Directed self-assembly of genomic sequences into monomeric and polymeric branched DNA structures† Ashok K. Nayak ab and Umakanta Subudhi * ab It is demonstrated that error-free hybridization between primers and its complementary sequences can act as the driving force to construct monomeric as well as polymeric branched DNA materials by molec- ular self-assembly. The mechanism, stability and application of the self-assembled products have been described. Deoxyribonucleic acid, the master molecule of heredity, is now considered as a powerful material in the eld of nanoscale engineering. 1 In the last 31 years, DNA hybridization-based self- assembly principles have been extensively explored to generate diverse nanostructures, 2 three dimensional objects, 3 DNA nanomachines, 4 and assembled nanomaterials. 5 Particularly, the breakthrough came with the concept of ‘DNA origami’, in which a long scaffold strand of M13 phage genome was folded with the help of hundreds of short staple strands into dened 2D shapes. 1b However, the development of more advanced structures and applications will require a number of issues to be addressed. The most signicant of which is the high-error rate of self-assembly. 6 We are interested in approaching the above issue in an alternative perspective. The error-free hybridization between primers (or probes) and its complementary sequences can be utilized for construction of DNA nanostructure. Such oligonucleotides have already proven to be highly specic during polymerase chain reaction, 7 microarrays 8 and in situ hybridization. 9 In cDNA synthesis or probe-hybridization reac- tion, a particular oligo selectively binds to its complementary sequences in the presence of thousands of diverse mRNAs. In the present study, these oligos are explored for molecular self- assembly. Moreover, evolutionary stable genomic DNA is the mother of all structural and functional diversities of protein, ribozyme, and different RNAs; hence, numerous stable nanostructures with diverse functions can be designed utilizing the genomic sequences for the application in DNA nanotechnology. Various structural and functional DNA tiles, 2D DNA origami and super- origami structures can thus be attained using linear genomic sequences as building blocks. In this communication, a remarkably simple strategy has been presented for the designing of oligos from the genomic sequences of Rattus norvegicus for the generation of monomeric and polymeric branched DNA (bDNA) materials. Hybridizing portion of each oligo was derived from the primers of different genes (b-actin, catalase, G3PDH, SOD1 and SOD2), which we have earlier 10 used for gene expression studies (Scheme 1). Currently, two sets of four oligos with 3T or 5T in the loop were designed to self-assemble for rigid or exible monomeric structure (Table 1, Fig. S1†). Since consecutive oligos have nearly 50% complementarity, self-assembly between two oligos either results into internal bubble or external single stranded overhangs (Scheme 2). Each monomer contains 15 nt long overhangs for the self-assembly to occur in one plane to form the two-dimensional arrays of polymeric bDNA materials. 11 A quick self-assembly process was followed for the generation of bDNA structures. 12 The mechanism, stability and application of the self-assembled products have been demonstrated through Scheme 1 Sequence design of the 4 oligos (strands A, B, C, and D with 3T loop and E, F, G, and H with 5T loop). The four different strands are derived from exon regions of b-actin, SOD1, SOD2, and CAT. a Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, Lab #229, Bhubaneswar 751 013, India. E-mail: usubudhi@immt.res.in b Academy of Scientic & Innovative Research (AcSIR), New Delhi 110 025, India † Electronic supplementary information (ESI) available. See DOI: 10.1039/c4ra08873e Cite this: RSC Adv. , 2014, 4, 54506 Received 19th August 2014 Accepted 6th October 2014 DOI: 10.1039/c4ra08873e www.rsc.org/advances 54506 | RSC Adv. , 2014, 4, 54506–54511 This journal is © The Royal Society of Chemistry 2014 RSC Advances COMMUNICATION