scholarly journals Utilizing DNA Strands for Secured Data-Hiding with High Capacity

2017 ◽  
Vol 11 (2) ◽  
pp. 88
Author(s):  
Samiha Abdelrahman Mohammed Marwan ◽  
Ahmed Shawish ◽  
Khaled Nagaty
Keyword(s):  
Dna Sequence ◽  
Data Storage ◽  
Data Extraction ◽  
High Capacity ◽  
Security Level ◽  
Full Data ◽  
High Data ◽  
Dna Strands ◽  
To Come ◽  
Dna Strand

There are continuous threats to network technologies due to its rapidly-changing nature, which raises the demand for data-safe transmission. As a result, the need to come up with new techniques for securing data and accommodating the growing quantities of information is crucial. From nature to science, the idea that genes themselves are made of information stimulated the research in molecular deoxyribonucleic acid (DNA). DNA is capable of storing huge amounts of data, which leads to its promising effect in steganography. DNA steganography is the art of using DNA as an information carrier which achieves high data storage capacity as well as high security level. Currently, DNA steganography techniques utilize the properties of only one DNA strand, since the other strand is completely dependent on the first one. This paper presents a DNA-based steganography technique that hides data into both DNA strands with respect to the dependency between the two strands. In the proposed technique, a key of the same length of the reference DNA sequence is generated after using the second DNA strand. The sender sends both the encrypted DNA message and its reference DNA sequence together into a microdot. If the recipient receives this microdot uncontaminated, the sender can safely send the generated key afterwards. The proposed technique doubles the amount of data stored and guarantees a secure transmission process as well, for even if the attacker suspects the first-sent DNA sequence, they will never receive the key, and hence full data extraction is nearly impossible. The conducted experimental study confirms the effectiveness of the proposed.

scholarly journals New Levenshtein-Marker Code for DNA-based Data Storage Capable of Correcting Multiple Edit Errors

2021 ◽  
Author(s):  
Yan Zihui ◽  
Cong Liang
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Error Rate ◽  
Decoding Algorithm ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Dna Strands ◽  
Marker Code ◽  
Dna Strand ◽  
Term Data

With the development of DNA synthesis and sequencing technologies, DNA becomes a promising medium forlong-term data storage. Three types of errors may occur in the DNA strand, insertions, deletions and substitutions,which we collectively call edit errors. It is still challenging to design a code that can correct multiple edit errors onnon-binary alphabets. In this paper, we propose a new coding schema for correcting multiple edit errors on DNAstrands by splitting the whole strand into consecutive blocks with appropriate length and correcting a single editerror in each block. Our method, called theDNA-LMcode, could be considered a generalization of the Levenshteincode combined with the marker code. We provide a linear encoding and decoding algorithm for ourDNA-LMcode.Compared to other encoding methods for DNA strands of several hundred base-pairs, ourDNA-LMcode achievedsimilar code rates and a much lower average nucleotide error rate in decoding.

scholarly journals New Levenshtein-Marker Code for DNA-based Data Storage Capable of Correcting Multiple Edit Errors

2021 ◽  
Author(s):  
Yan Zihui ◽  
Cong Liang
Keyword(s):  
Dna Synthesis ◽  
Data Storage ◽  
Error Rate ◽  
Decoding Algorithm ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Dna Strands ◽  
Marker Code ◽  
Dna Strand ◽  
Term Data

With the development of DNA synthesis and sequencing technologies, DNA becomes a promising medium forlong-term data storage. Three types of errors may occur in the DNA strand, insertions, deletions and substitutions,which we collectively call edit errors. It is still challenging to design a code that can correct multiple edit errors onnon-binary alphabets. In this paper, we propose a new coding schema for correcting multiple edit errors on DNAstrands by splitting the whole strand into consecutive blocks with appropriate length and correcting a single editerror in each block. Our method, called theDNA-LMcode, could be considered a generalization of the Levenshteincode combined with the marker code. We provide a linear encoding and decoding algorithm for ourDNA-LMcode.Compared to other encoding methods for DNA strands of several hundred base-pairs, ourDNA-LMcode achievedsimilar code rates and a much lower average nucleotide error rate in decoding.

