I. Structural studies of adenine tracts in DNA: Influence of length and sequence context. II. A method for selection of bent DNA molecules from a pool of random sequence DNA

Thesis/Dissertation · Fri Jan 01 04:00:00 EST 1993

OSTI ID:7042718

Price, M A

Short runs of adenines phased every 10--11 base-pairs cause DNA to bend. The structure of A-tracts of various lengths and in various sequence contexts was studied to understand the basis of DNA bending. Using hydroxyl radical cleavage, it was shown that short A-tracts in bent DNA adopt a structure that is a transition between the structure of poly(dA)[center dot]poly(dT) and that of mixed sequence DNA. The structure of an A-tract depends on its sequence context. Hydroxyl radical cleavage patterns show that the part of the A-tract near the central TA step in T[sub n]A[sub n] sequences has a B-DNA-like structure, unlike A-tracts in bent DNA. A model was formulated which explains the differences in the degree of bending caused by T[sub n]A[sub n] molecules. Adenine tracts of different lengths and in different sequence contexts have different susceptibilities to hydroxyl radical cleavage. The amount of decrease in hydroxyl radical cutting in different A-tracts relative to surrounding DNA by Fourier transformation of the cutting frequency data was determined. The degree of bending caused by A-tracts is directly related to the amount of decrease in hydroxyl radical cutting. To determine what feature of adenine tracts causes reduced reactivity to hydroxyl radical, relative hydroxyl radical cleavage rates were accurately determined at each position of a DNA duplex containing an A-tract for comparison to the structure determined by X-ray crystallography. Correlations were found between cutting frequency and solvent accessibilities of the 3[prime], 4[prime], and 5[prime] hydrogens. There is also a good correlation between cleavage frequency and minor groove width. The author was interested in knowing if sequences other than A-tracts could cause bending. She developed a method for selecting bent DNA molecules from a pool of molecules of random sequence. This method has allowed selection and characterization of several non-A tract sequences in addition to the expected A tracts.

• Research Organization: Johns Hopkins Univ., Baltimore, MD (United States)
• OSTI ID: 7042718
• Country of Publication: United States
• Language: English

Related Subjects

550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
ADENINES
AMINES
ANTIMETABOLITES
AROMATICS
AZAARENES
BENDING
CLEAVAGE
DEFORMATION
DNA
DNA SEQUENCING
DRUGS
HETEROCYCLIC COMPOUNDS
HYDROXYL RADICALS
MICROSTRUCTURE
MOLECULAR BIOLOGY
MOLECULAR STRUCTURE
NUCLEIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PURINES
RADICALS
STRUCTURAL CHEMICAL ANALYSIS