Analysing genetic information with DNA arrays.

The large amount of DNA sequence information produced in recent years has created a need for high-throughput methods in biology and genetics. These include sequencing, comparing gene sequences and genotyping. DNA arrays promise a highly parallel means for analysis of DNA that is fast and cost-effective, and offers scope for application to complex systems and processes. Recent years have seen continued transfer of technology from the microelectronics industry. Rapid application of the technology to genotyping, antisense oligonucleotide selection and gene expression analysis has illustrated the general power of this approach.

Variation in sebum fatty acid composition among adult humans.

Quartz capillary gas chromatography was used to analyze the wax ester fatty acids of 4 sebum samples collected at 2-week intervals from each of 10 adult human subjects. Marked differences in wax ester fatty acid composition between subjects were apparent. The greatest variation was present in the even-carbon-numbered iso-branched acids, which ranged from 1-22% of the monounsaturated acids and from 1-13% of the saturated acids. The anteiso chain structures formed 3-7.5% of the unsaturated acids and 3-13.5% of the saturated acids. Fatty acids bearing one or more methyl branches at other positions in the chain made up 12-22% of the saturated acids, but were not present in the unsaturated fatty acid fraction. This and other features of the composition of the unsaturated fatty acids indicate that the delta 6-desaturase that produces the monounsaturated fatty acids of human sebum requires a substrate having a straight chain of at least 12 carbon atoms extending from the carboxyl group. The differences in fatty acid composition between subjects and the constancy of composition for each of the subjects over the 2-month period indicate that the synthesis of each of the types of chain structure is under genetic control.

Migrant adjustment in Seoul, Korea: employment and housing.

PIP: To examine the role of the migrants in the job and housing markets, a sample survey of 1000 households in Seoul, Korea was conducted. For each sample household chosen, in an area probability sample based on the city registration lists, 1 household member, aged 15-45, was interviewed about employment, housing, migration and family histories, and the social and psychological adjustment in Seoul City of the respondent and his family members. Interveiws were completed for 978 cases in 2 rounds in 1974-75. An important feature of the sample was the inclusion of the control group of lifetime urban residents who were used as the standard by which migrants' adjustment was examined. This group comprised 27% of the sample. Additionally, the migrant group was subdivided according to length of residence in Seoul City. Those who resided there for fewer than 5 years were classified as recent migrants and comprised 20% of the sample. Longterm migrants, those with residence greater than 5 years, comprised 53% of the sample. Recent migrants were concentrated in the blue collar occupations, but there was virtually no difference between the occupational distributions of longterm migrants and lifetime urban residents. Lifetime urban residents showed higher unemployment rates and higher educational enrollment rates than either the recent or longterm migrants groups. There was a 10% differential favoring employment in modern industries (secondary and tertiary) among the lifetime urban residents; fewer than 40% of the recent migrants fell into the modern categories compared to 44% for longterm migrants, and over 50% for lifetime urban residents. Lifetime urban residents were significantly less likely to be employed in traditional service occupations than were recent migrants. Longer term migrants were intermediate for the tertiary traditional sector, but they were significantly less likely to be employed in the manufacturing or secondary sector, especially the modern secondary sector, possibly reflecting the job market upon their arrival in Seoul. Younger respondents were concentrated in blue collar occupations, but for those 25 years old and older more than half were employed in white collar occupations. The quality of dwellings for migrants and natives was measured in 3 areas: housing quality; neighborhood quality, and tenure status. To a certain extent migrants were in lower quality housing compared to urban natives, but this appeared to be due not to recency of migration itself but to other characteristics of the migrants. The relative position of recent, versus longterm migrants, was opposite to the expected pattern. The quality of the neighborhood of residence differed somewhat more for migrants and nonmigrants. The relative positions were as hypothesized: neighborhood quality increased with duration of residence. The range of differences was narrowed considerably when the effects of age, education, and income were removed. Owning or not owning one's house seemed related much more closely to the formation of attachments in the urban area, that is, commitment. Migrants through time do come to approximate the economic and housing patterns of lifetime urban residents.^ieng

Studies on the base pairing properties of deoxyinosine by solid phase hybridisation to oligonucleotides.

Extensive analyses of the base-pairing properties of deoxyinosine to A, C, G, and T were carried out by measuring the hybridisation of oligonucleotides with deoxyinosine in various positions to complementary sets of oligonucleotides made as an array on the surface of a glass microscope slide. With deoxyinosine in internal positions, results are consistent with previous studies, showing a preferential order for pairing of I-C > I-A > I-G approximately I-T. With two adjacent deoxyinosines in the centre of the oligonucleotide, the order in duplex yield is CC > CA > AA > AC > GC > GA > CG > TA > TC > CT = AG > AT > GT > TT. With deoxyinosine at the ends of the oligonucleotide, we find that at the 3' end there is the same order in duplex yield as for the deoxyinosine in internal positions, though with lower discrimination between the bases. When hybridisation is carried out in TMACI there is little base pairing discrimination with deoxyinosine, or indeed any of the four natural bases at the 5' end. Changing the cation to Na+ increased discrimination slightly.

Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield.

Effects of dangling ends on duplex yield have been assessed by hybridisation of oligonucleotides to an array of oligonucleotides synthesised on the surface of a solid support. The array consists of decanucleotides and shorter sequences. One of the decanucleotides in the array was fully complementary to the decanucleotide used as solution target. Others were complementary over seven to nine bases, with overhangs of one to three bases. Duplexes involving different decanucleotides had different overhangs at the 3' and 5' ends. Some duplexes involving shorter oligonucleotides had the same regions of complementarity as these decanucleotides, but with fewer overhanging bases. This analysis allows simultaneous assessment of the effects of differing bases at both 5' and 3' ends of the oligonucleotide in duplexes formed under identical reaction conditions. The results indicate that a 5' overhang is more stabilising than a 3' overhang, which is consistent with previous results obtained with DNA overhangs. However, it is not clear whether this is due to the orientation of the overhang or to the effect of specific bases.

Steric factors influencing hybridisation of nucleic acids to oligonucleotide arrays.

We have investigated the use of spacer molecules to reduce steric interference of the support on the hybridisation behaviour of immobilised oligonucleotides. These spacers are built up from a variety of monomeric units, using phosphoramidite chemistry, by condensation onto an amine-functionalised polypropylene support. The optimal spacer length was determined to be at least 40 atoms in length, giving up to 150-fold increase in the yield of hybridisation. The effects of different charged groups in the spacer were also examined, and it was shown that both positively and negatively charged groups in the spacer diminish the yield of hybridisation. Steric hindrance in hybridisation can also be a problem if the oligonucleotides attached to the support are too close to each other. Surface coverage was varied using a combination of cleavable and stable linkers, giving the highest hybridisation yields for surfaces containing approximately 50% of the maximum concentration of oligonucleotides.

Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids.

Arrays of oligonucleotides corresponding to a full set of complements of a known sequence can be made in a single series of base couplings in which each base in the complement is added in turn. Coupling is carried out on the surface of a solid support such as a glass plate, using a device which applies reagents in a defined area. The device is displaced by a fixed movement after each coupling reaction so that consecutive couplings overlap only a portion of previous ones. The shape and size of the device and the amount by which it is displaced at each step determines the length of the oligonucleotides. Certain shapes create arrays of oligonucleotides from mononucleotides up to a given length in a single series of couplings. The array is used in a hybridisation reaction to a labelled target sequence, and shows the hybridisation behaviour of every oligonucleotide in the target sequence with its complement in the array. Applications include sequence comparison to test for mutation, analysis of secondary structure, and optimisation of PCR primer and antisense oligonucleotide design.