GC-balanced polar codes correcting insertions, deletions and substitutions for DNA storage

Functional proteins coded by genes 46 and 47 are required for (i) continuation of deoxyribonucleic acid (DNA) synthesis in the late period of T4 infection and (ii) production of normal, late replicating DNA which contains strands with a sedimentation coefficient in alkaline sucrose greater than that of mature DNA (73S). Continued DNA synthesis in the late period in the absence of functional genes 46 or 47 can be achieved by inhibiting late protein synthesis either by using bacterio-phage with a second mutation in gene 55 or by adding chloramphenicol to the culture before the decline in the rate of DNA synthesis. However, when functional 46/47 proteins are absent throughout infection, no strands with a sedimentation coefficient greater than 73S (in alkaline sucrose) are produced. This is the case even when DNA synthesis is allowed to continue. DNA arrest is accompanied by conversion of rapidly sedimenting, replicating DNA to slower sedimenting forms. When 46/47 is absent from the beginning of infection, the conversion product has a smaller sedimentation coefficient than mature DNA both in neutral and alkaline sucrose. When DNA arrest occurs midway in infection by heat-inactivating the ts46 enzyme, the conversion product has a sedimentation coefficient (i) the same as mature DNA in both neutral (63S) and alkaline sucrose if capsid assembly is allowed to take place and (ii) close to 63S in neutral sucrose but heterogenous and relatively greater (up to 100S) in alkaline sucrose if capsid assembly is inhibited. The structure of this DNA is unknown.

A photochemical/chemical direct method of synthesizing high-performance deoxyribonucleic acid chips for rapid and parallel gene analysis

Convolutionally precoded polar codes known as polarization-adjusted convolutional (PAC) codes are a promising variant of polar codes for short block lengths. The precoding in PAC codes has demonstrated an effective reduction in the number of minimum weight codewords (a.k.a error coefficient) of polar codes. This reduction potentially improves the error correction performance significantly. From a codeword formation perspective, this reduction has limitations. Capitalizing on the understanding of the decomposition of minimum-weight codewords, this paper proposes a new coding scheme called reverse PAC (RPAC) codes that can effectively reduce minimum-weight codewords more than in PAC codes. Additionally, we propose a look-ahead list decoding for the RPAC codes, which maintains the same order of complexity as list decoding in PAC codes. Numerical results demonstrate that RPAC codes achieve significant improvements in block error rate over polar and PAC codes, especially in high-rate short-code scenarios where existing schemes are less effective.

Technology is transforming rapidly. Security during data transmission is an increasingly critical and essential factor for the integrity and confidentiality of data in the financial domain, such as e-commerce transactions and bank transactions, etc. We cannot overestimate the importance of encryption/decryption of information in the digital economy. The need to strengthen and secure the digital economy is urgent. Cryptography maintains the security and integrity of data kept on computers and data communicated over the internet using encryption/decryption. A new concept in cryptography named DNA cryptography has attracted the interest of information security professionals. The DNA cryptography method hides data using a DNA sequence, with DNA encryption converting binary data into the DNA sequence. Deoxy Ribonucleic Acid (DNA) is a long polymer strand having nitrogen bases adenine (A), thymine (T), cytosine (C), and guanine (G), which play an important role in plain text encoding and decoding. DNA has high storage capacity, fast processing, and high computation capacity, and is more secure than other cryptography algorithms. DNA cryptography supports both symmetric and asymmetric cryptography. DNA cryptography can encrypt numeric values, English language and unicast. The main aim of this paper is to explain different aspects of DNA cryptography and how it works. We also compare different DNA algorithms/methods proposed in a previous paper, and implement DNA cryptography using one-time pad (OTP) and amino acid sequence using java language. OTP is used for symmetric key generation and the DNA sequence is converted to an amino acid sequence to create confusion.

