Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.

Abstract

Structural parameters characterizing the bending propensity of trinucleotides were deduced from DNase I digestion data using simple probabilistic models. In contrast to dinucleotide‐based models of DNA bending and/or bendability, the trinucleotide parameters are in good agreement with X‐ray crystallographic data on bent DNA. This improvement may be due to the fact that the trinucleotide model incorporates more sequence context information than do dinucleotide‐based descriptions.

Distribution of bending propensity in DNA sequences

“…Recently, trinucleotide bending propensity parameters were deduced from deoxyribonuclease I (DNase I) digestion data [1,2]. DNase I, an enzyme with no pronounced sequence specificity, bends DNA towards the major groove [3,4].…”

“…A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenzae genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments -similar to artificially designed curved oligonucleotides -are extremely rare in natural DNA.bendable segments [2]. Bendability plots were drawn by first dividing a DNA sequence into overlapping trinucleotides, then assigning a bendability value given in Table 1 to the center of each trinucleotide.…”

“…bendable segments [2]. Bendability plots were drawn by first dividing a DNA sequence into overlapping trinucleotides, then assigning a bendability value given in Table 1 to the center of each trinucleotide.…”

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

“…Capital letters match the E. coli promoter consensus sequence TTGACAN [16][17][18] TATAAT. The 5 bp duplication generated upon insertion is shown as a stippled box alternating rigid and flexible regions (Pedersen et al 1998) as well as curved sequences (Brukner et al 1995). The presence of sequence-directed bends has been implicated in functionally relevant cellular processes including transcription (Cress and Nevins 1996), replication (Gimenes et al 2008), and recombination (Kusakabe et al 2001).…”

“…The corresponding p values were obtained from p ¼ erfc z j j= ffiffi ffi 2 p À Á ; where erfc is the complement error function. Curvature propensity plots were obtained by analyzing 200 bp sequences flanking the target sites with the bend.it server (Gabrielian et al 1997) (http://hydra.icgeb.trieste.it/dna/bend_it.html) using the DNAse I-based parameters of (Brukner et al 1995). Threedimensional reconstruction was performed with the model.it server (http://hydra.icgeb.trieste.it/dna/model_it.html) (Vlahovicek et al 2003), and the output was displayed and visualized with Polyview 3D (http://polyview.cchmc.org/ polyview3d.html) (Porollo et al 2004).…”