Hybridization methods for DNA sequencing

Data storage in DNA with fewer synthesis cycles using composite DNA letters

The density and long-term stability of DNA make it an appealing storage medium, particularly for long-term data archiving. Existing DNA storage technologies involve the synthesis and sequencing of multiple nominally identical molecules in parallel, resulting in information redundancy. We report the development of encoding and decoding methods that exploit this redundancy using composite DNA letters. A composite DNA letter is a representation of a position in a sequence that consists of a mixture of all four DNA nucleotides in a predetermined ratio. Our methods encode data using fewer synthesis cycles. We encode 6.4 MB into composite DNA, with distinguishable composition medians, using 20% fewer synthesis cycles per unit of data, as compared to previous reports. We also simulate encoding with larger composite alphabets, with distinguishable composition deciles, to show that 75% fewer synthesis cycles are potentially sufficient. We describe applicable error-correcting codes and inference methods, and investigate error patterns in the context of composite DNA letters.

A Novel Hypergraph-Based Genetic Algorithm (HGGA) Built on Unimodular and Anti-homomorphism Properties for DNA Sequencing by Hybridization

The sequencing by hybridization (SBH) of determining the order in which nucleotides should occur on a DNA string is still under discussion for enhancements on computational intelligence although the next generation of DNA sequencing has come into existence. In the last decade, many works related to graph theory-based DNA sequencing have been carried out in the literature. This paper proposes a method for SBH by integrating hypergraph with genetic algorithm (HGGA) for designing a novel analytic technique to obtain DNA sequence from its spectrum. The paper represents elements of the spectrum and its relation as hypergraph and applies the unimodular property to ensure the compatibility of relations between l-mers. The hypergraph representation and unimodular property are bound with the genetic algorithm that has been customized with a novel selection and crossover operator reducing the computational complexity with accelerated convergence. Subsequently, upon determining the primary strand, an anti-homomorphism is invoked to find the reverse complement of the sequence. The proposed algorithm is implemented in the GenBank BioServer datasets, and the results are found to prove the efficiency of the algorithm. The HGGA is a non-classical algorithm with significant advantages and computationally attractive complexity reductions ranging to [Formula: see text] with improved accuracy that makes it prominent for applications other than DNA sequencing like image processing, task scheduling and big data processing.

Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries

In this paper, a problem of isothermic DNA sequencing by hybridization (SBH) is considered. In isothermic SBH a new type of oligonucleotide libraries is used. The library consists of oligonucleotides of different lengths depending on an oligonucleotide content. It is assumed that every oligonucleotide in such a library has an equal melting temperature. Each nucleotide adds its increment to the oligonucleotide temperature and it is assumed that A and T add 2 degrees C and C and G add 4 degrees C. The hybridization experiment using isothermic libraries should provide data with a lower number of errors due to an expected similarity of melting temperatures. From the computational point of view the problem of isothermic DNA sequencing with errors is hard, similarly like its classical counterpart. Hence, there is a need for developing heuristic algorithms that construct good suboptimal solutions. The aim of the paper is to propose a heuristic algorithm based on tabu search approach. The algorithm solves the problem with both positive and negative errors. Results of an extensive computational experiment are presented, which prove the high quality of the proposed method.

DNA sequencing with positive and negative errors

The problem addressed in this paper is concerned with DNA sequencing by hybridization. An algorithm is proposed that solves a computational phase of this approach in the presence of both positive and negative errors resulting from the hybridization experiment. No a priori knowledge of the nature and source of these errors is required. An extensive set of computational experiments showed that the algorithm behaves surprisingly well if only positive errors appear. The general case, where positive and negative errors occur, can be also solved satisfactorily for an error rate up to 10%.

Hybridization of glass-tethered oligonucleotide probes to target strands preannealed with labeled auxiliary oligonucleotides

