In living cells, genomic DNA is organized into multiple topological domains that restrict the rotation of the double helix and cause DNA supercoiling. DNA topology is important for the intranuclear DNA packaging and plays a role in the regulation of gene expression. Particular cellular proteins are involved in the maintenance and the control of topological DNA organization. In turn, DNA topology can affect the functioning of DNA-processing proteins. That is why various aspects of the topology-mediated interrelationship between DNA and proteins attract a great deal of attention.Three interesting papers touching on this subject from different directions were published in the January and February issues of Nucleic Acids Research. Pavlov et al. report on the finding and cloning of a new DNA-binding protein isolated from hyperthermophilic archaebacterium [1xIdentification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri. Pavlov, N.A et al. Nucleic Acids Res. 2002; 30: 685–694Crossref | PubMedSee all References][1]. This protein, termed 7kMk, bends DNA, leading to the formation of ∼140-bp nucleosome-like loops with negative constrained DNA supercoiling. The change in DNA topology is most likely to be due to a left-handed orientation of the DNA loop, similar to a histone core of eukaryotic or archaeal nucleosomes. The 7kMk–DNA complex adds to the list of nucleoprotein structures with looped DNA configuration that are thought to be involved in DNA packaging and in transcription regulation.Bentin and Nielsen examined whether the rotary constraints within DNA topological domains affect the performance of RNA polymerase [2xIn vitro transcription of a torsionally constrained template. Bentin, T and Nielsen, P.E. Nucleic Acids Res. 2002; 30: 803–809Crossref | PubMedSee all References][2]. To model transcription of a torsionally constrained template in vitro, they immobilized covalently closed, circular DNA to streptavidin-coated beads using a peptide nucleic acid (PNA)–biotin conjugate, stably targeted to a specific DNA site. For synthesis of RNAs up to 900 nt, the rate of constrained transcription elongation was as high as with rotary free DNA. Preliminary data (not shown in the paper) suggested that this could also be the case for even longer RNAs. The authors therefore concluded that genes can be transcribed in vivo by some RNA polymerases with high efficiency, despite the fact that newly synthesized RNA is entangled around the template in the narrow confines imposed by DNA topology.In another study on proteins, DNA and topology, Kuhn et al. addressed the important question of whether the rolling DNA synthesis known as RCA is inhibited by topological constraints [3xRolling-circle amplification under topological constraints. Kuhn, H et al. Nucleic Acids Res. 2002; 30: 574–580Crossref | PubMedSee all References][3]. For this, the PNA-assisted assembly of topologically linked, earring-like DNA constructs has been applied. The RCA efficiency was unaffected when the linked templates were employed. The finding that certain DNA polymerases can carry out replicative synthesis in a topologically constrained setting could have practical implications in the area of DNA diagnostics.These recent studies on the interplay of DNA topology and DNA-binding proteins will stimulate more research on the theme covering its various aspects, with a rewarding impact on molecular biotechnology.