Intrinsically curved DNA structures are often found in or around transcriptional control regions of eukaryotic genes, and curved DNA may be common to all class I gene promot ers. Although not all class II gene promoters contain curved DNA structures, both TATAbox- containing and TATA-box-less...

Fragile X mental retardation syndrome and Friedreich ataxia belong to a group of genetic disorders known as the Repeat Expansion Diseases. These diseases all result from expansion of a specific tandem repeat. These repeats form a variety of secondary structures that have been suggested to play...

Readout of eukaryotic genomes is soft-wired, leading to many different messages from a single gene. Z-DNA and double-stranded RNA (dsRNA) are both examples where genetic information is encoded by shape rather than by sequence. The use of these two conformational motifs to produce...

The placement of nucleosomes along genomic DNA is determined by signals that can be specific or degenerate at the level of sequence; the latter signals are harder to find using conventional methods. In recent years, the development of sophisticated machine learning techniques that can extract...

Nucleoid-associated protein H-NS has emerged as one of the most intriguing and versatile global regulators of enterobacterial gene expression acting primarily yet not exclusively at the transcriptional level where it generally acts as a repressor. H-NS is also believed to contribute to the...

Transcription and supercoiling of the template DNA are closely related each other. DNA supercoiling affects transcription and transcription affects supercoiling of the template DNA. Furthermore, packaging of genomic DNA into chromatin in eukaryotes raises another type of relation. DNA...

DNA bending is universal in biology—both the storage and the retrieval of information encoded in the base-pair sequence require significant deformations, particularly bending, of the double helix. The A-tract curvature, which modulates these processes, has thus been a subject of...

Certain DNA sequences preferentially adopt multistranded, non-B-form structures under physiological conditions. These include three-stranded DNA triplexes and four-stranded DNA quadruplexes. Several lines of evidence suggest that multiplex structures can form in vivo, either from the addition...

Intrinsically curved DNA structures often occur in or around origins of DNA replication, regions that regulate transcription, and DNA recombination loci, and are found in a wide variety of cellular and viral genomes from bacteria to man. In bacterial promoters, bent DNA structures are often...

The human testis-determining gene Sry, a single-copy gene on the short arm of the Y chromosome, encodes a high-mobility-group (HMG) box, a DNA-bending motif conserved among architectural transcription factors. The SRY-DNA complex exhibits a dramatic reorganization of the double helix. Although...

Local structural transitions from the common B-DNA conformation into other DNA forms can be functionally important. This chapter describes the structures of DNA forms called alternative DNA conformations that are different from the canonical B-DNA helix. Also discussed are the requirements for...

The structural and mechanical properties of DNA influence nucleosome positioning and the manner in which DNA is organized in chromatin. Curved DNA structures, poly(dA•dT) sequences, and Z-DNA-forming sequences frequently occur near transcription start sites. Many reports have indicated that...

The eukaryotic abundant high mobility group HMGA and HMGB proteins can act as architectural transcription factors by promoting the assembly of higher-order protein- DNA complexes which can either activate or repress gene expression. The structural organisation of both classes of protein is...

In bacteria, RecA protein is indispensable for recombination, mutagenesis and for the induction of SOS genes. Curiously, anti-RecA antibodies recognize kin17, a human nuclear Zn-finger protein of 45 kDa that preferentially binds to curved DNA and participates in a general response to diverse...