This is very possible as long as your bios supports booting to USB devices. Many current bioses do not. You should simply be able to boot to dos off a floppy drive and sys the drive letter of the pen drive (given that your bios is smart enough to treat it like a hard drive) and then be able to reboot. If worse comes to worse, you can probably copy command.com, io.sys, msdos.sys to the drive, do a attrib +h +s +r on the .sys files, then get a utility called bootpart to "restore" a dos boot sector on the drive.
Good luck..
P.S. I haven't had DOS booting off my 64 mb pen drive, but I had OS9 booting off my pen drive on my iBook.