In this article we introduce a strategy of preannealing labeled auxiliary oligonucleotides to single-stranded target DNA, prior to hybridization of the DNA target to oligonucleotide arrays (genosensors) formed on glass slides for the purpose of mutation analysis. Human genomic DNA samples from normal individuals and cystic fibrosis (CF) patients (including homozygous delta F508 and heterozygous delta F508/wild type (wt) in the region examined) were used. A PCR fragment of length 138 bp (wt) or 135 bp (mutant) was produced from exon 10 in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, using a new pair of polymerase chain reaction (PCR) primers. This fragment contains four of the most frequent mutation sites causing the disease (Q493X, delta I507, delta F508, and V520F). Each of these mutations was tested using a pair of nonamer (9-mer) probes covalently attached to glass slides, representing the normal (wt) and the mutant alleles. Single-stranded target DNA was isolated from the PCR fragment using one PCR primer labeled with biotin and a streptavidin minicolumn to capture the biotin-labeled strand. Prior to hybridization to the 9-mer array on a glass slide, the unlabeled target strand was preannealed with one, three, or four auxiliary oligonucleotides, at least one being labeled with 32P. As observed previously in several laboratories, the discrimination between normal (wt) and mutant alleles at each site using oligonucleotide array hybridization ranged from very good to poor, depending on the number and location of mismatches between probe and target. Terminal mismatches along the probe were difficult to discriminate, internal mismatches were more easily discriminated, and multiple mismatches were very well discriminated. An exceptionally intense hybridization signal was obtained with a 9-mer probe that hybridized contiguously (in tandem) with one auxiliary oligonucleotide preannealed to the target DNA. The increased stability is apparently caused by strong base stacking interactions between the "capture probe" and the auxiliary oligonucleotide. The presence of the delta F508 mutation was detected with this system, including discrimination between homozygous and heterozygous conditions. Base mismatch discrimination using the arrayed 9-mer probes was improved by increasing the temperature of hybridization from 15 to 25 degrees C. Auxiliary oligonucleotides, preannealed to the single-stranded template, may serve several purposes to enable a more robust genosensor-based DNA sequence analysis: 1. A convenient means of introducing label into the target DNA molecule. 2. Disruption of interfering short-range secondary structure in the region of analysis. 3. Covering up of redundant binding sites in the target strand (i.e., where a given probe has more than one complement within the target). 4. Tandem hybridization with the capture probe (providing contiguous stacking) as a means for achieving efficient mismatch discrimination at the terminal position of the capture probe (adjacent to the auxiliary oligonucleotide). By use of multiple auxiliary oligonucleotides, all of the above benefits can be derived simultaneously.

Efficiency of sequencing by hybridization on oligonucleotide matrix supplemented by measurement of the distance between DNA segments

DNA sequencing by hybridization on oligonucleotide microchip (SHOM) allows the determination of a spectrum of overlapping oligonucleotides constituting a DNA fragment that hybridizes to form perfect duplexes with an array of immobilized oligonucleotides and, as a result, enables reconstitution of the nucleotide sequence of the fragment. In longer DNA fragments, unambiguous reconstitution of DNA sequence is often impeded by the presence of repetitive regions and simple sequence repeats. Here it is demonstrated that SHOM supplemented by measurement of the distance between certain sites (for example, restriction sites or priming sites for PCR) within the analyzed DNA enables sequencing of much longer DNA fragments, containing repeats of different complexity.

A DNA sequencing strategy that requires only five bases of known terminal sequence for priming

We have previously reported an enhanced version of sequencing by hybridization (SBH), termed positional SBH (PSBH). PSBH uses partially duplex probes containing single-stranded 3' overhangs, instead of simple single-stranded probes. Stacking interactions between the duplex probe and a single-stranded target allow us to reduce the probe sizes required to 5-base single-stranded overhangs. Here we demonstrate the use of PSBH to capture relatively long single-stranded DNA targets and perform standard solid-state Sanger sequencing on these primer-template complexes without ligation. Our results indicate that only 5 bases of known terminal sequence are required for priming. In addition, the partially duplex probes have the ability to capture their specific target from a mixture of five single-stranded targets with different 3'-terminal sequences. This indicates the potential utility of the PSBH approach to sequence mixtures of DNA targets without prior purification.

DNA fingerprinting by hybridisation to oligonucleotide arrays

Most methods for analysing variation in DNA sequences rely on gel electrophoresis, a method which is difficult to automate and to quantify. Hybridisation to oligonucleotides bound to a solid surface offers alternatives, with the advantage that they can be more readily automated and lend themselves to powerful statistical analytical procedures. In this paper, we discuss a number of different ways in which oligonucleotide arrays could be used for DNA typing for applications in forensic science.

Sequencing potential of nested strand hybridization

The capability of the sequencing by nested strand hybridization (SNSH) method to sequence unseparated pools of DNA fragments was assessed in computer simulation experiments. The results demonstrate the high resolving power of the method and its tolerance to false-positive errors. We determine the optimal proportion between the fragment length and the pool size at a given length of oligonucleotide probes, compare SNSH to the standard SBH, and suggest the best experimental setting for the special case of sequencing of long isolated fragments.

