Review
Making contacts on a nucleic acid polymer

https://doi.org/10.1016/S0968-0004(01)01978-8Get rights and content

Abstract

The interaction of proteins bound at distant sites on a nucleic acid chain plays an important role in many molecular biological processes. Contact between the proteins is established by looping of the intervening polymer, which can comprise either double- or single-stranded DNA or RNA, or interphase or metaphase chromatin. The effectiveness of this process, as well as the optimal separation distance, is highly dependent on the flexibility and conformation of the linker. This article reviews how the probability of looping-mediated interactions is calculated for different nucleic acid polymers. In addition, the application of the equations to the analysis of experimental data is illustrated.

Section snippets

Calculating the local concentration for circular and linear polymers

In many aspects, sufficiently long polymers behave similar to an idealized chain of n segments of length l, where the chain segments are not restricted in their torsional movement with respect to one another. Such a chain is termed a Gaussian or freely jointed chain (FJC) 2, 19. The parameter l is called the statistical segment length or Kuhn length after the Swiss scientist Werner Kuhn who developed the concept and much of the theoretical description of the FJC model in the 1930s [2]. The

Applying the approximations to a specific polymer

The expressions in Eq. (2) and Eq. (3) are independent of the characteristics of a specific polymer. To calculate jM for a certain circular or linear nucleic acid chain, the flexibility of the polymer as given by the Kuhn length l needs to be known. Values for l that have been determined experimentally are summarized in Table 1. In addition, the site-separation distance n, as well as the circle length N, have to be expressed by a corresponding number of nucleic acid monomer units, such as, for

Double-stranded DNA

Protein–protein contacts between distant binding sites are often mediated by looping of dsDNA (for reviews see Refs 1, 15, 23, 24, 25, 26, 27, 28). The theoretical framework outlined above has been used successfully for a quantitative analysis in various systems, including the interaction between lac repressor complexes 28, 29, the in vitro and in vivo frequency of site-specific recombination by FLP recombinase [20], and transcription activation of E. coli RNA polymerase·σ54 holoenzyme by the

Single-stranded RNA

Various protein–protein contacts have been reported that are mediated by looping of a ssRNA chain (for examples see Refs 10, 11, 12). One example refers to the mechanism by which RNA splicing enhancers operate. These RNA elements are usually located within 100 nucleotides of the 3′ splice position. They are thought to constitute binding sites for protein factors that interact with the general splicing machinery at the nearby intron 10, 31. An experimental analysis of the effect of varying the

Interphase chromatin fibers

In eukaryotes, the DNA is structured by histone proteins into a chain of nucleosomes, in which ∼146 base pairs of DNA are wrapped around a histone octamer complex. This nucleosome chain associates under physiological conditions into a condensed fiber with a diameter of ∼30 nm [13]. The 30 nm fiber adopts a complex and dynamic structure that is modified by a large number of protein complexes. To estimate the local concentration of one site in the proximity of another site for chromosomal DNA,

Conclusions

The optimal separation distances for looping-mediated interactions with their respective jM values are summarized for the various nucleic acid polymers in Table 2. It is evident that single-stranded DNA or RNA are much more effective in promoting protein–protein interactions (jM=10−4 to 10−3 m, 10–20 nucleotides separation distance) than their double-stranded forms (jM≈10−7 m at ∼500 base pairs). This is because of the highly increased flexibility of the single-stranded nucleic acids. In fact,

Acknowledgements

I thank John Schellman, Peter von Hippel, Konstantin Klenin, Job Dekker, Malte Wachsmuth and Jörg Langowski for helpful discussions and comments to the manuscript. The review was written at the division ‘Biophysik der Makromoleküle’ of the German Cancer Research Center. Financial support from the DFG (grant Ri-828/1) and the Volkswagen Foundation in the programme ‘Junior Research Groups at German Universities’ is gratefully acknowledged.

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