Chapter 8: DNA Electrophoresis

negatively charged molecule

negatively charged molecule

DNA is a _______ in an aqueous environment, with the phosphate groups of DNA nucleotides carrying negative charges.

Electrical Potential

A measure of the work required to move a charged molecule in an electric field, is the force responsible for moving the charged macromolecules during electrophoresis.

electrophoretic mobility

The ________ of macromolecules is primarily determined by their charge-to-mass ratios and their shapes.

Matrix

A physical support material used by most variants of electrophoresis.

Agarose

It is a linear polymer composed of alternating residues of D-galactose and L-galactose.

gelatinized agarose

A _______ forms a three-dimensional sieve with pores from 50 to 200 nm in diameter.

electrophoretic mobility

The _______ of double-stranded DNA through agarose gel matrices is inversely proportional to the log10 of the size of DNA fragments ranging from 50 to 20,000 base pairs.

inversely proportional

The electrophoretic mobility of a linear DNA fragment is also _____ to the concentration of agarose in the gel.

larger pores

A low concentration of agarose in a gel forms ______, allowing the separation of larger DNA fragments.

smaller pore sizes

Polyacrylamide produces much _____ than agarose gels and thus has a much higher resolving power than agarose gels for low-molecular-weight DNA molecules.

polyacrylamide gel matrix

A ______ is formed by the polymerization and cross-linking reactions.

Polymerization Reaction

Long linear chains of polyacrylamide are polymerized from acrylamide monomers.

Cross-Linking Reaction

Three-dimensionally cross-linked polyacrylamide chains can be formed with the use of cross-linking agents, such as N,N′— methylenebisacrylamide.

Denaturing Polyacrylamide Electrophoresis

Electrophoresis that is performed under the conditions of single-stranded DNA is called denaturing electrophoresis.

Agarose Gel Electrophoresis

One forensic application of agarose gel electrophoresis is restriction fragment length polymorphism (RFLP) analysis of VNTR loci.

Polyacrylamide Gel Electrophoresis

The forensic application of this apparatus is the separation of STR fragments and DNA sequencing reaction products of mtDNA.

Capillary Electrophoresis

It can be utilized to separate charged macromolecules, such as DNA, RNA, polysaccharides, and proteins.

Capillary

A thin hollow tube made of fused silica.

Electrokinetic Mechanism

An injection based on the charge of molecules.

Microfluidic devices

control the movement of samples and reagents in a small, geometrically constrained environment and carry out biochemical reactions and analysis.

microfabrication technology

This technology fabricates miniature structures historically used for integrated circuit fabrication in semiconductor manufacturing.

electrophoretic assay

The ______ is carried out on a modular microfluidic chip format using the same basic principle of capillary electrophoresis.

single-use chip

The _______ contains wells for samples, a sieving polymer matrix for electrophoresis, and size standards.

polymer matrix

The _______ contains fluorescent dye molecules that intercalate with DNA in a sample, which can be detected by laser-induced fluorescence.

automated process

An integrated system is a fully _______. It also reduces the risk of contamination from laboratory sources.

rapid DNA instrument

Full integration of all the constituent steps required for forensic STR DNA analysis has been achieved by a _______.

Microquantitative PCR

utilizes the Taqman real-time quantitative PCR technique. During amplification, multiplex PCR is accomplished using commercial STR kits.

fluorescently labeled DNA fragments

The ________ are detected based on laser-induced fluorescence.

Rapid DNA instruments

are fully automated platforms that are designed to process a single-source sample such as a buccal swab to generate a DNA profile and database search in less than 2h.

relative mobility (Rf)

The _______ of a DNA molecule during electrophoresis can be calculated as the distance of band migration divided by the distance of tracking dye migration.

DNA band migration

The ______ is the distance from the sample origin to the center of the band.

Local Southern method

The _______ is used to generate standard curves for determining the sizes of DNA fragments.

internal size standard

The size of a DNA fragment is determined by an ______ that is a set of synthetic fragments with known molecular weight.

standard

The _____ is labeled with a different colored dye so that it can be spectrally distinguished from DNA fragments of unknown size.

standard curve

To determine the sizes of DNA fragments, a _______ using the internal size standards must be established based on the reciprocal relationship between the electrophoretic mobility and the sizes of DNA fragments.