Analysis of protein–nucleic acid interactions by photochemical cross‐linking and mass spectrometry

I. Introduction 163 II. Photochemical Cross‐Linking 165 III. Structural Analysis of Protein–Nucleic Acid Heteroconjugates 165 IV. Analytical Challenges 168A. Ionization of Peptide–Oligonucleotide Heteroconjugates 168   1.  MALDI MS Analysis of Heteroconjugates 168   2.  Electrospray Ionization (ESI) MS Analysis of Heteroconjugates 170B. Mass Analysis and Sequencing of Heteroconjugates 170C. Photochemical Reaction Mechanisms 170 V. Mass Spectrometric Analysis of Photochemically Cross‐Linked Heteroconjugates 171A. Analysis of Intact Protein–Oligonucleotide Heteroconjugates by MS 171B. Mass Analysis of Peptide–Oligonucleotide Heteroconjugates 174C. Sequence Information by MS 174   1.  MALDI MS‐Based Sequencing of Peptide–Nucleic Acid Heteroconjugates 174   2.  Sequence Information by ESI MS/MS 175   3.  Other Mass Spectrometric Techniques for the Analysis of Protein/Peptide–Oligonucleotide Heteroconjugates 176 VI. Conclusions and Perspectives 178 Acknowledgments 179 Abbreviations 179 References 179Photochemical cross‐linking is a commonly used method for studying the molecular details of protein‐nucleic acid interactions. Photochemical cross‐linking aids in defining nucleic acid binding sites of proteins via subsequent identification of cross‐linked protein domains and amino acid residues. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross‐linking sites in proteins. The present review of the field describes a number of MS‐based approaches for the characterization of cross‐linked protein‐nucleic acid complexes and for sequencing of peptide‐nucleic acid heteroconjugates. The combination of photochemical cross‐linking and MS provides a fast screening method to gain insights into the overall structure and formation of protein‐oligonucleotide complexes. Because the analytical methods are continuously refined and protein structural data are rapidly accumulating in databases, we envision that many protein‐nucleic acid assemblies will be initially characterized by combinations of cross‐linking methods, MS, and computational molecular modeling. © 2002 Wiley Periodicals, Inc., Mass Spec Rev 21:163–182, 2002; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/mas.10024