Two-point-one-line modularized strategy combined with Holliday-junction button probes for multiloci SNPs long-range distribution analysis.

• Rapid analysis for long-range multi-site haplotypes was developed. • Thermodynamically designed LNA-button probes combine high specificity and yield. • Rapidly determine whether SNP sites apart > 1000 bp are located on the same DNA strand. • Rapid analysis of all haplotype combinations of two DNA strands. • Modularized algorithm proposed is highly scalable for different setting and platform. Some combinations of statistically related SNPs (tag SNPs) distributed within individual chromosomes may reflect richer medical and genetic information than isolated SNPs, called haplotypes. However, unlike the rapidly growing number of rapid SNP tests, determining whether SNP loci separated thousands of bases are located on the same chromosome is so difficult and time-consuming that its personalized application in clinical settings is slow. First, we designed special targets that retain modularized haplotype information; through DNA nanotechnology, we developed Holliday-junction button probes that specifically identify much longer double-stranded targets; through exploration of thermodynamic mechanisms, we overcame the paradox of probe specificity and yield to significantly improve detection; through mathematical logic reasoning, we designed modular algorithms to simplify difficult long-range multilocus haplotype analysis. The multidisciplinary intersection allows us to quickly and accurately read known haplotypes. Most importantly, haplotype analysis based on mathematical logic is universally applicable, and other effective molecular biological techniques can be combined with our algorithm to obtain more professional results. This study provides a new perspective on the field's efforts to solve the thorny problem of haplotype analysis. It is promising to contribute to the development of personalized applications of haplotype analysis. [ABSTRACT FROM AUTHOR]