scholarly journals CLE against SOA with Better Data Security Storage to Cloud 5G

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Huige Wang ◽  
Xing Chang ◽  
Kefei Chen
Keyword(s):  
Data Storage ◽  
Data Privacy ◽  
Privacy Preservation ◽  
Smart Cities ◽  
Security Level ◽  
High Data ◽  
Security Proof ◽  
Security Standard ◽  
Soa Security

Cloud 5G and Cloud 6G technologies are strong backbone infrastructures to provide high data rate and data storage with low latency for preserving QoS (Quality of Service) and QoE (Quality of Experience) in applications such as driverless vehicles, drone-based deliveries, smart cities and factories, remote medical diagnosis and surgery, and artificial-intelligence-based personalized assistants. There are many techniques to support the aforementioned applications, but for privacy preservation of Cloud 5G, the existing methods are still not sufficient. Public key encryption (PKE) scheme is an important means to protect user data privacy in Cloud 5G. Currently, the most common PKE used in Cloud 5G is CCA or CPA secure ones. However, its security level maybe not enough. SOA security is a stronger security standard than CPA and CCA. Roughly speaking, PKE with SOA security means that the adversary is allowed to open a subset of challenger ciphertexts and obtains the corresponding encrypted messages and randomness, but the unopended messages and randomness remain secure in the rest of the challenger ciphertexts. Security against SOA in PKEs has been a research hotspot, especially with the wide discussion in Cloud 5G. We revisited the SOA-CLE and proposed a new security proof, which is more concise and user friendly to understand privacy preservation in Cloud 5G applications.

scholarly journals NOREC4DNA: using near-optimal rateless erasure codes for DNA storage

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peter Michael Schwarz ◽  
Bernd Freisleben
Keyword(s):  
Data Storage ◽  
Dna Sequences ◽  
Storage Systems ◽  
High Capacity ◽  
Digital Data ◽  
Erasure Codes ◽  
Software Framework ◽  
Digital Information ◽  
Dna Storage ◽  
Dna Strands

Abstract Background DNA is a promising storage medium for high-density long-term digital data storage. Since DNA synthesis and sequencing are still relatively expensive tasks, the coding methods used to store digital data in DNA should correct errors and avoid unstable or error-prone DNA sequences. Near-optimal rateless erasure codes, also called fountain codes, are particularly interesting codes to realize high-capacity and low-error DNA storage systems, as shown by Erlich and Zielinski in their approach based on the Luby transform (LT) code. Since LT is the most basic fountain code, there is a large untapped potential for improvement in using near-optimal erasure codes for DNA storage. Results We present NOREC4DNA, a software framework to use, test, compare, and improve near-optimal rateless erasure codes (NORECs) for DNA storage systems. These codes can effectively be used to store digital information in DNA and cope with the restrictions of the DNA medium. Additionally, they can adapt to possible variable lengths of DNA strands and have nearly zero overhead. We describe the design and implementation of NOREC4DNA. Furthermore, we present experimental results demonstrating that NOREC4DNA can flexibly be used to evaluate the use of NORECs in DNA storage systems. In particular, we show that NORECs that apparently have not yet been used for DNA storage, such as Raptor and Online codes, can achieve significant improvements over LT codes that were used in previous work. NOREC4DNA is available on https://github.com/umr-ds/NOREC4DNA. Conclusion NOREC4DNA is a flexible and extensible software framework for using, evaluating, and comparing NORECs for DNA storage systems.

scholarly journals Targeting of the Activation-Induced Cytosine Deaminase Is Strongly Influenced by the Sequence and Structure of the Targeted DNA

2005 ◽  
Vol 25 (24) ◽  
pp. 10815-10821 ◽  
Author(s):  
Hong Ming Shen ◽  
Sarayu Ratnam ◽  
Ursula Storb
Keyword(s):  
Dna Sequence ◽  
Somatic Hypermutation ◽  
Cytosine Deaminase ◽  
Target Sequence ◽  
Cytosine Deamination ◽  
Dna Strands ◽  
Activation Induced Deaminase ◽  
Dna Strand