Due to the unsatisfactory block error rate (BLER) performance of short or moderate block , the further development of polar codes is limited. In this paper, the parity-check codes concatenated cyclic redundancy check aided successive cancellation list (CA-SCL) decoding algorithms are studied. Then, an efficient concatenated method, double-parity-check CA-SCL (DP-CA-SCL) polar codes, is proposed according to exiting parity-check decoding algorithms. Not only can this new method improve the BLER performance in short or moderate block, but also it can guarantee the reduction of complexity relative to original CA-SCL method. The simulations in additive white Gaussian noise channel with binary phase shift keying modulation reveal that the DP-CA-SCL polar codes can provide significant performance gains. Comparing to the original CA-SCL decoding, there are 0.5 dB performance gains using proposed method at BLER of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> with (128, 64) polar codes. For another moderate block (256, 128) polar codes, it can also guarantee performance gains at least 0.18 dB.

As the next generation sequencing and deoxyribonucleic acid (DNA) synthesis technologies rapidly develop, DNA engineering became faster and cheaper with higher accuracy than before. External information such as secret messages or digital archives can be embedded into the DNA sequence by mutating its molecular sequence according to a certain algorithm. This study presents a sector‐based DNA steganography method using non‐coding regions of the DNA sequence as the host for carrying binary data. The aim of the sector‐based embedding is to have a high level of security, data capacity, and error handling while preserving the organism's life information. A sector consists of reference bases, segmented message bases, and parity bases. The parity bases can detect and handle mutation errors in each sector. The sector length controls the data capacity and security. Our in silico experiments verified that the bit‐per‐nucleotide of our method can be [1.2, 2.0] by controlling the sector length, which is 0.2 point higher than that of conventional methods. As many as 104 base mutations in the DNA sequence can be handled for perfect message retrieval. Furthermore, the probability for message detection without keys is lower than 1.3949 × 10−62, which is very low. Copyright © 2016 John Wiley &amp; Sons, Ltd.

Deoxyribonucleic acid (DNA) synthesis was examined in asynchronous and synchronous cultures of a number of cdc (cell division cycle) temperature-sensitive mutant strains. The kinetics of DNA synthesis after a shift to the restrictive temperature was compared with that obtained after inhibition of protein synthesis at the permissive temperature, a condition that specifically blocks the initiation of new rounds of DNA replication, but does not block those in progress. Mutations in three genes (cdc 4, 7, and 28) appear to block a precondition for DNA synthesis since cells carrying these lesions cannot start new rounds of DNA replication after a shift from permissive to restrictive temperature, but can finish rounds that were in progress. These three genes are classified as having roles in the "initiation" of DNA synthesis. Mutations in two genes (cdc 8 and 21) block DNA synthesis, itself, since cells harboring these lesions that had started DNA synthesis at the permissive temperature arrest synthesis abruptly upon a shift to the restrictive temperature. Mutations in 13 other cdc genes do not impair DNA synthesis in the first cell cycle at the restrictive temperature.

The products of the deoxyribonucleic acid (DNA) polymerase associated with Rous sarcoma virus and avian myeloblastosis virus were characterized by correlative analyses with equilibrium centrifugation and stepwise elution from hydroxyapatite. The initial enzymatic product consists of nascent DNA chains which are hydrogen-bonded to 70S viral ribonucleic acid (RNA), whereas the final enzymatic product is double-stranded DNA. Appreciable amounts of free single-stranded DNA were not detected at any point during the course of the enzymatic reaction, but the data in this regard are not decisive. The time course of synthesis of DNA:RNA hybrids and double-stranded DNA has been analyzed. It is concluded that the synthesis of double-stranded DNA is a sequel to and is probably dependent upon the synthesis of DNA:RNA hybrid.

