ArticleslgStudy

chemistry

NUPACK

NUPACK is a chemistry topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand NUPACK rather than just read about it. In short: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally for non-commercial academic use.

NUPACK — main illustration
NUPACK — illustration

Key takeaways

  • NUPACK belongs to chemistry; place it in that map before memorising details.
  • Learn the definition first, then one example that makes the definition concrete.
  • Connect NUPACK to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of NUPACK from memory before moving on to harder problems.

Reference excerpt

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally for non-commercial academic use. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble.

Secondary structure model

The secondary structure of multiple interacting strands is defined by a list of base pairs. A polymer graph for a secondary structure can be constructed by ordering the strands around a circle, drawing the backbones in succession from 5’ to 3’ around the circumference with a nick between each strand, and drawing straight lines connecting paired bases. A secondary structure is pseudoknotted if every strand ordering corresponds to a polymer graph with crossing lines. A secondary structure is connected if no subset of the strands is free of the others. Algorithms are formulated in terms of ordered complexes, each corresponding to the structural ensemble of all connected polymer graphs with no crossing lines for a particular ordering of a set of strands. The free energy of an unpseudoknotted secondary structure is calculated using nearest-neighbor empirical parameters for RNA in 1M Na+ or for DNA in user-specified Na+ and Mg++ concentrations; added parameters are employed for the analysis of pseudoknots (single RNA strands only).

Web server

Analysis The Analysis page allows users to analyze the thermodynamic properties of a dilute solution of interacting nucleic acid strands in the absence of pseudoknots (e.g., a test tube of DNA or RNA strand species). For a dilute solution containing multiple strand species interacting to form multiple species of ordered complexes, NUPACK calculates for each ordered complex:

the partition function, the minimum free energy (MFE) secondary structure, the equilibrium base-pairing probabilities, its equilibrium concentration, including rigorous treatment of distinguishability issues that arise in the multi-stranded setting.

Design The Design page allows users to design sequences for one or more strands intended to adopt an unpseudoknotted target secondary structure at equilibrium. Sequence design is formulated as an optimization problem with the goal of reducing the ensemble defect below a user-specified stop condition. For a candidate sequence and a given target secondary structure, the ensemble defect is the average number of incorrectly paired over the structural ensemble of the ordered complex. For a target secondary structure with N nucleotides, the algorithm seeks to achieve an ensemble defect below N/100. Empirically, the design algorithm exhibits asymptotic optimality as N increases: for sufficiently large N, the cost of sequence design is typically only 4/3 the cost of a single evaluation of the ensemble defect.

Utilities The Utilities page allows users to evaluate, display, and annotate the equilibrium properties of a complex of interacting nucleic acid strands. The page accepts as input either sequence information, structure information, or both, performing diverse functions based on the information provided, including automatic layout and rendering of secondary structures with or without ideal helical geometry. In either case, the structure layout can be edited dynamically within the web application.

Implementation The NUPACK web application is programmed within the Ruby on Rails framework, employing Ajax and the Dojo Toolkit to implement dynamic features and interactive graphics. Plots and graphics are generated using NumPy and matplotlib. The site is supported on current versions of the web browsers Safari, Chrome, and Firefox. The NUPACK library of analysis and design algorithms is written in the programming language C. Dynamic programs are parallelized using Message Passing Interface (MPI).

Terms of use The NUPACK web server and NUPACK source code are provided for non-commercial research purposes and is with this restriction not Free and open source software.

Funding NUPACK development is funded by the National Science Foundation via the Molecular Programming Project and by the Beckman Institute at the California Institute of Technology (Caltech).

See also RNA RNA structure List of RNA structure prediction software Comparison of nucleic acid simulation software

External links Official website Source download page Molecular Programming Project Homepage The Beckman Institute at Caltech

References

Illustrations

NUPACK: An example secondary structure drawing (left) and the corresponding polymer graph (right). Backbones are represented by thick colored lines and bases and base pairs are represented by thin black lines.
An example secondary structure drawing (left) and the corresponding polymer graph (right). Backbones are represented by thick colored lines and bases and base pairs are represented by thin black lines.
NUPACK: The Utilities page enables depicting secondary structures with ideal helical geometry for stacked base pairs, as for this complex of three RNA strands with A-form helices (left) or three DNA strands with B-form helices (right).
The Utilities page enables depicting secondary structures with ideal helical geometry for stacked base pairs, as for this complex of three RNA strands with A-form helices (left) or three DNA strands with B-form helices (right).

Worked examples

Example 1 — a first encounter with NUPACK

Start with the simplest possible case. Write down what NUPACK claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to NUPACK before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about NUPACK ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of NUPACK

In research
NUPACK appears in chemistry research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry
Engineering practice reuses NUPACK in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom
NUPACK is common in secondary-school and first-year university syllabi. It links to neighbouring topics DNA nanotechnology, Molecular modelling software, so understanding it makes those chapters shorter.
In everyday life
Look for NUPACK outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study NUPACK in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what NUPACK means in your own words.
  3. Compare your version with the excerpt and mark what you missed.
  4. Work through the three examples above with pen and paper.
  5. Explain NUPACK out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is NUPACK in simple terms?

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. Jobs can be run online on the NUPACK webserver or NUPACK source code can be downloaded and compiled locally for non-commercial academic use.

Why does NUPACK matter?

Because it connects several chemistry ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study NUPACK?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on NUPACK.

Tags

  • DNA nanotechnology
  • Molecular modelling software

Keep exploring