Nucleic acid structure and recognition

Ch. 1. Methods for studying nucleic acid structure

1.1. Introduction

1.2. X-ray diffraction methods for structural analysis

1.3. NMR methods for studying nucleic acid structure and dynamics

1.4. Molecular modelling and simulation of nucleic acids

1.5. Chemical and enzymatic probes of structure

1.6. Sources of structural data

Ch. 2. The building-blocks of DNA and RNA

2.1. Introduction

2.2. Base pairing

2.3. Base and base pair flexibility

2.4. Sugar puckers

2.5. Conformations about the glycosidic blood

2.6. The backbone torsion angles and correlated flexibility

Ch. 3. DNA structure as observed in fibres and crystals

3.1. Structural fundamentals

3.2. Polynucleotide structures from fibre diffraction studies

3.3. B-DNA oligonucleotide structure as seen in crystallographic analyses

3.4. A-DNA oligonucleotide crystal structures

3.5. Z-DNA

left-handed DNA

3.6. Bent DNA

3.7. Concluding remarks

Ch. 4. DNA-DNA recognition: non-standard and higher order DNA structures

4.1. Mismatches in DNA

4.2. DNA triple helices

4.3. Guanine quadruplexes

4.4. DNA junctions

Ch. 5. Principles of small molecule-DNA recognition

5.1. Introduction

5.2. DNA-water interactions

5.3. General features of DNA-drug and small-molecule recognition

5.4. Intercalative binding

5.5. Intercalative-type binding to higher order DNAs

5.6. Groove binding molecules

5.7. Covalent bonding

Ch. 6. The RNA structural world

6.1. Introduction

6.2. Fundamentals of RNA structure

6.3. Transfer RNA Structures

6.4. Ribozymes

6.5. The ribosome, a ribozyme machine

6.6. RNA motifs

Ch. 7. Principles of protein-DNA recognition

7.1. Introduction

7.2. Direct protein-DNA contacts

7.3. Major-groove interactions

the [alpha]-helix as the recognition element

7.4. Zinc-finger recognition modes

7.5. Other major-groove recognition motifs

7.6. Minor-groove recognition

7.7. DNA bending and protein recognition