The regulation of gene expression is controlled by multiple mechanisms. The primary level of control is embedded within the sequence itself, as the transcription factors bind specific deoxyribonucleic acid (DNA) sequences at the gene regulatory regions and either activate or silence the genes. A secondary level of control includes enhancer sequences, which may lie megabases away from the gene and are necessary for the induction of gene expression in the human genome 1. A third level of control is the three-dimensional structure of chromatin, which can bring enhancers and promoters into contact with one another and can be restricted by the CCCTC-binding factor (CTCF) that insulates chromatin segments into topologically associated domains. A number of novel methodological approaches have recently hastened characterisation of the regulatory elements in the genome 2. One commonly used approach is to couple the chromatin immunoprecipitation sequencing of the transcription factors with gene expression profiling to study the transcription factor fusion targets in leukaemia 3, 4. In comparison, the assay named global nuclear run-on sequencing allows simultaneous exploration of the dynamics of gene expression and regulatory element activity. In a cell model with inducible ETS variant 6-runt-related transcription factor 1 (ETV6-RUNX1) fusion, we were able to follow up the interplay of the enhancer elements and their host genes that occur downstream of this structural variation, which is the most common one found in childhood leukaemias 5. The ETV6-RUNX1 fusion bound the predominantly RUNX1 motif containing DNA sequences and caused repression of the enhancer activity as measured by the enhancer ribonucleic acid (RNA) levels. Interestingly, in most cases, the repression at the enhancers led to lower transcription at the nearby gene loci. In particular, the ETV6-RUNX1 aberration predominantly altered the expression of genes regulating B-cell adhesion and signalling. Furthermore, we noted a significantly higher repression of cluster of differentiation (CD)19/20 associated super-enhancers, in comparison with stem cell-linked CD34 super-enhancers 5. Super-enhancers are regions of the genome with clusterings of multiple enhancer sites and are deemed essential for lineage specification 6. They could provide a possible explanation for the disruption of B-cell differentiation, which is a hallmark of precursor leukaemias. A significant number of somatic mutations in leukaemia are located outside the coding regions of the genome. Mansour et al. 7 identified a small insertional mutation in a regulatory element at the T-cell acute lymphocytic leukaemia protein 1 (TAL1) gene locus in patients with T-cell acute lymphoblastic leukaemia. The mutation introduced a novel transcription factor binding site, for transcription factor myeloblastosis (MYB), thereby creating an aberrant super-enhancer that led to gross overexpression of the TAL1 gene. Such changes at the binding sites may also be inherited, as exemplified by the risk of neuroblastomas associated with a common single nucleotide polymorphism that alters a site where GATA transcription factors bind with DNA in a super-enhancer region of the LIM domain-only 1 (LMO1) gene 8. Moreover, the regulatory boundaries at the oncogene loci may be lost during disruption of the CTCF binding sites by mutations, as shown in T-cell acute lymphoblastic leukaemia 9, which leads to aberrant transcriptional activity. In addition to explaining the aberrant activation of oncogenes in leukaemic cells, highly active enhancers may create genetic instability. We explored the transcriptional features associated with structural variation sites in precursor B-cell leukaemias, which are represented by deletions, insertions, translocations and inversions. Structural variation sites tended to accumulate at certain loci in the leukaemia genomes and were more prevalent at actively transcribed regions. We discovered that simultaneous transcription from both DNA strands was often associated with these recurring structural variation sites 10. Enhancers that overlapped gene regions displayed this feature, which was accompanied by polymerase II stalling, access to DNA cleavage motifs and R-loop formation, a DNA:RNA hybrid formed during the transcription, which could lead to double-stranded DNA breaks that promote off-target cleavage by recombination-activating genes and activation-induced cytidine deaminase complexes. Stalled polymerases were found within the first intron of many key regulators of cell differentiation and tumour suppressor genes, including paired box protein 5 (PAX5) and B-cell translocation gene 1 (BTG1) protein 10, 11. The preleukaemic cells arrested at the pre-B stage are thereby vulnerable to secondary lesions at such genomic regions. Taken together, these observations highlighted that altered activity or mutations in both coding and noncoding regions can have a profound effect on the regulatory network that governs lymphoid cell differentiation. With the power of ever-developing sequencing techniques, these alterations, which may lead to childhood leukaemia, are now being elucidated at a genomewide scale. It is also tempting to speculate that the detection of changes in the regulatory elements of the genome might guide us to put patients in more specific stratifications as well as increase our understanding of the leukaemia as a disease.

