Poly (dA: dT) tracts: major determinants of nucleosome organization

E Segal, J Widom - Current opinion in structural biology, 2009 - Elsevier
Homopolymeric stretches of deoxyadenosine nucleotides (A's) on one strand of double-
stranded DNA, referred to as poly (dA: dT) tracts or A-tracts, are overabundant in eukaryotic …

The unique structure of A-tracts and intrinsic DNA bending

TE Haran, U Mohanty - Quarterly reviews of biophysics, 2009 - cambridge.org
Short runs of adenines are a ubiquitous DNA element in regulatory regions of many
organisms. When runs of 4–6 adenine base pairs ('A-tracts') are repeated with the helical …

Curved DNA without AA: experimental estimation of all 16 DNA wedge angles.

A Bolshoy, P McNamara… - Proceedings of the …, 1991 - National Acad Sciences
The principal sequence feature responsible for intrinsic DNA curvature is generally assumed
to be runs of adenines. However, according to the wedge model of DNA curvature, each …

Bending and curvature calculations in B-DNA.

DS Goodsell, RE Dickerson - Nucleic acids research, 1994 - ncbi.nlm.nih.gov
A simple program, BEND, has been written to calculate the magnitude of local bending and
macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired …

[PDF][PDF] Intrinsically bent DNA

DM Crothers, TE Haran, JG Nadeau - J. Biol. Chem, 1990 - taliharan.net.technion.ac.il
Intrinsically bent or curved DNA molecules result when special base sequences or structural
motifs are repeated in phase with the DNA helical repeat (~ 10.5 bp'/turn). This places the …

Temperature dependence of the raman spectrum of DNA. Part I—Raman signatures of premelting and melting transitions of poly (dA–dT)· poly (dA–dT)

L Movileanu, JM Benevides… - Journal of Raman …, 1999 - Wiley Online Library
Abstract Poly (dA–dT)· poly (dA–dT) is a double‐helical B DNA containing A· T and T· A
base pairs in alternating sequence. Although Raman spectra of this structure have been …

Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature

P De Santis, A Palleschi, M Savino, A Scipioni - Biochemistry, 1990 - ACS Publications
Revised Manuscript Received May 14, 1990 abstract: The validity of a theoretical nearest-
neighbor model based on conformational energy calculations, for translating the …

The complex architecture of p53 binding sites

A Senitzki, J Safieh, V Sharma… - Nucleic Acids …, 2021 - academic.oup.com
Sequence-specific protein-DNA interactions are at the heart of the response of the tumor-
suppressor p53 to numerous physiological and stress-related signals. Large variability has …

The toxbox: specific DNA sequence requirements for activation of Vibrio cholerae virulence genes by ToxT

JH Withey, VJ DiRita - Molecular microbiology, 2006 - Wiley Online Library
The Gram‐negative, curved rod Vibrio cholerae causes the severe diarrhoeal disease
cholera. The two major virulence factors produced by V. cholerae during infection are the …

On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules

B Luisi, M Orozco, J Sponer, FJ Luque… - Journal of molecular …, 1998 - Elsevier
Crystallographic studies of duplex DNA have indicated that opposing exocyclic amino
groups may form close NH⋯ N contacts. To study the nature of such interactions, we have …