Engineering polymerases and reaction conditions for modified incorporation properties

A multi-modal sequencing method, comprising:

• performing a first template dependent sequencing reaction in a first mode comprising a first set of reaction conditions;
• collecting initial sequencing information produced by the first sequencing reaction;
• performing a second sequencing reaction of the template, or a copy thereof, in a second mode comprising a second set of reaction conditions;
• collecting additional sequencing information produced by the second sequencing reaction;
• and,
• compiling the initial and additional sequencing information to provide a sequence of at least a portion of the template.

A method of determining which of two or more labeled nucleotides is incorporated at a site during a template-dependent polymerization reaction, the method comprising:

• incorporating the nucleotide into a nucleic acid polymer produced by the polymerization reaction, whereby signal pulses or signatures are generated;
• monitoring the pulses or signatures;
• and,
• using the presence of multiple pulses corresponding to the nucleotide, or identical molecules thereof, to assign which labeled nucleotide is incorporated at the site.

A nucleic acid sequencing system that, during operation of the system, sequences a nucleic acid, the system comprising:

• a signal detector, which detector detects at least signal pulses or signatures from branch fraction nonincorporation events during sequencing of a template nucleic acid;
• system instructions or software that assign a sequence based upon detection of at least signal pulses or signatures from branch fraction nonincorporation events;
• and,
• a user output module that displays the sequence to the user.

A composition comprising a modified recombinant nucleic acid polymerase, which modified recombinant polymerase exhibits an altered property selected from:

• a) an increased branching fraction during a polymerization by the polymerase;
• b) an altered translocation property of the polymerase during a polymerization reaction;
• and,
• c) a combination of any of (a)-(b),
• wherein the altered property is altered as compared to a corresponding wild-type polymerase.