Solid nanopore-based deoxyribonucleic acid (DNA) sequencing has led to low-cost, fast, reliable, controlled, and amplified or label-free and high-resolution recognition and identification of DNA nucleotides. Solid-state materials and biological nanopores have a low signal-to-noise ratio (SNR) and generally are too thick to read at single-nucleotide resolution. The issue with solid-state nanopores is that the DNA strands stick to the nanopore sides and on the surface during the translocation process. The coexistence of DNA nucleotides on the surface and the nanopore sides will complicate the ionic current signals, making nucleotide detection difficult. Therefore, different sized nanogaps can be promising to overcome some of these issues. Using all-atom molecular dynamics (MD) simulations, we have studied the translocation of single-stranded (ss) DNA through solid-state nanogaps embedded in a graphene membrane device. A nucleotide-specific DNA sequencing technique is proposed based on unique differences in the ionic current responses for all the four ssDNA nucleotides (dAMP16, dGMP16, dTMP16, and dCMP16). As the individual homogeneous ssDNA translocate through the nanogaps, characteristic changes are observed in the ionic current. Our results show that ssDNA nucleotides can translocate through the proposed graphene nanogap devices by applying an external electric field. In addition, the sticking issue can be resolved using graphene nanogaps during the ssDNA translocation processes. Therefore, the significant difference in ionic current sensitivity and the translocation event/time yielded by the graphene nanogap-based devices reveal possibilities for utilizing it for ultrafast nanogap-based DNA sequencing.

Bacterial deoxyribonucleic acid (DNA) polymerase I is a family of enzymes involved in bacterial DNA synthesis and lesion repair. These enzymes have a multidomain structure, consisting of a single polypeptide chain that encompasses a distinct polymerase domain, a proofreading 3′–5′ exonuclease and/or a 5′–3′ exonuclease activity. Members of the polymerase I family have been investigated extensively, both because of their vital role in replicating and maintaining bacterial chromosomes, and because of their importance as tools in molecular biology, in particular for the polymerase chain reaction (PCR) and DNA sequencing. Studies on the Escherichia coli DNA polymerase I in particular have yielded significant insights into the mechanism of DNA polymerisation which is shared by almost all other nucleotide polymerases. Key Concepts: Bacterial DNA polymerase I enzymes are multidomain proteins with separate polymerisation, proofreading and 5′–3′ exonuclease functions. They perform a vital function in bacteria by carrying out DNA repair and some aspects of chromosomal replication. Polymerases incorporate one nucleotide at a time to the 3′ end of the primer DNA strand in a template‐directed manner. Members of the DNA polymerase I family are able to replicate DNA with far greater accuracy than base pairing alone can account for. The polymerisation reaction is a multistep process during which the enzyme switches between substrate binding and nucleotide incorporation conformations. The 5′–3′ exonuclease allows the polymerase to degrade RNA primers and to assist with DNA repair. Thermostable family I DNA polymerases are used extensively in polymerase chain reaction to amplify DNA and for DNA sequencing.

The synthesis of deoxyribonucleic acid (DNA) during in vivo infection of chick epithelium with fowlpox virus was examined by incorporation of tritiated thymidine into the acid-insoluble fraction. The proportion of precursor incorporated into host and viral DNA at various times after infection was determined by chromatography on columns of methylated albumin-kieselguhr. The first 60-hr period of infection was characterized by the synthesis of predominantly host DNA, the rate of production of which increased markedly over the control between 36 and 48 hr postinoculation (PI). Although the replication of viral DNA began between 12 and 24 hr PI, the rate of synthesis was very low during the first 60 hr. In contrast, an abrupt increase in the rate of viral DNA synthesis occurred between 60 and 72 hr PI, concomitantly with a sharp decline of host DNA synthesis. Subsequently, between 72 and 96 hr, the ratio of synthesis of viral DNA to host DNA progressively increased to a maximum of greater than 2:1. The temporal relationship of this biphasic pattern of host and viral DNA synthesis to hyperplasia and viral replication is discussed.

