Lysov Iu P, Chernyĭ A A, Balaev A A, Beattie K L, Florent'ev V L, Mirzabekov A D
Houston Advanced Research Center.
Mol Biol (Mosk). 1993 Sep-Oct;27(5):1126-38.
The efficiency of additional rounds of continuous stacking hybridization in DNA sequence reconstruction by hybridization with oligonucleotide matrix (SHOM) is considered. At first, DNA is hybridized with a matrix of oligonucleotides of the length L. The overlapping of the tuples which have formed perfect duplexes with the DNA, on the one hand, has enabled us to reconstruct unambiguously a part of the sequence, and on the other hand, suggested a modified scheme for reconstructing the remaining part. Then the additional hybridizations should be carried out in the presence of shorter oligonucleotides of the length l, that are able to form perfect duplexes of the length L + l in continuous hybridization closely to matrix tuples. In this case the stability of a duplex consisting of l-tuples and long DNA is enhanced due to stacking interaction. The information obtained about the succession of L + l sites considerably increases the efficiency of reconstruction, which can eventually reach the efficiency of a matrix consisting of (L + l)-tuples. We propose here an algorithm for compiling such a set of l-tuples to be added that the number of additional hybridizations can be appreciably diminished. For an octanucleotide matrix and different sets of pentanucleotides to be used for continuous stacking hybridization, the length of unambiguously sequenced DNA undergoes a rise from 200 to some thousands bp.
研究了通过与寡核苷酸矩阵杂交进行DNA序列重建（SHOM）时额外轮次连续堆积杂交的效率。首先，将DNA与长度为L的寡核苷酸矩阵进行杂交。一方面，与DNA形成完美双链体的元组的重叠使我们能够明确重建部分序列，另一方面，也为重建其余部分提出了一种改进方案。然后，应在长度为l的较短寡核苷酸存在的情况下进行额外的杂交，这些较短寡核苷酸能够在与矩阵元组紧密连续杂交中形成长度为L + l的完美双链体。在这种情况下，由于堆积相互作用，由l元组和长DNA组成的双链体的稳定性得到增强。关于L + l个位点顺序获得的信息大大提高了重建效率，最终可达到由（L + l）元组组成的矩阵的效率。我们在此提出一种算法，用于编译这样一组要添加的l元组，从而可以显著减少额外杂交的次数。对于八核苷酸矩阵和用于连续堆积杂交的不同五核苷酸组，明确测序的DNA长度从200 bp增加到数千bp。
