What is dideoxyribonucleoside triphosphate when we sequence DNA?

Answer 1

They are ddNTPs (ddATP, ddGTP, ddTTP, ddCTP) that also lack a 3' hydroxyl (OH) group in their deoxyribose sugar. This allows them to terminate the complementary nucleotide sequence (forming antiparallel to the template strand) that starts with the oligonucleotide (primer) and continues with dNTPs (deoxynucleoside triphosphate) attached by DNA polymerase. ddNTPs terminate the sequence at different positions which results in sequences of different lengths that each end with a different ddNTP. As these sequences are ran through a capillary electrophoresis gel, they are sorted by length, with the shortest sequence exiting the capillary tube first, and so on. Since each ddNTP is dyed a different color and fluoresces differently, the sequencing machine reads the ddNTP at the end of each sequence, determines its nucleotide (A, G, T, or C), and writes out the sequence one nucleotide at a time. Below is a link to a wonderful interactive animation that teaches about this method of sequencing.