The effects of treatment with live or inactivated Shope fibroma virus on host cell deoxyribonucleic acid (DNA) synthesis were determined. The incorporation of (3)H-thymidine into nuclear DNA was suppressed by both active and inactivated virus, although live virus was more effective. During the early phase of infection, stimulation of host nuclear DNA synthesis of up to 240% of control value was observed in cells infected with active virus. Inhibition of DNA synthesis began at about the 8th h and was maximal by 12 h postinfection. Virus inactivated by ultraviolet-irradiation or heat treatment did not induce viral DNA synthesis but was, nevertheless, able to suppress host DNA synthesis.

A promoter is a brief stretch of DNA (100–1,000 bp) where RNA polymerase starts to transcribe a gene. A DNA (Deoxyribonucleic Acid) base pair is a fundamental unit of DNA structure and represents the pairing of two complementary nucleotide bases within the DNA double helix. The four DNA nucleotide bases are adenine (A), thymine (T), cytosine (C), and guanine (G). DNA base pairs are the building blocks of the DNA molecule, and their complementary pairing is central to the storage and transmission of genetic information in all living organisms. Normally, a promoter is found at the 5′ end of the transcription initiation site or immediately upstream. Numerous human disorders, particularly diabetes, cancer, and Huntington’s disease, have been shown to have DNA promoter as their root cause. The scientific community has long been interested in learning crucial information about protein-coding genes. Finding the promoters is therefore the first step in finding genes in DNA sequences. The scientific world has always been attracted by the effort to glean crucial knowledge about protein-coding genes. Consequently, identifying promoters has emerged as an intriguing challenge that has caught the interest of numerous researchers in the field of bioinformatics. We proposed Gaussian Decision Boundary Estimation in machine learning models to detect transcription start sites (promoters) in the DNA sequences of a common bacteria, Escherichia coli. The best features are identified through a score-based function to select relevant nucleotides that are directly responsible for promoter recognition, in order maximise the models’ performance. The Gaussian Decision Boundary Estimation based support-vector-machine model is trained with these features and finds the best hyperplane that separates the data into different classes. Throughout this study, promoter regions could be identified with high accuracy 99.9% which is better compared to other state of art algorithms. The comparison of machine learning classification models is another major emphasis of this paper in order to identify the model that most accurately predicts DNA sequence promoters. It provides analysis for further biological research as well as precision medicine.

Deoxyribonucleic acid (DNA) profiling uses various molecular biological techniques to identify, classify, and study the ecology and evolution of organisms based on differences in DNA sequence. These differences in DNA sequence are known as polymorphisms, which may be as simple as a single nucleotide at a given nucleotide position within the genome or as complex as variant numbers of tandem repeat sequences or the presence of an interspersed repetitive element. Individuals, populations or species‐specific DNA polymorphisms are used as targets to generate fingerprint patterns suitable for the differentiation of individuals and populations. Data generated by DNA profiling methods are used to provide quantitative or qualitative information for population genetics, human diseases, diversity, phylogeny, epidemiological, forensics and conservation management purposes. Key Concepts: DNA profiling methodologies allow for the classification of organisms based on polymorphisms in DNA sequences at a given loci. DNA profiling methods that can be used to detect single nucleotide and repetitive element polymorphisms include: amplified and restriction fragment length polymorphisms (AFLP/RFLP), multilocus fingerprinting using hybridisation, random amplified polymorphic DNA and denaturing gradient and pulse field gel electrophoresis (DGGE/PFGE). DNA profiling patterns can be used to identify individuals, determine kinship and genealogy, examine inbreeding, and bottlenecks and differentiate populations.