Oligonucleotide arrays: new concepts and possibilities

Advances in solid-phase oligonucleotide synthesis and hybridization techniques have led to an incipient technology based on the use of oligonucleotide arrays. The inclusion of a large number of oligonucleotide probes within a single array greatly reduces the cost of their synthesis and allows thousands of hybridizations to be carried out simultaneously. The range of potential applications of oligonucleotide arrays was expanded by the realization that nucleic acids can be sequenced by hybridizing them to all possible oligonucleotides of a given length. Additional possibilities are offered by novel types of oligonucleotide arrays that are capable of parallel sorting, isolating, and manipulating thousands, and even millions, of nucleic acid species. Fields, such as site-directed mutagenesis, protein engineering, and recombinant DNA technology, would benefit from using these arrays. Further, these approaches could enable the analysis of entire genomes by preparing ordered fragment libraries, and by sequencing complex pools of nucleic acids, in a novel approach that provides long-range sequence information by generating nested nucleic acids and then surveying the oligonucleotides contained in the nested strands. This would allow large diploid genomes to be sequenced directly in a completely automated procedure that does not require fragment cloning or chromosome mapping.

Rearrangements of DNA sequences and SBH

Despite recent advances in DNA sequencing by hybridization it is still a random shotgun method. Even if one manages to routinely sequence short DNA fragments by SBH these fragments have to be assembled into the final genomic sequence. Recently different additional biochemical experiments were suggested which potentially may drastically increase the resolving power of SBH. However biologists frequently cannot estimate the computer science limitations of the proposed additional experiments and no computational studies of additional experiments for SBH were provided yet. The paper discusses a combinatorial technique which might help a biologist to analyze different additional biochemical experiments and to combine these data with SBH data to increase the resolving power of SBH.

Parallel synthesis and analysis of large numbers of related chemical compounds: applications to oligonucleotides

This review presents methods for addressing the issue of molecular complexity in biological systems. Biomolecules immobilised on solid phases can be used to probe biological interactions. As a specific example, arrays of large numbers of oligonucleotides allow the analysis of DNA sequences and complex populations of DNA molecules. The specific embodiments of this new method are presented, research up to mid-1992 outlined and requirements for future development discussed.

Enhanced DNA sequencing by hybridization

An enhanced version of DNA sequencing by hybridization (SBH), termed positional SBH (PSBH), has been developed. PSBH uses duplex probes containing single-stranded 3' overhangs, instead of simple single-stranded probes. Stacking interactions between the duplex probe and a single-stranded target should provide enhanced stringency in distinguishing perfectly matched 3' sequences. A second enhancement is the use of enzyme-catalyzed steps, instead of pure physical hybridization. The feasibility of this scheme has been investigated using biotinylated duplex probes containing single-stranded 5-base 3' overhangs, immobilized on streptavidin-coated magnetic beads. Ligation of a single-stranded target, hybridized to the single-stranded region of the duplex probes, provided enhanced discrimination of perfectly matched targets from those containing mismatches. In distinction to the serious complications caused by base composition effects in ordinary SBH, there was little effect of base composition in PSBH. The hardest mismatch to discriminate was the one furthest from the phosphodiester bond formed by ligation. However, mismatches in this position were efficiently discriminated by 3' extension of the duplex probe using a template-dependent DNA polymerase. These results demonstrate that PSBH offers considerable promise to facilitate actual implementations of SBH.

DNA sequencing by hybridization to oligonucleotide matrix. Calculation of continuous stacking hybridization efficiency

In this paper we consider the efficiency of additional rounds of "continuous stacking" hybridization in DNA sequence reconstruction by hybridization with oligonucleotide matrix (SHOM). After the initial hybridization of target DNA with the matrix of oligonucleotides of fixed length L some additional hybridizations should be carried out in the presence of fluorescently labeled oligonucleotides of another length l. These additional oligonucleotides can hybridize in tandem with matrix tuples (continuous stacking hybridization) thus forming an extended duplex with the target DNA strand. The additional data obtained allows resolutions of branching points arising in the reconstruction procedure. Multiple rounds of continuous stacking hybridization considerably increase the efficiency of the sequencing method, eventually approaching the power of (L+l)-matrix. We develop here an algorithm that allows us to minimize the number of additional hybridization steps, by assembling sets of l-tuples to be added together in each round of continuous stacking hybridization. For SHOM using a matrix of octanucleotides, continuous stacking hybridization with pentanucleotides increases the length of unambiguously sequenced DNA from 200 to several thousands of base pairs.

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.