ABSTRACT Activation-induced deaminase (AID) initiates immunoglobulin somatic hypermutation (SHM). Since in vitro AID was shown to deaminate cytosines on single-stranded DNA or the nontranscribed strand, it remained a puzzle how in vivo AID targets both DNA strands equally. Here we investigate the roles of transcription and DNA sequence in cytosine deamination. Strikingly different results are found with different substrates. Depending on the target sequence, the transcribed DNA strand is targeted as well as or better than the nontranscribed strand. The preferential targeting is not related to the frequency of AID hot spots. Comparison of cytosine deamination by AID and bisulfite shows different targeting patterns suggesting that AID may locally unwind the DNA. We conclude that somatic hypermutation on both DNA strands is the natural outcome of AID action on a transcribed gene; furthermore, the DNA sequence or structure and topology play major roles in targeting AID in vitro and in vivo. On the other hand, the lack of mutations in the first ∼100 nucleotides and beyond about 1 to 2 kb from the promoter of immunoglobulin genes during SHM must be due to special conditions of transcription and chromatin in vivo.

scholarly journals 3′ → 5′ Exonucleases of DNA Polymerases ϵ and δ Correct Base Analog Induced DNA Replication Errors on Opposite DNA Strands in Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 717-726 ◽  
Author(s):  
Polina V Shcherbakova ◽  
Youri I Pavlov
Keyword(s):  
Dna Replication ◽  
Dna Polymerases ◽  
Replication Errors ◽  
Dna Strands ◽  
Base Analog ◽  
Chromosome Iii ◽  
Dna Strand ◽  
Dna Replication Errors ◽  
Yeast Mutants ◽  
Lagging Strand

Abstract The base analog 6-N-hydroxylaminopurine (HAP) induces bidirectional GC → AT and AT → GC transitions that are enhanced in DNA polymerase ϵ and δ 3′ → 5′ exonuclease-deficient yeast mutants, pol2-4 and pol3-01, respectively. We have constructed a set of isogenic strains to determine whether the DNA polymerases δ and ϵ contribute equally to proofreading of replication errors provoked by HAP during leading and lagging strand DNA synthesis. Site-specific GC → AT and AT → GC transitions in a Pol→, pol2-4 or pol3-01 genetic background were scored as reversions of ura3 missense alleles. At each site, reversion was increased in only one proofreading-deficient mutant, either pol2-4 or pol3-01, depending on the DNA strand in which HAP incorporation presumably occurred. Measurement of the HAP-induced reversion frequency of the ura3 alleles placed into chromosome III near to the defined active replication origin ARS306 in two orientations indicated that DNA polymerases ϵ and δ correct HAP-induced DNA replication errors on opposite DNA strands.

scholarly journals Nanoscale optical writing through upconversion resonance energy transfer

2021 ◽  
Vol 7 (9) ◽  
pp. eabe2209
Author(s):  
S. Lamon ◽  
Y. Wu ◽  
Q. Zhang ◽  
X. Liu ◽  
M. Gu
Keyword(s):  
Graphene Oxide ◽  
Energy Transfer ◽  
Energy Consumption ◽  
Data Storage ◽  
High Capacity ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
High Energy ◽  
Optical Data ◽  
Upconversion Nanoparticles

Nanoscale optical writing using far-field super-resolution methods provides an unprecedented approach for high-capacity data storage. However, current nanoscale optical writing methods typically rely on photoinitiation and photoinhibition with high beam intensity, high energy consumption, and short device life span. We demonstrate a simple and broadly applicable method based on resonance energy transfer from lanthanide-doped upconversion nanoparticles to graphene oxide for nanoscale optical writing. The transfer of high-energy quanta from upconversion nanoparticles induces a localized chemical reduction in graphene oxide flakes for optical writing, with a lateral feature size of ~50 nm (1/20th of the wavelength) under an inhibition intensity of 11.25 MW cm−2. Upconversion resonance energy transfer may enable next-generation optical data storage with high capacity and low energy consumption, while offering a powerful tool for energy-efficient nanofabrication of flexible electronic devices.

scholarly journals Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double Strand

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3986
Author(s):  
Cécilia Hognon ◽  
Antonio Monari
Keyword(s):  
Dna Cleavage ◽  
Catalytic Mechanism ◽  
Dna Lesions ◽  
Cleavage Reaction ◽  
Dynamic Simulations ◽  
Important Target ◽  
System Adaptation ◽  
Dna Strands ◽  
Dna Strand ◽  
Dna Substrate

Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.

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