Dinitrophenyl (DNP) derivatives of amino acids (specifically epsilon-DNP-lysine)
Does "epsilon-DNP-lysine" refer to a product where the DNP is bound only to the epsilon amino group (but not to the amino terminus), or does it refer to a product where DNP is bound simultaneously to the epsilon amino group and to the amino terminus?


Good question.  &epsilon;-DNP-lysine usually refers to a lysine in which the dinitrophenyl substituent is bound only to the &epsilon; atom, i.e., to the side-chain nitrogen.  

The reason is that in lysine-focused derivatization methods, the reaction with DNP can be done prior to protein hydrolysis.  Thus, during DNP derivatization, the vast majority of lysine residues will have no free &alpha;-amino terminus because they are part of polypeptide chains.  Only the &epsilon;-amino groups are free to react with DNFB.  Derivatization forms DNP-ylated proteins where the peptide bonds are intact.  Later steps in the procedure hydrolyze all the peptide bonds.  During this step, free &alpha;-amino groups are created.  But no DNFB is used in these later steps.

I found a paper from 1963 which describes the derivatization procedure in detail.


  ...Care was taken to
  deposit the sample at the bottom of
  the flask. Ten milliliters of bicarbonate
  solution were added, care being taken
  that no meal adhered to the side of the
  flask. The contents were then thoroughly
  mixed by gentle swirling, and the
  suspension was permitted to stand for 10
  minutes. A solution of 0.3 ml. of
  DNFB in 10 ml. of ethanol was then
  added and the contents of the flask
  were thoroughly mixed by gentle
  swirling. The side of the flask was
  rinsed with 3 ml. of absolute ethanol
  and then the contents were shaken in
  subdued light for two hours on a shaker
  with a wrist-like motion. Previous
  work (10) has established that 2 hours
  reaction time is sufficient for substantially
  complete reaction between DNFB
  arid the free epsilon amino groups of
  lysine. alcohol and most of the
  water were removed by evaporation
  under an air stream, and the residue was extracted with four 50-ml. portions
  of anhydrous, peroxide-free diethyl
  ether. The ether in each case was
  removed from the residue by decantation
  and the residue in the flask was dried at ambient temperature by
  aeration.


The ether washings will remove the vast majority of unreacted DNFB.


  ... Two hundred milliliters of
  constant-boiling aqueous HCl nere
  added to the flask, and the resulting
  mixture was boiled overnight at the
  reflux temperature, cooled and then filtered through a sintered glass funnel
  directly into a 250-ml. volumetric flask.
  The filtrate, and washings from the
  filtrate, were made up to 250 mi. with
  distilled water.
  An aliquot (2.0 to 4.0 ml.) of the
  hydrolyzate containing from 0.1 to 0.3
  mg. of epsilon-dinitrophenyllysine...


Now for your other question:


  Also, can the same thing happen with other amino acids that have an amino group in the side chain? i.e. can there be epsilon-DNP-arginine, for instance, or is this behavior unique to lysine?


DNFB is not reactive with arginine.  The arginine side-chain is best viewed as a guanidine, not as an amino group.  Guanidine is considerably less nucleophilic than lysine.