Origins of life: a route to nanotechnology.

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.

Self-programmable, self-assembling two-dimensional genetic matter.

Putative two-dimensional coding systems can be constructed from aqueous solutions of purine and pyrimidine nucleic acid bases evaporated at moderate temperatures on the surfaces of inorganic solids. The resultant structures are monolayers which are formed spontaneously by molecular self-assembly and they have been observed with molecular resolution by scanning tunnelling microscopy (STM). When formed from solutions of a single base, the monolayers of adenine and uracil have crystalline characteristics and the STM images can be interpreted in terms of the geometrical placement of planar arranged molecules that interact laterally by intermolecular hydrogen bonding. When formed from solutions containing a mixture of adenine and uracil, the monolayers have aperiodic structures. Small crystalline domains within these monolayers can be interpreted in terms of the single phase configurations of the molecules and the remaining aperiodic structures can presumably be interpreted, geometrically, in terms of the 21 theoretically possible adenine-adenine, uracil-uracil and adenine-uracil hydrogen bonding interactions. We propose that combinatorial arrangements of planar arranged purine and pyrimidine bases could provide the necessary complexity to act as a primitive genetic mechanism and may have relevance to the origin of life.

Methylation sequencing analysis refines the region of H19 epimutation in Wilms tumor.

Differential DNA methylation of the parental alleles has been implicated in the establishment and maintenance of the monoallelic expression of imprinted genes. H19 and IGF2 are oppositely imprinted with only the maternal and the paternal alleles expressed, respectively. In Wilms tumor, a childhood renal neoplasm, loss of the H19/IGF2 imprinted expression pattern results in silencing of H19 and biallelic expression of IGF2. This was shown to be associated with biallelic methylation of the H19 promoter in the tumor and the adjacent kidney tissue suggesting that epigenetic H19 silencing is an early event in Wilms tumorigenesis. An imprinting mark region characterized by paternal allele-specific methylation has been suggested to reside in a GC-rich region of 400-base pair direct repeats starting at -2 kilobase pairs (kb) relative to the H19 transcription start and extending upstream. The upstream boundary of the potential paternal methylation imprint of the H19 gene has yet to be defined. We sought to define this upstream imprint boundary and investigate whether Wilms tumors with loss of imprinting are biallelically methylated in this imprinting mark region. The analysis of 6.6 kb of new upstream H19 sequence determined in this study identified a series of the direct 400-base pair repeats that extends to approximately -5.3 kb relative to the transcription start. DNA methylation analyses indicated that the upstream boundary of the potential imprint may coincide with the 5' end of the direct repeats. We found that Wilms tumors with loss of imprinting are biallelically methylated in the H19 upstream repeat region, and we suggest that pathological methylation in this region is the epigenetic error that initiates H19 silencing.

Scanning tunnelling microscopy and molecular modelling of xanthine monolayers self-assembled at the solid-liquid interface: relevance to the origin of life.

The development of scanning tunnelling microscopy (STM) has allowed examination of inorganic crystalline surfaces and their interactions with organic adsorbates with unparalleled resolution. As a novel technique in origin of life studies, the application of STM is detailed with particular attention paid to the methods employed in the analysis of organic monolayer structures. STM imaging and molecular modelling of self-assembled monolayers of the purine base, xanthine, formed on the surfaces of graphite and molybdenum disulfide are presented as an example. The putative role of such structures in the origin of life is discussed.

Is gene deletion in eukaryotes sequence-dependent? A study of nine deletion junctions and nineteen other deletion breakpoints in intron 7 of the human dystrophin gene.

Although large deletions comprise 65% of the mutations that underlie most cases of Duchenne and Becker muscular dystrophies, the DNA sequence characteristics of the deletions and the molecular processes leading to their formation are largely unknown. Intron 7 of the human dystrophin gene is unusually large (110 kb) and a substantial number of deletions have been identified with endpoints within this intron. The distribution of 28 deletion endpoints was mapped to local sequence elements by PCR. The break points were distributed among unique sequence, LINE-1, Alu, MIR, MER and microsatellite sequences with frequencies expected from the frequency of those sequences in the intron. Thus, deletions in this intron are not associated primarily with any one of those sequences in the intron. Nine deletion junctions were amplified and sequenced. Eight were deletions between DNA sequences with minimal homology (0-4 bp) and are therefore unlikely to be products of homologous recombination. In the ninth case, a complex rearrangement was found to be consistent with unequal recombinational exchange between two Alu sequences coupled with a duplication. We have hypothesized that a paucity of matrix attachment regions in this very large intron expanded by the insertion of many mobile elements might provoke a chromatin structure that stimulates deletions (McNaughton et al., 1997, Genomics 40, 294-304). The data presented here are consistent with that idea and demonstrate that the deletion sequences are not usually produced by homologous DNA misalignments.

The Arg506Gln mutation (FV Leiden) among a cohort of 4188 unselected Danish newborns.

