Detection of non-covalent interaction of single and double stranded DNA with peptides by MALDI-TOF

Shanhua Lin, Robert J. Cotter, Amina S. Woods

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


DNA-histone interaction facilitates packaging of huge amounts of DNA in the confined space of the nucleus. The importance of this interaction underscores the need for new analytical techniques to acquire a better understanding of nuclear dynamics. Electrospray-ionization mass spectrometry made it possible to investigate non-covalently-bound biopolymers. We are enlarging the scope of available analytical tools by studying noncovalent interaction between single and double stranded DNA and peptides with matrix- assisted laser desorption/ionization (MALDI) mass spectrometry. The interaction is an ionic one, between the negatively charged sugar-phosphate backbone of single stranded DNA and positively charged side chains of Arg- and Lys-rich peptides as demonstrated by Vertes' group with the dipeptides Arg-Lys and His-His. We replicated Lecchi and Pannell's work, which showed that double stranded DNA could be seen by MALDI using 6-aza-2-thiothymine (ATT) as matrix. We tried various peptides and found that as was demonstrated in DNA-histone interaction, a certain ratio and arrangement of basic residues was needed in order to generate ionic binding between DNA and peptide. We tested various single and double stranded DNA with the peptide of choice, and found that other variables such as pH value of solution, ionic strength, and matrix system did play a role.

Original languageEnglish (US)
Pages (from-to)12-21
Number of pages10
JournalProteins: Structure, Function and Genetics
Issue numberSUPPL. 2
StatePublished - Jan 1 1998


  • DNA
  • Non-covalent interaction
  • Peptides

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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