Bent helical structure in kinetoplast DNA.
TLDR
It is proposed that this molecule contains a region of systematically bent B-DNA, which accounts for the fragment's difficulty in snaking through the pores of a polyacrylamide gel, its ease in diffusing into Sephacryl beads, and its smaller rotational relaxation time.Abstract:
We have investigated the unusual physical properties of a restriction fragment of Leishmania tarentolae kinetoplast DNA. A gel-purified fragment comprising slightly more than half of a minicircle was determined by Maxam-Gilbert sequence determination to be 490 base pairs (bp) in length. This fragment has dramatically anomalous electrophoretic behavior; it has an apparent size of 450 bp on a 1% agarose gel but migrates as 1,380 bp on a 12% polyacrylamide gel. However, in gel filtration on Sephacryl S-500, the fragment elutes with an apparent size of 375 bp. Finally, it behaves anomalously in electric dichroism experiments. Field-free rotational relaxation times from transient electric dichroism studies are highly sensitive to effective molecular dimensions. The rotational relaxation time of the kinetoplast fragment is smaller than that of a 309-bp control fragment from pBR322. Because rigorous control experiments rule out the possibility that this fragment is modified, these anomalous properties must be dictated by the sequence itself. Fragment behavior indicates that it has an unusually compact configuration; we propose that this molecule contains a region of systematically bent B-DNA. This model accounts for the fragment's difficulty in snaking through the pores of a polyacrylamide gel, its ease in diffusing into Sephacryl beads, and its smaller rotational relaxation time. Bending of this molecule may be caused by periodicities in the DNA sequence.read more
Citations
More filters
Journal ArticleDOI
The locus of sequence-directed and protein-induced DNA bending
Hen-Ming Wu,Donald M. Crothers +1 more
TL;DR: The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence symmetrically distributed about it, with a repeat interval of 10 base pairs.
Journal ArticleDOI
DNA bending at adenine . thymine tracts.
TL;DR: Intrinsic bending of DNA molecules results from local structural polymorphism in regions of homopolymeric dA · dT which are at least 4 base pairs long; the A · T tracts must be repeated in phase with the helix screw.
Book
DNA Structure and Function
TL;DR: This chapter discusses the structure and function of DNA, which is a right handed helix of two individual antiparallel DNA strands that is the source of all intrinsic genetic information.
Journal ArticleDOI
The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids
Richard Lavery,Heinz Sklenar +1 more
TL;DR: An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment by definition of a function describing simultaneously the curvature of the nucleic acids segment and the corresponding stepwise variation of helicoidal parameters along the segment.
Journal ArticleDOI
Crystal structure of trp repressor/operator complex at atomic resolution.
Zbyszek Otwinowski,Schevitz Rw,Rui Zhang,Lawson Cl,Andrzej Joachimiak,R. Q. Marmorstein,Ben F. Luisi,Paul B. Sigler +7 more
TL;DR: The crystal structure of the trp repressor/operator complex shows an extensive contact surface, including 24 direct and 6 solvent-mediated hydrogen bonds to the phosphate groups of the DNA as mentioned in this paper.
References
More filters
Journal ArticleDOI
Crystal structure analysis of a complete turn of B-DNA
Richard M. Wing,Richard M. Wing,Horace R. Drew,Tsunehiro Takano,Chris Broka,Shoji Tanaka,Keiichi Itakura,Richard E. Dickerson +7 more
TL;DR: This work reports the first single-crystal structure analysis of more than a complete turn of right-handed B-DNA, with the self-complementary dodecamer sequence d(CpGpCpC pGpApApTpTpCPGp CpG) or CGCGAATTCGCG.
Journal ArticleDOI
The anatomy of A-, B-, and Z-DNA
Richard E. Dickerson,Horace R. Drew,Benjamin N. Conner,Richard M. Wing,Albert V. Fratini,Mary L. Kopka +5 more
TL;DR: Single-crystal x-ray analyses of double-stranded DNA molecules of predetermined sequence, with 4 to 12 base pairs, are carried out for understanding of the mode of bending of DNA in chromatin, and the way in which specific DNA sequences are recognized by drug molecules and repressor proteins.
Journal ArticleDOI
The pitch of chromatin DNA is reflected in its nucleotide sequence.
TL;DR: A correlation analysis of chromatin DNA nucleotide sequences reveals the clear tendency of some of the dinucleotides to be repeated along the sequences with periods of 3 and about 10.5 bases, interpreted as a reflection of the deformational anisotropy of the DNA molecule that facilitates its smooth folding in chromatin.
Journal ArticleDOI
Left-handed double helical DNA: variations in the backbone conformation
TL;DR: Four different crystals of d(CpGpCp GpC GpG) have been solved by x-ray diffraction analysis and all form similar left-handed double helical Z-DNA molecules in the crystal lattice, as the phosphates are found either facing the helical groove or rotated away from it.
Journal ArticleDOI
Investigation of the flexibility of DNA using transient electric birefringence.
TL;DR: There is no strong ionic strength dependence of the persistencelength for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å.
Related Papers (5)
The locus of sequence-directed and protein-induced DNA bending
Hen-Ming Wu,Donald M. Crothers +1 more