Resistance to activated protein C (APC) is the most prevalent single phenomenon associated with thromboembolic disease. It is caused by a single point mutation in the factor V gene (Arg506Gln or FV Leiden), replacing an Arg506 with a Gln at the APC-cleavage site in factor V. In this study we present a prevalence study of the Arg506Gln mutation in a large Danish cohort. By screening 4188 newborns (8376 alleles) we identified 3.4% alleles (95% CI: 3.0-3.8) of the Arg506Gln mutation, corresponding to a heterozygous prevalence of 6.6% (95% CI: 5.9-7.4) in Denmark. This is significantly lower than what has been reported from southern Sweden. The birth cohort has been selected from the entire country, providing representative and accurate estimates of the gene frequencies. Equal gender distribution was found, and the Arg506Gln mutation is probably not a considerable risk factor in fetal life in the general population.

The evolution of an intron: analysis of a long, deletion-prone intron in the human dystrophin gene.

The sequence of a 112-kb region of the human dystrophin (DMD/BMD) gene encompassing the deletion prone intron 7 (110 kb) and the much shorter intron 8 (1.1 kb) has been determined. Recognizable insertion sequences account for approximately 40% of intron 7. LINE-1 and THE-1/LTR sequences occur in intron 7 with significantly higher frequency than would be expected statistically while Alu sequences are underrepresented. Intron 7 also contains numerous mammalian-wide interspersed repeats, a diverse range of medium reiteration repeats of unknown origin, and a sequence derived from a mariner transposon. By contrast, the shorter intron 8 contains no detectable insertion sequences. Dating of the LI and Alu sequences suggests that intron 7 has approximately doubled in size within the past 130 million years, and comparison with the corresponding intron from the pufferfish (Fugu rubripes) suggests that the intron has expanded some 44-fold over a period of 400 million years. The possible contribution of the insertion elements to the instability of intron 7 is discussed.

Chiral symmetry breaking during the self-assembly of monolayers from achiral purine molecules.

Scanning tunneling microscopy was used to investigate the structure of the two-dimensional adsorbate formed by molecular self-assembly of the purine base, adenine, on the surfaces of the naturally occurring mineral molybdenite and the synthetic crystal highly oriented pyrolytic graphite. Although formed from adenine, which is achiral, the observed adsorbate surface structures were enantiomorphic on molybdenite. This phenomenon suggests a mechanism for the introduction of a localized chiral symmetry break by the spontaneous crystallization of these prebiotically available molecules on inorganic surfaces and may have some role in the origin of biomolecular optical asymmetry. The possibility that purine-pyrimidine arrays assembled on naturally occurring mineral surfaces might act as possible templates for biomolecular assembly is discussed.

An improved method for the synthesis of mercurated dUTP. Enzymic synthesis of Hg-labelled DNA of high molecular weight suitable for use in an image based DNA sequencing strategy.

The development of high-resolution scanning-probe microscopes has reawakened interest in the possibility of sequencing large nucleic acid molecules by direct imaging. Such an approach would be facilitated by the availability of effective methods for increasing contrast by labelling specific nucleotides, and the utility of introducing mercury atoms into complete DNA molecules through the enzymic polymerisation of mercurated pyrimidine deoxynucleoside triphosphates has been re-investigated. A simplified and improved method for the synthesis of a heat- and thiol-stable, mercurated derivative of deoxyuridine triphosphate in high yield and the incorporation of this precursor into full-length copies of a single-stranded phage M13 template are described. The DNA product has been fully characterised and the quantitative and specific replacement of thymidylic acid residues by the mercurated analogue demonstrated.

Selective miscarriage of Down's syndrome fetuses in women aged 35 years and older.

OBJECTIVE: To estimate the fetal loss of Down's syndrome fetuses between the time of chorionic villus sampling (10 weeks gestation) and the time of amniocentesis (16 weeks gestation) and term in women aged 35 years and older. DESIGN: The age specific prevalence rates in the first trimester of Down's syndrome were estimated using the Danish cytogenetic register in combination with results from four published studies. These were compared with the reported prevalence at the time of amniocentesis and at birth. SUBJECTS: 5927 singleton pregnancies undergoing chorionic villus sampling (71 cases of Down's syndrome and 5856 unaffected cases). This was combined with published data on a further 231 cases of Down's syndrome and 16,620 unaffected cases. MAIN OUTCOME MEASURES: Age specific prevalences at the time of chorionic villus sampling. Proportion of pregnancies lost between the time of chorionic villus sampling and the time of amniocentesis and term. RESULTS: Thirty-two percent of Down's syndrome pregnancies are lost between the time of chorionic villus sampling (10 weeks) and the time of amniocentesis (16 weeks) and 54% are lost by term. CONCLUSIONS: The high fetal loss rates of Down's syndrome between the time of chorionic villus sampling and term introduce problems when evaluating first trimester screening tests with respect to their effective detection rates at term. A recommendation for quoting term risks is made.

Phylogenetic relationships among transposon-like elements in human and primate DNA.

