of all of the above, which can be generated using a HELM editor.

Sapio’s advanced molecular biology toolkit is seamlessly integrated with the recently announced multimodal registration, assisting scientists in bridging the divide between small molecules and large molecules. It enables the efficient management of natural and non-natural biologics, diverse conjugates, peptides, and small molecules.

Sequence Analysis

Genome Browser

A general-purpose genome browser is available within the Sapio Molecular Biology Toolkit. It supports a wide range of visualization features, including multiple sequence alignments, reading frames, and protein translations. Beyond variant visualization, it can also display genomic features such as exons, introns, and regulatory elements. Additionally, it accommodates various experimental data types—such as RNA-seq and ATAC-seq—allowing users to view how these datasets align with genome coordinates.

Genome Browser Multiple Sequence Alignment

Compare and align multiple nucleotide or amino acid sequences with industry-standard algorithms including MAFFT, MUSCLE, Clustal Omega, and BioMSA. Visualize results with rich, interactive graphics featuring annotated pileups, sequence features, and translations. Seamlessly integrated with our Protein Sequence Editor for a streamlined analysis workflow.

AI Tools

NVIDIA BioNeMo

Machine learning and structural biology and chemistry can enable predictions with high accuracy before entering the lab. The integration of NVIDIA BioNeMo into the Sapio Platform equips scientists with advanced in silico tools embedded directly within their experimental workflows. This includes access to powerful AI-driven models such as DiffDock, an AI-powered molecular docking model, and MolMIM, which enables the design and optimization of small molecules.

These tools allow researchers to generate novel candidate molecules early in the research process, predict their 3D protein targets using AlphaFold2, and evaluate docking interactions with target proteins—all within a unified, science-aware platform. This iterative feedback cycle can help refine molecular models, enabling the development of high-efficacy therapeutics.

By consolidating these capabilities in a single environment, the Sapio Platform streamlines molecular modeling accelerates the path from discovery to development and empowers scientists to innovate with greater speed and precision.