This paper elucidates a new approach for aligning multiple sequences using DNA operations. A new distance metric using DNA hybridization melting temperature that gives approximate solutions for the multiple sequence alignment (MSA) problem is proposed. This paper provides proof for the proposed distance metric using the distance function properties. With this distance metric, a distance matrix is constructed that generates a guide tree for the alignment. Providing an accurate solution in less computational time is considered to be a challenging task for the MSA problem. Developing an algorithm for the MSA problem is essentially a trade-off between finding an accurate solution and that can be completed in less computational time. In order to reduce the time complexity, the Bio-inspired technique called the DNA computing is applied in calculating the distance between the sequences. The main application of this multiple sequence alignment (MSA) is to identify the sub-sequences for the functional study of the whole genome sequences. The detailed theoretical study of this approach is explained in this paper.