Cloning and characterization of DNAs with palindromic sequences

The human genome-wide distribution of DNA palindromes

In this work, we performed a systematic study of perfect and nonspacer palindromes present in human genomic DNA, and we investigated palindrome distribution over the entire human genome and over the functional regions such as the exon, intron, intergenic, and upstream regions (2,000 bp upstream from translational start site). We found that 24 palindrome-abundant intervals are mostly located on G-bands, which condense early, replicate late, and are relatively A+T rich. In general, palindromes are overrepresented in introns but underrepresented in exons. Upstream region has enriched palindrome distribution, where palindromes can serve as transcription factor binding sites. We created a Human DNA Palindrome Database (HPALDB) which is accessible at http://vhp.ntu.edu.sg/hpaldb . It contains 12,556,994 entries covering all palindromes in the human genome longer than 6 bp. Queries can be performed in different ways. Each entry in the database is linked to its location on NCBI's human chromosome Map Viewer.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus

The nature of any long palindrome that might exist in the human genome is obscured by the instability of such sequences once cloned in Escherichia coli. We describe and validate a practical alternative to the analysis of naturally-occurring palindromes based upon cloning and propagation in Saccharomyces cerevisiae. With this approach we have investigated an intronic sequence in the human Neurofibromatosis 1 (NF1) locus that is represented by multiple conflicting versions in GenBank. We find that the site is highly polymorphic, exhibiting different degrees of palindromy in different individuals. A side-by-side comparison of the same plasmids in E.coli versus. S.cerevisiae demonstrated that the more palindromic alleles were inevitably corrupted upon cloning in E.coli, but could be propagated intact in yeast. The high quality sequence obtained from the yeast-based approach provides insight into the various mechanisms that destabilize a palindrome in E.coli, yeast and humans, into the diversification of a highly polymorphic site within the NF1 locus during primate evolution, and into the association between palindromy and chromosomal translocation.

Effects of adeno-associated virus DNA hairpin structure on recombination

Hairpin DNA ends are evolutionarily conserved intermediates in DNA recombination. The hairpin structures present on the ends of the adeno-associated virus (AAV) genome are substrates for recombination that give rise to persistent circular and concatemeric DNA episomes through intramolecular and intermolecular recombination, respectively. We have developed circularization-dependent and orientation-specific self-complementary AAV (scAAV) vectors as a reporter system to examine recombination events involving distinct hairpin structures, i.e., closed versus open hairpins. The results suggest that intramolecular recombination (circularization) is far more efficient than intermolecular recombination (concatemerization). Among all possible combinations of terminal repeats (TRs) involved in intermolecular recombination, the closed-closed TR structures are twice as efficient as the open-open TR substrates for recombination. In addition, both intramolecular recombination and intermolecular recombination exhibit the common dependency on specific DNA polymerases and topoisomerases. The circularization-dependent and orientation-specific scAAV vectors can serve as an efficient and controlled system for the delivery of DNA structures that mimic mammalian recombination intermediates and should be useful in assaying recombination in different experimental settings as well as elucidating the molecular mechanism of recombinant AAV genome persistence.

Cloning and sequencing of defective particles derived from the autonomous parvovirus minute virus of mice for the construction of vectors with minimal cis-acting sequences

The production of wild-type-free stocks of recombinant parvovirus minute virus of mice [MVM(p)] is difficult due to the presence of homologous sequences in vector and helper genomes that cannot easily be eliminated from the overlapping coding sequences. We have therefore cloned and sequenced spontaneously occurring defective particles of MVM(p) with very small genomes to identify the minimal cis-acting sequences required for DNA amplification and virus production. One of them has lost all capsid-coding sequences but is still able to replicate in permissive cells when nonstructural proteins are provided in trans by a helper plasmid. Vectors derived from this particle produce stocks with no detectable wild-type MVM after cotransfection with new, matched, helper plasmids that present no homology downstream from the transgene.

Mutation in Escherichia coli under starvation conditions: a new pathway leading to small deletions in strains defective in mismatch correction

Strains of Escherichia coli carrying the mutY mutation lack a mismatch correction glycosylase that removes adenines from various mismatch situations. In growing bacteria, 8-oxoguanine-adenine mispairs persist and can give rise to G-->T transversions during subsequent replication cycles. We now show that when trpA23 mutY bacteria are held under tryptophan starvation conditions the tryptophan-independent mutants that arise include small in-frame deletions in addition to transversions. The trpA23 reversion system appears to be unusual in that small in-frame deletions occurring in a particular region of the gene can lead to the production of a functional protein. We suggest that this is a consequence of the deletion causing the polar group on the arginine at the trpA23 site to be pulled away from the active site of the enzyme. Such deletions are also found with starved bacteria defective in methyl-directed mismatch correction activity (mutH, mutL or mutS), and deletion mutations are also found among the much lower number of mutants that arise in bacteria wild-type for mismatch correction. There is thus a pathway, hitherto undetected, leading to deletions probably from mismatches under conditions of growth restraint. RecA, UmuC, UvrA, MutH,L,S, SbcC and SbcD proteins are not required for the operation of the deletion pathway. A possible explanation is that the deletion pathway is not dependent upon further replication and that it fails to be discernible in growing cells because it is relatively slow acting and mismatches are likely to encounter a DNA replication fork before the initial step of the deletion pathway.