{"cells": [{"cell_type": "markdown", "metadata": {}, "source": ["# Exercise 3.2: Restriction enzyme cut sites\n", "\n", "<hr>"]}, {"cell_type": "markdown", "metadata": {}, "source": ["**[Restriction enzymes](https://en.wikipedia.org/wiki/Restriction_enzyme)** cut DNA at specific locations called **restriction sites**. The sequence at a restriction site is called a **recognition sequence**. Here are the recognition sequences of some commonly used restriction enzymes.\n", "\n", "|Restriction enzyme | Recognition sequence|\n", "|:----|:----|\n", "|[HindIII](https://en.wikipedia.org/wiki/HindIII) | `AAGCTT` |\n", "|[EcoRI](https://en.wikipedia.org/wiki/EcoRI)| `GAATTC` |\n", "|KpnI| `GGTACC` |\n", "\n", "\n", "**a)** [New England Biosystems](https://www.neb.com/products/n3011-lambda-dna#Product%20Information) sells purified DNA of the genome of \u03bb-phage, a bacteriophage that infect _E. coli_. You can download the FASTA file containing the sequence [here](https://www.neb.com/-/media/nebus/page-images/tools-and-resources/interactive-tools/dna-sequences-and-maps/text-documents/lambdafsa.txt). Use the function you wrote in [Exercise 3.1](exercise_3.1.ipynb) to extract the sequence.\n", "\n", "**b)** Write a function with call signature\n", "\n", "```python\n", "restriction_sites(seq, recoq_seq)\n", "```\n", "\n", "that takes as arguments a sequence and the recognition sequence of a restriction enzyme sites and returns the indices of the first base or each of the restriction sites in the sequence. Use this function to find the indices of the restriction sites of \u03bb-DNA for HindIII, EcoRI, and KpnI. Compare your results with those given [here](https://www.bioinformatics.nl/molbi/SCLResources/LambdaBE_restrct_alphab.htm), which contain a comprehensive list of locations of restriction sites for a variety of enzymes.\n", "\n", "<!--Compare your results to those reported on the [New England Biosystems datasheet](https://www.neb.com/-/media/nebus/page-images/tools-and-resources/interactive-tools/dna-sequences-and-maps/lambda_sites.pdf).-->"]}, {"cell_type": "markdown", "metadata": {}, "source": ["<br />"]}], "metadata": {"anaconda-cloud": {}, "kernelspec": {"display_name": "Python 3", "language": "python", "name": "python3"}, "language_info": {"codemirror_mode": {"name": "ipython", "version": 3}, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.10"}}, "nbformat": 4, "nbformat_minor": 4}