Repair of thymine.guanine and uracil.guanine mismatched base-pairs in bacteriophage M13mp18 DNA heteroduplexes

Repair of thymine.guanine (T.G) and uracil.guanine (U.G) mismatched base-pairs in bacteriophage M13mp18 replicative form (RF) DNA was compared upon transfection into repair-proficient or repair-deficient Escherichia coli strains. Oligonucleotide-directed mutagenesis was used to prepare covalently closed circular heteroduplexes that contained the mismatched base-pair at a restriction recognition site. The heteroduplexes were unmethylated at dam (5'-GATC-3') sites to avoid methylation-directed biasing of repair. In an E. coli host containing uracil-DNA glycosylase (ung+), about 97% of the transfecting U.G-containing heteroduplexes had the U residue excised by the uracil-excision repair system. With the analogous T.G mispair, mismatch repair operated on almost all of the transfecting heteroduplexes and removed the T residue in about 75% of them when the mismatched T was on the minus strand of the RF DNA. Similar preferential excision of the minus-strand's mismatched base was observed whether the heteroduplex RF DNA molecules had only one or both strands unmethylated at dcm (5'-CC(A/T)GG-3') sites and whether the RF DNA was prepared by primer extension in vitro or by reannealing mutant and non-mutant DNA strands. Also, the extent and directionality of repair was the same at a U.G mispair in ung- host cells as at the analogous T.G mispair in ung- or ung+ cells. Only in a mismatch repair-deficient (mutH-) host was the plus strand of the transfecting M13mp18 heteroduplex DNA preferentially repaired. It is suggested that the plus strand nick made by the M13-encoded gene II protein might be employed by a mutH- host to initiate repair on that strand.

Hydrolysis by restriction endonucleases at their DNA recognition sequences substituted with mismatched base pairs

Restriction endonucleases were tested for their ability to catalyze the cleavage of mismatch-containing recognition sites in DNA. These mismatched base pairs were T.G, U.G, or A.C in covalently closed, circular heteroduplexes prepared by in vitro extension of chemically synthesized oligonucleotide primers annealed to a bacteriophage M13-derived viral DNA. None of the restriction enzymes was able to completely cleave the mismatch-containing recognition sites under standard conditions. However, three of them, SmaI, SalI, and SstI, catalyzed partial digestion leading to an accumulation of DNA singly nicked at the mismatched recognition site. The ability of SmaI and SstI to partially cleave at a mismatch was shown to depend on the nature and position of the mismatch within the corresponding recognition site. In contrast, little or no digestion was obtained with AccI, HincII, HindIII, and KpnI at mismatch-containing sites. Therefore, in some cases a transition-type substitution in only one strand of a recognition site inhibits restriction endonuclease-catalyzed digestion at that site although in others partial digestion occurs.

Isolation of in vitro synthesized covalently closed circular double-stranded DNA by selective denaturation and filtration

Based upon their resistance to irreversible denaturation, covalently closed circular (CCC) DNA (non-nicked, double-stranded circular molecules) can be purified by alkaline denaturation, neutralization, and filtration through a nitrocellulose membrane. This procedure offers a simple means of isolating in vitro synthesized CCC DNA molecules. The preparations of molecules obtained by this method consisted of 91-97% CCC DNA and contained no detectable inhibitors of biological activity or enzymatic digestion.

A protein from human placental nuclei binds preferentially to 5-methylcytosine-rich DNA

The methylation of vertebrate DNA at the 5-position of approximately 3-10% of its cytosine residues occurs in a sequence-specific and tissue-specific manner and has been implicated in the control of transcription. How these differences are established and how they mediate the initiation or maintenance of transcription are unknown. DNA methylation might also have other roles, such as modulating DNA replication, transposition, DNA repair or chromosome configuration. These other roles suggested for DNA methylation would be consistent with the finding that tissue-specific differences in methylation of certain gene regions, highly repeated satellite DNA sequences and whole genomes often do not correlate with transcriptional activity. For DNA methylation to modulate the expression, maintenance or duplication of chromosomes, there should be effector macromolecules, presumably proteins, which specifically recognize 5-methylcytosine (m5C) residues in DNA. We describe here the first identification of a mammalian protein that binds preferentially to m5C-rich DNA sequences.

DNA methylation inhibits the transfecting activity of replicative- form phi X174 DNA

Replacement of virtually all the cytosine residues with 5-methylcytosine residues in the complementary strand of the replicative form (RF) of phi X174 DNA caused a 300- to 500-fold loss in its transfecting activity. Similar results were obtained with analogously methylated M13 RF. Transfection experiments with phi X RF hemimethylated in only part of the molecule, as assessed by analysis with restriction endonucleases, indicated that gene A of phi X, which needs to be nicked at a specific site by the gene A protein for RF replication, was not the main target for this inhibition by DNA methylation. We propose that the loss of transfecting activity was due to hemimethylation of the phi X RF interfering with the processively catalyzed movement of the replication fork.

Light and ultrastructural studies of renal oncocytic adenoma

An asymptomatic renal oncocytoma was found in the upper left quadrant of an eighty-five-year-old woman during a routine physical examination. Ultrastructurally, the tumor was composed entirely of epithelial cells filled with normal and abnormal mitochondria. Selective renal angiography showed two renal arteries supplying a lobulated, highly vascular mass. The mass contained irregular and tortuous vessels without any arteriovenous shunting.

Arteriovenous malformation of the cecum: report of six cases

Patients who have chronic lower gastrointestinal bleeding with negative conventional work-ups should undergo superior mesenteric arteriography to look for arteriovenous malformations. Once the diagnosis is made, treatment is immediate conventional right hemicolectomy. Six patients with arteriovenous malformations described in this report have had no recurrence of rectal bleeding in one to five years.