Field Trips at DNALC NYC

DNA Restriction Analysis

The DNA restriction analysis experiment demonstrates that DNA can be precisely manipulated with enzymes that recognize and cut specific target sequences. In this lab, restriction enzymes—the scissors of molecular biology—are used to digest DNA from the bacteriophage lambda. After cutting, the DNA fragments are visualized by agarose gel electrophoresis, allowing students to identify a “mystery” enzyme through comparison with controls.

DNA Fingerprint

Human DNA is more alike than different, so how do we find the differences? Restriction enzymes are proteins that recognize specific DNA sequences and can be used to determine whether a particular DNA sequence is present. In this lab, DNA from “evidence” and “suspects” will be compared using restriction enzyme digest and agarose gel electrophoresis. DNA analysis will then be combined with crime scene data to draw conclusions about each suspect. This is an introductory lab, appropriate for classes with little or no experience in molecular biology.

Detecting a Jumping Gene

This lab examines  a region of DNA from chromosome 16 that can contain a short nucleotide sequence called Alu within a noncoding region of the chromosome. Alu insertions are segments of DNA that “jump” around in the genome. Students will prepare a sample of their own DNA from cells obtained by saline mouthwash, use PCR to amplify the targeted locus, and agarose gel electrophoresis to determine the presence or absence of this Alu, which jumped into the chromosome tens of thousands of years ago. Class data can be used as part of an exploration of allele frequencies and population genetics and to identify classmates who are related.

Human Mitochondrial Sequencing

Comparison of the control region within the human mitochondrial genome reveals that people have distinct patterns of single nucleotide polymorphisms (SNPs). These sequence differences, in turn, are the basis for far-ranging investigations on human DNA diversity and the evolution of hominids. In this lab, students prepare a sample of their own DNA from cells obtained by saline mouthwash, use PCR to amplify a section of their own mitochondrial DNA and agarose gel electrophoresis to confirm the result. DNA is then sent for sequencing, and results are uploaded to the DNALC’s BioServers website. Back at school, students can perform bioinformatic analysis of their own DNA sequences to explore the theories behind how modern humans evolved and how related they are to their classmates and people from around the world.

Forensic DNA Profiling

This lab examines a highly variable tandem repeat polymorphism on chromosome 1 called D1S80, similar to what the FBI uses to create a genetic profile. Students will prepare a sample of their own DNA from cells obtained by saline mouthwash. After amplification by PCR, the improved size resolution of a DNA chip allows students to identify their genotype, something impossible with traditional agarose gel electrophoresis. This is an advanced lab, appropriate for classes with some background in molecular biology and genetics.

Bioinformatics: Using Alu Insertions to Study Population Genetics

Students will learn about Alu insertions—segments of DNA that “jump” around in the genome—and use real population data to study variation in alleles, calculate allele frequencies, and examine Hardy-Weinberg equilibrium in populations. Computer simulations will be used to model genetic drift.

Bioinformatics: Tracing Human Evolution

Students will analyze mitochondrial sequence data to test models of human evolution. Were Neanderthals direct ancestors of modern humans? Did we all arise from a single founding population in Africa? Students will be guided through BioServers and DNA Subway to help answer these questions and more!

Bioinformatics: Barcoding & Phylogenetics

Phylogenetics is the practice of determining the evolutionary relatedness of groups of organisms. Much of this work is done utilizing DNA data. In this lab activity, students will learn about different methods of building phylogenetic trees and practice building them using both morphological and genetic data. Students will use sample data on the bioinformatics platform DNA Subway to compare species and build phylogenetic trees.

GMO: Detecting Genetically Modified Foods

Genes that encode herbicide resistance, insect resistance, drought tolerance, frost tolerance, and other traits have been added to many commercial plants – including most of the corn and soybeans grown in the United States. In this laboratory, students isolate DNA from processed food products. Then, polymerase chain reaction (PCR) and gel electrophoresis are used to identify a promoter that drives the expression of most plant transgenes. During the lab, bioinformatics tools allow students to predict the outcome of the experiment and discover genes and functions transferred into GM plants. Students have the option of bringing in a processed snack food to test for the presence of the transgene promoter.

PTC: Using a SNP to Predict Bitter Tasting Ability

The ability to taste the bitter compound PTC (phenylthiocarbamide) is often used to illustrate Mendelian inheritance. Three SNPs (single nucleotide polymorphisms) in the gene encoding the PTC taste receptor strongly affect tasting ability. In this experiment, students extract DNA from cheek cells* and use PCR to amplify a short region of the gene. After a diagnostic restriction digest, student genotypes are scored on an agarose gel, allowing them to predict their phenotypes. Students then test their tasting ability and compare genotypes and phenotypes, allowing them to discover that PTC tasting is genetically more complex than the model. This experiment is a close analog to how “precision or personalized medicine” uses genotypes to predict drug response.

Barcoding: Using DNA Barcodes to Identify and Classify Living Things

Just as unique universal product codes (UPC) identify products, unique "DNA barcodes" use specific DNA sequences to identify living things. In this laboratory, students use DNA barcoding to identify plants, fungi, or animals—or products containing them. DNA is extracted from samples, the barcode region is amplified by PCR, and the PCR product is sequenced. DNA Subway, an online bioinformatics site, is used to search a DNA database for close matches to sample sequences and to construct phylogenetic trees that show evolutionary relatedness. Students have the option of bringing in their own samples to test, providing the opportunity for mini-projects to sample local environments or to test food products.

Extended Jumping Genes: Using an Alu Insertion Polymorphism to Study Human Populations

(extension of Detecting a Jumping Gene)

The DNA from any two people varies at many sites. These polymorphic sequences that make each person’s DNA unique are used in the study of human evolution. This experiment examines a polymorphism that is caused by the insertion of an Alu transposon, the most common DNA sequence in the human genome. DNA is extracted from student cheek cells*, and PCR is used to amplify the region containing the Alu insertion site. Students score their genotypes on an agarose gel, and the compiled class results are used as a case study in human population genetics. On the BioServers Internet site, students use tools to test Hardy-Weinberg equilibrium, explore the geographic distribution of the insertion in world populations, and simulate the inheritance of a new Alu insertion.