Abstract
| I. | Introduction | 163 |
| II. | Photochemical Cross‐Linking | 165 |
| III. | Structural Analysis of Protein–Nucleic Acid Heteroconjugates | 165 |
| IV. | Analytical Challenges | 168 |
| | A. Ionization of Peptide–Oligonucleotide Heteroconjugates | 168 |
| | 1. MALDI MS Analysis of Heteroconjugates | 168 |
| | 2. Electrospray Ionization (ESI) MS Analysis of Heteroconjugates | 170 |
| | B. Mass Analysis and Sequencing of Heteroconjugates | 170 |
| | C. Photochemical Reaction Mechanisms | 170 |
| V. | Mass Spectrometric Analysis of Photochemically Cross‐Linked Heteroconjugates | 171 |
| | A. Analysis of Intact Protein–Oligonucleotide Heteroconjugates by MS | 171 |
| | B. Mass Analysis of Peptide–Oligonucleotide Heteroconjugates | 174 |
| | C. 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 | 179 |
Photochemical 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