+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Sequence-dependent variability of DNA structure. Influence of flanking sequences and fragment length on digestion by conformationally sensitive nucleases



Sequence-dependent variability of DNA structure. Influence of flanking sequences and fragment length on digestion by conformationally sensitive nucleases



Journal of Biological Chemistry 263(17): 8458-8463



DNase I and 1,10-phenanthroline-copper are two nucleolytic activities which are sequence-dependent in their scission reaction yet are not nucleotide-specific at their site of cutting. When these two nucleases are used to digest identical sequences in 18-base pair oligonucleotides and in restriction fragments 10-fold longer, the digestion patterns are similar at sequence positions in the interior of the fragment. Changes in reactivity to 1,10-phenanthroline-copper associated with mutational changes in the lac promoter in biochemically functional restriction fragments are duplicated in 18-base pair oligonucleotides. The structural variability of a given DNA sequence detected by these conformationally sensitive nucleolytic activities is therefore encoded in local sequence and not sensitive to fragment length. Digestion patterns of a repeated 7-base pair sequence within a longer sequence have the same characteristic except for the two nucleotides at the 5' periphery of the direct repeat. This conclusion is based on the digestion pattern of a restriction fragment which contains the polyadenylation site of the mouse immunoglobulin mu heavy chain gene. Two pairs of different 7-base pair sequences repeated in this fragment retain their distinctive digestion patterns. DNA sequences which comprise the binding sites of regulatory proteins, retain a characteristic structure only influenced at their peripheries by two to three bases of the flanking sequence.

Please choose payment method:






(PDF emailed within 1 workday: $29.90)

Accession: 041336234

Download citation: RISBibTeXText

PMID: 3131344


Related references

Restriction fragment length polymorphisms in shigella species genomic dna detected with ipah structural gene and flanking dna sequence probes. Abstracts of the General Meeting of the American Society for Microbiology 91: 82, 1991

Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities. Nucleic Acids Research 13(12): 4445-4467, 1985

Sequence changes in both flanking sequences of a pre-tRNA influence the cleavage specificity of RNase P. Journal of Molecular Biology 217(4): 637-648, 1991

Influence of flanking sequences on variability in expression levels of an introduced gene in transgenic tobacco plants. Nucleic Acids Research 16(19): 9267-9283, 1988

Flanking region sequences and internal repeat structure of the pYNH24 (D2S44) 2 kbp insert analyzed by polymerase chain reaction and partial digestion with RsaI. Electrophoresis 16(10): 1881-1885, 1995

Flanking-sequence exponential anchored-polymerase chain reaction amplification: a sensitive and highly specific method for detecting retroviral integrant-host-junction sequences. CytoTherapy 10(5): 526-539, 2008

Dna fragment sizes of mouse tlt hepatoma chromatin after auto digestion or treatment with various nucleases. Journal of Supramolecular Structure SUPPL: 1, 1977

Possible correlation between non-insulin dependent diabetes mellitus (NIDDM) and restriction fragment length polymorphism (RFLP) of the 5'-flanking region of insulin gene in Korean diabetic population. Korean Journal of Internal Medicine 2(2): 140-146, 1987

Structure-specific nuclease activity of RAGs is modulated by sequence, length and phase position of flanking double-stranded DNA. Febs Journal 282(1): 4-18, 2015

Human DNA sequences isolated with an immunoglobulin switch region probe: sequence, chromosomal localization, and restriction fragment length polymorphisms. Human Genetics 73(2): 104-109, 1986

Genetic variability within and among populations of the golden crayfish (Orconectes luteus): a comparison using amplified fragment length polymorphisms (AFLPs) and mitochondrial 16s gene sequences. Freshwater Crayfish, 12: 396-412, 1999

Assessing genetic variability among Brazilian strains of Xanthomonas axonopodis pv. manihotis through restriction fragment length polymorphism and amplified fragment length polymorphism analyses. Canadian Journal of Microbiology 45(9): 754-763, 1999

Asexual genetic variability in Agavaceae determined with inverse sequence-tagged repeats and amplification fragment length polymorphism analysis. Plant Molecular Biology Reporter 24(2): 205-217, 2006

Nucleotide sequence of a fragment of sv 40 dna that contains the origin of dna replication and specifies the 5 prime ends of early and late viral rna part 2 sequences of t 1 and pancreatic rnase digestion products of rna transcripts prepared from sub fragments of eco r ii g. Journal of Biological Chemistry 252(1): 340-354, 1977

Terminal restriction fragment length measurement errors are affected mainly by fragment length, G+C nucleotide content and secondary structure melting point. Journal of Microbiological Methods 82(3): 223-228, 2010