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This is a post I lost on my old blog and am trying to reconstruct, better, faster, stronger. Work in progress. Here’s the state of the science:

Gel Electrophoresis

The standard: Gel electrophoresis
Can separate and measure DNA reliably. This involves floating a flat piece of gelatin in a box full of buffer, and running an electric current through. It’s messy, takes about an hour, and is a pain to get your DNA out once you put it in.

Tweaks:
To stain your otherwise-invisible dna, use SYBR Safe instead of ethidium bromide (EtBr). EtBr is a carcinogen and using it requires that you follow the proper safety guidelines. Why not use something non-toxic instead? Norman Wang has suggestions for using SYBR published on OpenWetWare

I want to join 2 genetic parts together!
Biobricks 3A ligation – designed as a workaround for gel electrophoresis when combining biological parts. Using Biobrick Standard parts, you can simply digest 2 parts and a vector and ligate them together without ever extracting the part using a gel.
http://openwetware.org/wiki/Synthetic_Biology:BioBricks/3A_assembly 

I want to determine the length of my DNA!
Sequence everything, inadvertently determine the length

I want to isolate DNA from a genome!
If possible, look up the genome for the species, and have the relevant genes synthetsized 

Is there any DNA in my sample?
SYBR Green stain, expose it to UV light 

Up coming technologies:

1. Capillaries used in DNA synthesis used to separate DNA
This cool machine does 94 or 384 samples at time – factory scale stuff, and it costs about $200k

http://www.caliperls.com/products/labchip-systems/labchip90.htm

2. Microfluidics chips – these are great but seem confined to the lab from what I’ve read. They involve microfab/nanofabriaction of a specific design. Pricey, though perhaps there is a more common material with the needed nanoscale features that could be used to separate DNA.