Intermittent detection during analytical reactions

A method of performing an analytical reaction, comprising:

• a) preparing a reaction mixture containing components of the analytical reaction, wherein at least a first of the components is a detectable component that is detectable during one or more detection periods during the analytical reaction, and further wherein at least a second of the components is a clocking component that is detectable during one or more non-detection periods during the analytical reaction;
• b) initiating the analytical reaction in the reaction mixture to begin progression of the analytical reaction;
• and
• c) maintaining conditions that allow the analytical reaction to proceed while subjecting the reaction mixture to at least one detection period and at least one non-detection period during the progression of the analytical reaction, wherein the detectable component and the clocking component are present during both said detection period and said non-detection period, thereby performing the analytical reaction.

A method of sequencing a template nucleic acid, comprising:

• a) subjecting the template nucleic acid to methylation to generate at least one methylated base;
• b) subjecting the methylated base to base excision to generate at least one abasic site in the template nucleic acid;
• c) annealing a primer to the template nucleic acid;
• d) contacting the template nucleic acid with a polymerase enzyme in a manner that promotes extension of the primer in a template-dependent manner;
• e) monitoring the extension of the primer in real time to generate a nucleotide sequence read complementary to the template nucleic acid;
• f) extending the primer until the abasic site is encountered by the polymerase enzyme, at which time the polymerase enzyme pauses on the template nucleic acid;
• g) reinitiating primer extension by facilitating abasic site bypass by the polymerase;
• h) repeating steps e-h until a desired number of nucleotide sequence reads is generated and collected;
• and
• i) analyzing the desired number of nucleotide sequence reads to determine the sequence of the template nucleic acid, thereby sequencing the template nucleic acid.

A method of performing an illuminated reaction, comprising:

• a) preparing a reaction mixture comprising multiple optically detectable components that are distinguishable from one another based upon their individual signal emissions;
• b) initiating the illuminated reaction in the reaction mixture to begin progression of the illuminated reaction;
• and
• c) maintaining conditions that allow the illuminated reaction to proceed while subjecting the reaction mixture to at least one maximal illuminated period and at least one modified illuminated period during the progression of the illuminated reaction, wherein at least a portion of the optically detectable components are detectable during both the maximal illuminated period and the modified illuminated period.