S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32(1998)287-387 6. Chemical shifts 322 6. 1. Chemical shifts; qualitative aspects 6.2. Theory 324 6.3. shifts 6.4. Structurally important H shifts 5. N and c shifts in dna and rna 6.6. shifts 330 7. Assignment methods 330 7. 1. Assignment without isotope labeling 7.2. Assignment with isotope labeling 335 7.2.1. NOE-based correlation 7.2.2. Through-bond correlation 337 7.2.2. 1. Coherence transfer functions 337 7.2.2.2. Through-bond amino/imino to non-exchangeable proton correlation 7.2.2.3. Through-bond H2-H8 correlation 344 7.2.2.4. Through-bond base sugar correlation 347 7.2.2.5. Through-bond sugar correlation 7.2.2.6. Through-bond sequential backbone assignment 357 7. 2.3. X-filter techniques 361 8. Relaxation and dynamics 363 9. Calculation of structures 375 10. Prospects for larger systems 378 11. Concl 383 References 383 Keywords: NMR; Conformational studies, Nucleic acids; RNA; DNA; Labeling; Assignment; Structure 1. Introduction However. the alternate rna and dNA structures associated with many of the different processes Nucleic acid molecules play a central role in cell mentioned above, are less well known. Only> in biological processes. DNA s main role is to act as the the early 1990s have technological advances in carrier of genetic information. Furthermore, DNA is sample preparation, such as isotope labeling and transcribed into RNa by a carefully regulated process, developments in crystallization, made such structural and it is duplicated on cell division. RNAs main role data available, and allowed the structural basis of the Is to communicate the genetic information for protein biological functions of DNA and rNa to be synthesis to the ribosomes RNA is, however, very addressed versatile. It can also take on the role of dna as the In the past ten years, we have witnessed an carrier of genetic information, and it can function as explosion in the number of crystal and solution struc an enzyme. It has even been hypothesized that early in tures of proteins determined by X-ray crystallography evolution, life was based entirely on RNA(see, for and NMr, respectively. In comparison, the increase in example, Ref. [I]). All these different processes the number of nucleic acid structures determined by require different structures. The basic structural either X-ray or NMR has been relatively small. This elements of rna and dna are well established. ie. can be attributed to the difficulties encountered when DNA forms a B-helix, while RNa may be either trying to crystallize nucleic acids for detailed X-ray single-stranded or may form an A-type helix. analysis and to the problem of extensive resonanceKeywords: NMR; Conformational studies; Nucleic acids; RNA; DNA; Labeling; Assignment; Structure 1. Introduction Nucleic acid molecules play a central role in cell biological processes. DNA’s main role is to act as the carrier of genetic information. Furthermore, DNA is transcribed into RNA by a carefully regulated process, and it is duplicated on cell division. RNA’s main role is to communicate the genetic information for protein synthesis to the ribosomes. RNA is, however, very versatile. It can also take on the role of DNA as the carrier of genetic information, and it can function as an enzyme. It has even been hypothesized that early in evolution, life was based entirely on RNA (see, for example, Ref. [1]). All these different processes require different structures. The basic structural elements of RNA and DNA are well established, i.e. DNA forms a B-helix, while RNA may be either single-stranded or may form an A-type helix. However, the alternate RNA and DNA structures, associated with many of the different processes mentioned above, are less well known. Only since the early 1990s have technological advances in sample preparation, such as isotope labeling and developments in crystallization, made such structural data available, and allowed the structural basis of the biological functions of DNA and RNA to be addressed. In the past ten years, we have witnessed an explosion in the number of crystal and solution struc￾tures of proteins determined by X-ray crystallography and NMR, respectively. In comparison, the increase in the number of nucleic acid structures determined by either X-ray or NMR has been relatively small. This can be attributed to the difficulties encountered when trying to crystallize nucleic acids for detailed X-ray analysis and to the problem of extensive resonance 6. Chemical shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322 6.1. Chemical shifts; qualitative aspects . . . . . . . . . . . . . . . . . . . . . . . . . . 324 6.2. Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324 6.3. 1 H shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327 6.4. Structurally important 1 H shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327 6.5. 15N and 13C shifts in DNA and RNA . . . . . . . . . . . . . . . . . . . . . . . . . 329 6.6. 31P shifts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 7. Assignment methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 7.1. Assignment without isotope labeling. . . . . . . . . . . . . . . . . . . . . . . . . . 330 7.2. Assignment with isotope labeling . . . . . . . . . . . . . . . . . . . . . . . . . . . 335 7.2.1. NOE-based correlation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336 7.2.2. Through-bond correlation . . . . . . . . . . . . . . . . . . . . . . . . . . . 337 7.2.2.1. Coherence transfer functions . . . . . . . . . . . . . . . . . . . . . . 337 7.2.2.2. Through-bond amino/imino to non-exchangeable proton correlation . . . . . . 337 7.2.2.3. Through-bond H2-H8 correlation . . . . . . . . . . . . . . . . . . . . 344 7.2.2.4. Through-bond base ¹ sugar correlation . . . . . . . . . . . . . . . . . 347 7.2.2.5. Through-bond sugar correlation. . . . . . . . . . . . . . . . . . . . . 355 7.2.2.6. Through-bond sequential backbone assignment . . . . . . . . . . . . . . 357 7.2.3. X-filter techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 8. Relaxation and dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363 9. Calculation of structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375 10. Prospects for larger systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378 11. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382 Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383 288 S.S. Wijmenga, B.N.M. van Buuren/Progress in Nuclear Magnetic Resonance Spectroscopy 32 (1998) 287–387