Reversible DNA codes from skew cyclic codes over a ring of order 256

We introduce skew cyclic codes over the finite ring $\R$, where $u^{2}=0,v^{2}=v,w^{2}=w,uv=vu,uw=wu,vw=wv$ and use them to construct reversible DNA codes. The 4-mers are matched with the elements of this ring. The reversibility problem for DNA 4-bases is solved and some examples are provided

On DNA Codes Over the Non-Chain Ring Z4+uZ4+u2Z4\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4 with u3=1u^3=1

In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first study and analyze a distance conserving map defined over the ring $R$ into the length-$3$ DNA sequences. Then, we derive some conditions on the generator matrix of a linear code over $R$, which leads to a DNA code with reversible, reversible-complement, homopolymer $2$-run-length, and $\frac{w}{3n}$-GC-content constraints for integer $w$ ($0\leq w\leq 3n$). Finally, we propose a new construction of DNA codes using Reed-Muller type generator matrices. This allows us to obtain DNA codes with reversible, reversible-complement, homopolymer $2$-run-length, and $\frac{2}{3}$-GC-content constraints.Comment: This paper has been presented in IEEE Information Theory Workshop (ITW) 2022, Mumbai, INDI

On Conflict Free DNA Codes

DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a special constraint. Each codeword of the DNA code has a specific property that any two consecutive sub-strings of the DNA codeword will not be the same (a generalization of homo-polymers constraint). This is in addition to the usual constraints such as Hamming, reverse, reverse-complement and $GC$-content. We believe that the new constraint will help further in reducing the errors during reading and writing data into the synthetic DNA strings. We also present a construction (based on a variant of stochastic local search algorithm) to calculate the size of the DNA codes with all the above constraints, which improves the lower bounds from the existing literature, for some specific cases. Moreover, a recursive isometric map between binary vectors and DNA strings is proposed. Using the map and the well known binary codes we obtain few classes of DNA codes with all the constraints including the property that the constructed DNA codewords are free from the hairpin-like secondary structures.Comment: 12 pages, Draft (Table VI and Table VII are updated

Transcriptional response of O⁶-methylguanine methyltransferase deficient yeast to methyl-N-nitro-N-nitrosoguanidine (MNNG)

Thesis (S.M.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004.Includes bibliographical references (leaves 66-75).(cont.) of transcription factors and subsequently, induction of RNA processing (35% of genes incrementally induced) and kinases involved in protein phosphorylation. In the WT, the response was restricted to a transient repression of fundamental biochemical processes. Interestingly, a gene whose repression is known to mimic apoptosis was found to be repressed in the WT. The overwhelming induction of ribosomal protein synthesis genes in both WT and mgtl in response to MNNG is an unexpected result that could signify a successful recovery following wide-spread cellular damage.Damage to DNA can occur by means of endogenous biochemical processes or exogenous chemicals such as alkylating agents. If left unrepaired, alkylated bases, most notably, O⁶ Methylguanine (O⁶MeG) can be mutagenic and cytotoxic to the cell. Luckily, DNA methyltransferase (encoded by the gene MGT1 in yeast), repairs this damage. By using transcriptional profiling as a tool, an attempt to elucidate the role of MGT1 has been made. First, the basal expression profile of the mgtl was established. Then, the response of wild-type (WI) yeast and yeast lacking MGT1 (mgt1) to the alkylating agent, MNNG was studied using exponentially growing WT and mgti cultures which were exposed to 30[mu]g/ml of MNNG for 10 to 60 minutes. Basal expression profile of yeast lacking MGT1 showed up-regulation of RETV7, a gene implicated in spontaneous mutagenesis. Response to MNNG was invoked immediately and was dramatic and widespread involving 30% of the genome in both WT and mgt1. Cell-cycle checkpoints, damage signal amplifiers, DNA repair genes (nucleotide excision repair, photoreactive repair, mismatch repair) and chromatin remodeling genes were induced. Genes involved in maintaining mitochondrial structure and mitochondrial genome were also induced. Intriguingly, RPN4, a key regulator of proteasomal system was found to be repressed. Environmental stress response genes were culled out to examine the effects of MNNG on WT and mgtl, more carefully. Temporal gene expression profiles in WT and mgtl were informative in delineating differences in the distinct responses mounted by WT and mgtl. The magnitude of response in mgt1 is more profound than in WT. The differences in the dynamic trends between the two suggest that mgt1 initiates a coordinated response involving repressionby Anoop Rao.S.M