A THE-1 sequence in intron 7 of the human dystrophin gene has been found to represent a new subfamily of THE-1 elements. The sequence is closely related to the MstII family of repetitive sequences and is more like single-copy sequences found in the galago genome than any other THE-1 sequence previously reported. This new THE-1 sequence has been compared with two other complete THE-1 sequences and three related long-terminal repeat elements that we have previously found in intron 7 of the dystrophin gene, and with members of the same family from elsewhere in the primate genome. Parsimony and deletion analysis show that the cluster of THE-1 sequences in intron 7 of the dystrophin gene has arisen from at least three individual insertion events, rather than from the insertion and duplication of a single progenitor sequence.

Sequence of a transposon identified as Tn1000 (gamma delta).

We report the complete sequence of a transposon found in a cosmid clone of a human DNA sequence. The transposon is identified as the Escherichia coli transposon Tn1000 (also known as gamma delta) on the basis of the identity of the restriction map of the new sequence with that previously recorded for Tn1000 and homology between parts of the new sequence and that of published fragments of Tn1000 sequence. The transposon, which comprises 5,981 nucleotides including two 35 bp inverted terminal repeat sequences (ITRs), contains three open reading frames. The sequence of the resolvase coding region (tnpR) is identical to that published by others. A second reading frame can be identified as the tnpA gene, coding for the transposase, on the grounds of its strong homology with the corresponding gene from transposon Tn3. The third reading frame has the potential to code for a protein of unknown function containing 698 amino acids.

A cluster of transposon-like repetitive sequences in intron 7 of the human dystrophin gene.

A 32 kilobase-pair fragment of intron 7 of the human dystrophin gene has been sequenced and analysed for the presence of repetitive elements and open reading frames. Two transposon-like human elements (THE-1 sequences), and three intervening, and related, long terminal repeat elements, together with three Alu sequences and a LINE sequence have been identified. These represent an unexpected clustering of highly-repetitive sequences within this single segment of intron DNA. Amplification of a region of chimpanzee genomic DNA by the polymerase chain reaction has provided evidence that at least one of the THE-1 sequences is present in the same position in the chimpanzee genome and the high homology between the human and chimpanzee sequences indicates that this element was fixed within the ancestral genome before the divergence of the two species. The possible role of repetitive, transposon-like sequences in natural mutagenesis of the dystrophin gene is discussed.

Characterization of two sheep insulin-like growth factor II cDNAs with different 5'-untranslated regions.

We have isolated two sheep IGF-II clones which have the same coding regions but have different 5'-untranslated regions. There is no homology between these 5'-UTR sequences which are homologous to exons 5 and 6 of the human IGFII gene. In humans these exons are transcribed only during fetal development, but in the sheep these transcripts were detected up to 28 weeks after parturition. The sizes of the sheep IGF-II mRNA transcripts are the same as those observed for the human gene, suggesting structural and transcriptional similarity between the human and sheep IGF-II genes. The sheep could therefore be a good model system in which to study IGF-II expression.

Ring chromosome 22 and neurofibromatosis.

Variable constitutional mosaicism, mos45,XY,-22/46,XY,-22,+mar/46,XY,-22,+r(22)/47,XY,-22,+r(22)+mar/ 47, XY,-22,+r(22)*2, was found in PHA-stimulated peripheral blood, in a lymphoblastoid cell line and in cultured skin fibroblasts from a mentally retarded patient with neurofibromatosis. Both the ring chromosome and the small extra marker chromosome stained positively by in situ hybridization with a chromosome 14/22-specific alphoid repeat probe. DNA dosage analysis showed constitutional loss of one copy of the arylsulfatase A gene (ARSA), consistent with its terminal location on 22q. There was no evidence of constitutional loss of D22S1 or D22S28 which flank the neurofibromatosis type 2 (NF2) locus. Analysis of two DNA samples from a skin neurofibroma indicated retainment of two copies of D22S1, whereas the results were ambiguous with respect to tumor-specific loss of one copy of D22S28. It is suggested that the development of neurofibromatosis of unclear type in two r(22) carriers might be associated with somatic mutation of the NF2 locus due to instability of the ring chromosome(s), and in analogy, that somatic mutation of either NF1 or NF2 may account for some cases of neurofibromatosis which do not meet the criteria of either NF1 or NF2. The occurrence of seminoma in the proband may be fortuitous, but could also be due to the presence of a seminoma-associated locus on chromosome 22.

Ovine follistatin: characterization of cDNA and expression in sheep ovary during the luteal phase of the oestrous cycle.

We have isolated ovine follistatin cDNA from an ovarian follicle cDNA library and determined its sequence. The deduced amino acid sequence of the ovine follistatin precursor is highly homologous (greater than 97%) to the porcine, human and rat follistatins. Northern analysis was used to characterize follistatin gene expression in ovaries of adult ewes, collected from days 11 to 13 of the oestrous cycle. Two major (about 2.7 kb and 1.5 kb) and one minor (about 0.5 kb) transcripts were detected in polyadenylated RNA extracted from ovarian follicles and corpora lutea. The degree of expression of the transcripts varied in the two ovarian compartments, with the 2.7 kb species predominating in the follicles and the 1.5 kb species being more abundant in the corpora lutea. No transcripts were detected in stromal tissue containing preantral follicles of less than 1 mm.