The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5' to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of approximately 20 degrees, twist angles of approximately 17 degrees). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, approximately 46 degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.
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http://dx.doi.org/10.1016/j.jmb.2005.12.051 | DOI Listing |
Phys Rev Lett
October 2024
Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.
The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong nonlinear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that kink formation entails a mixed spool-nematic ordering of double-stranded DNA or RNA in spherical capsids, consisting of an outer spool domain and an inner, twisted nematic domain. These findings explain the experimentally observed nematic domains in viral capsids and imply that nonlinear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles.
View Article and Find Full Text PDFFront Biosci (Landmark Ed)
April 2024
Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
Background: Although the role of dynamic factors in DNA function still remains unclear, research in this direction is a rapidly developing area of molecular biology. In this work, the genetic constructions Y_red and Y_green, based on the plasmid pPF1 and containing a fragment of () DNA with predicted promoter-like regions, are considered complex dynamic systems in which local sites of double helix unwinding, called open states, can arise and propagate. The purpose of the article is to show the existence of a connection between the dynamics of open states and the functioning of predicted promoters.
View Article and Find Full Text PDFSci Rep
March 2024
Department of Mathematics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 602 105, India.
The present research investigates the double-chain deoxyribonucleic acid model, which is important for the transfer and retention of genetic material in biological domains. This model is composed of two lengthy uniformly elastic filaments, that stand in for a pair of polynucleotide chains of the deoxyribonucleic acid molecule joined by hydrogen bonds among the bottom combination, demonstrating the hydrogen bonds formed within the chain's base pairs. The modified extended Fan sub equation method effectively used to explain the exact travelling wave solutions for the double-chain deoxyribonucleic acid model.
View Article and Find Full Text PDFJ Biol Chem
December 2023
Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan. Electronic address:
RNA polymerase II (RNAPII) transcribes DNA wrapped in the nucleosome by stepwise pausing, especially at nucleosomal superhelical locations -5 and -1 [SHL(-5) and SHL(-1), respectively]. In the present study, we performed cryo-electron microscopy analyses of RNAPII-nucleosome complexes paused at a major nucleosomal pausing site, SHL(-1). We determined two previously undetected structures, in which the transcribed DNA behind RNAPII is sharply kinked at the RNAPII exit tunnel and rewrapped around the nucleosomal histones in front of RNAPII by DNA looping.
View Article and Find Full Text PDFAdv Mater
July 2023
Center for Artificial Low Dimensional Electronic Systems, Institute for Basic Science (IBS), 37673, Pohang, Republic of Korea.
Kinks, point-like geometrical defects along dislocations, domain walls, and DNA, are stable and mobile, as solutions of a sine-Gordon wave equation. While they are widely investigated for crystal deformations and domain wall motions, electronic properties of individual kinks have received little attention. In this work, electronically and topologically distinct kinks are discovered along electronic domain walls in a correlated van der Waals insulator of 1T-TaS .
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