SYNTHETIC DEOXYRIBO-OLIGONUCLEOTIDES AS TEMPLATES FOR THE DNA POLYMERASE OF ESCHERICHIA COLI: NEW DNA-LIKE L-POLYMERS CONTAINING REPEATING NUCLEOTIDE SEQUENCES

Short tandem repeat stutter model inferred from direct measurement of in vitro stutter noise

Short tandem repeats (STRs) are polymorphic genomic loci valuable for various applications such as research, diagnostics and forensics. However, their polymorphic nature also introduces noise during in vitro amplification, making them difficult to analyze. Although it is possible to overcome stutter noise by using amplification-free library preparation, such protocols are presently incompatible with single cell analysis and with targeted-enrichment protocols. To address this challenge, we have designed a method for direct measurement of in vitro noise. Using a synthetic STR sequencing library, we have calibrated a Markov model for the prediction of stutter patterns at any amplification cycle. By employing this model, we have managed to genotype accurately cases of severe amplification bias, and biallelic STR signals, and validated our model for several high-fidelity PCR enzymes. Finally, we compared this model in the context of a naïve STR genotyping strategy against the state-of-the-art on a benchmark of single cells, demonstrating superior accuracy.

Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs

A number of applications of analysis of human Y-chromosome microsatellite loci to human evolution and forensic science require reliable estimates of the mutation rate and knowledge of the mutational mechanism. We therefore screened a total of 4,999 meioses from father/son pairs with confirmed paternity (probability >/=99. 9%) at 15 Y-chromosomal microsatellite loci and identified 14 mutations. The locus-specific mutation-rate estimates were 0-8. 58x10-3, and the average mutation rate estimates were 3.17x10-3 (95% confidence interval [CI] 1.89-4.94x10-3) across 8 tetranucleotide microsatellites and 2.80x10-3 (95% CI 1.72-4.27x10-3) across all 15 Y-chromosomal microsatellites studied. Our data show a mutational bias toward length increase, on the basis of observation of more repeat gains than losses (10:4). The data are in almost complete agreement with the stepwise-mutation model, with 13 single-repeat changes and 1 double-repeat change. Sequence analysis revealed that all mutations occurred in uninterrupted homogenous arrays of >/=11 repeats. We conclude that mutation rates and characteristics of human Y-chromosomal microsatellites are consistent with those of autosomal microsatellites. This indicates that the general mutational mechanism of microsatellites is independent of recombination.

Isolation and characterization of a bacteriophage specific for Sphaerotilus natans which contain an unusual base in its deoxyribonucleic acid

A bacteriophage was isolated specific for Sphaerotilus natans, an organism for which bacteriophages have not been previously described. This phage (designated SN1) was found to infect both the single-cell (S-type) and filamentous (R-type) forms of the host, although the sheath appeared to provide R-type cells with a degree of physical protection from infection. SN1 had a hexagonal head and a long flexible tail resembling most closely the phages in Bradley's group B. The nucleic acid was found to be deoxyribonucleic acid and contained an unusual base which substituted for 35% of the guanine. Deoxyribonucleic acid base composition was 56% cytosine plus guanine.

Comparative ability of RNA and DNA to prime DNA synthesis in vitro: role of sequence, sugar, and structure of template-primer

The priming efficiency of oligo(RNA) vs. oligo(DNA) in a homopolymer template-homooligomer primer system was compared using four DNA polymerases. The templates included (dT)n, (dA)n, (dC)n, and (dI)n. Primers were the oligomers of the complementary DNA OR RNA with chain lengths of 6 to 23. The DNA polymerases used were from Micrococcus luteus, avian myeloblastosis virus (AMV), and Escherichia coli (polymerase I and polymerase III). The polymerases demonstrated a preference for the DNA primers with (dC)n, (dA)n, and (dI)n templates. However, when (dT)n was the template, all but the AMV polymerase preferred (rA)11 more than 200-fold better than (dA)12. This preference was due to the physical structure of the initiation complex. The structures of the oligo-polymer complexes were characterized by mixing curves, melting curves, and analytical bouyant density analyses. (rA)11 + (dT)n formed predominatly a duplex structure, whereas (dA)12 + (dT)n formed the three- stranded structure, (dA12-2(dT)n. The Km of the duplex with E. coli Pol III was 2.9 mugM (rA)11. The Ki of the triplex was 2.2 mugM (dA)12, indicating that Pol III could bind to the triplex but would not elongate the (dA)12 primer. The influence of structure on priming also was demonstrated with longer oligomers, (dA)23 and (rA)23, where the (dA)23 formed more duplex-like structures and primed more than the (dA)12.(dT)10 + (dA)n complexes also were shown to form triplex structures that inhibited priming. These results show that template-primer structure has more influence on priming than the sugar moiety or the sequence of the nucleic acid.