Selection of oligonucleotide probes and experimental conditions for multiplex hybridization experiments

Different DNA probes hybridize under different conditions. I examine the constraints of the design of oligonucleotide probes that are meant to hybridize to different unique sites in human genomic DNA under a single set of hybridization conditions as a parallel array. In 522 kb of human genomic DNA, 75% of 12-base and 89% of 22-base are unique, as opposed to 90% and 100% as expected of unstructured DNA, and this is not due solely to repetitive elements in the DNA. Hybridization in TMAC to reduce A+T content effects on melting temperature allows only 90% of unique targets to be hybridized under one set of conditions if a 2 degrees C difference between matched and mismatched sequences is required. Standard hybridization conditions allow no more than 60% of unique probes to be used together. This suggests that probe, hybridization conditions, and instrument design for multiple-probe hybridization applications will be harder than previously suggested.

Mixed hybridization and conventional strategies for DNA sequencing

Oligonucleotide hybridization can be used to sequence short regions of DNA. In this report, I examine the extent to which this method can be used to sequence genomic DNA, using simulation experiments performed on known human genomic DNA sequences, and show that segments of sequence of up to 800-bp length may be unambiguously sequenced using 65,536 mixed 11-mers. Conventional sequencing or hybridization to specific, longer oligonucleotides can extend this limit in a mixed strategy that can sequence 10-kb DNA sequences with 5-7 conventional sequencing reactions and hybridization to a mixed 12-mer probe array.

Characterizing and sequencing cDNAs using oligonucleotide hybridization

Hybridization of a large panel of oligonucleotides to a target DNA could be used to determine the sequence of that target. The inherent ambiguity of the reconstruction limits the length of DNA that can be sequenced by such an approach. Here I show that constraining the reconstruction by assuming that the target DNA contains an open reading frame allows longer DNAs to be sequenced. In the case of ideal hybridization using mixed 11-mer probes, the amount of DNA that can be sequenced is extended from 700 bases to 2400 bases. This is sufficient to sequence substantial portions of most cDNA clones, and suggests that oligonucleotide hybridization could be a practical method of generating large amounts of sequence data from cDNA libraries.

Current methods of mutation detection

Mutation detection is important in all areas of biology. Detection of unknown mutations can involve sequencing of kilobases of DNA, often in many patients. This has lead to the development of methods to screen DNA for mutations as well as methods to detect previously described mutations. This review discusses current methods used for such purposes with special emphasis on genetic diseases of humans. However, savings can be made by similar means in other areas of biology where repetitive or extensive sequencing for comparative purposes needs to be done. This review covers the methods used for detection of unknown mutations, namely the ribonuclease, denaturing gradient-gel electrophoresis, carbodiimide, chemical cleavage, single-strand conformation polymorphism, heteroduplex and sequencing methods. Once mutations have been defined they can be searched for repeatedly by methods referred to as diagnostic methods. Such methods include allele-specific oligonucleotide hybridization, allele-specific amplification, ligation, primer extension and the artificial introduction of restriction sites. We can now choose from a range of excellent methods, but the choice will usually depend on the background of the laboratory and/or the application in hand. Screening methods are evolving to more satisfactory forms, and the diagnostic methods can be automated to screen whole populations inexpensively.

Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes

An immediately applicable variant of the sequencing by hybridization (SBH) method is under development with the capacity to determine up to 100 million base pairs per year. The proposed method comprises six steps: (i) arraying genomic or cDNA M13 clones in 864-well plates (wells of 2 mm); (ii) preparation of DNA samples for spotting by growth of the M13 clones or by polymerase chain reaction (PCR) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly smaller wells; (iii) robotic spotting of 13,824 samples on an 8 x 12 cm nylon membrane, or correspondingly more, on up to 6 times larger filters, by offset printing with a 96 or 864 0.4 mm pin device; (iv) hybridization of dotted samples with 200-2000 32P-labeled probes comprising 16-256 10-mers having a common 8-mer, 7-mer, or 6-mer in the middle (20 probes per day, each hybridized with 250,000 dots); (v) scoring hybridization signals of 5 million sample-probe pairs per day using storage phosphor plates; and (vi) computing clone order and partial-to-complete DNA sequences using various heuristic algorithms. Genome sequencing based on a combination of this method and gel sequencing techniques may be significantly more economical than gel methods alone.

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models

An efficient method was developed for making complete sets of oligonucleotides of defined length, covalently attached to the surface of a glass plate, by synthesizing them in situ. A device carrying all octapurine sequences was used to explore factors affecting molecular hybridization of the tethered oligonucleotides, to develop computer-aided methods for analyzing the data, and to test the feasibility of using the method for sequence analysis. Further development is needed before the method can be used routinely, but our work shows that it has a number of potential advantages over gel-based methods: it should be easy to automate; the quality of the sequence results can be evaluated statistically; it provides a powerful way of comparing related sequences and detecting mutation; it can be applied to both DNA and RNA; and specific motifs can be incorporated into all sequences of the array to focus analysis on sequences of biological interest.