The present invention encompasses methods for producing a modified
polynucleotide sequence that comprises a (e.g., one or more)
phosphorothiolate linkage, methods for determining a polynucleotide
sequence comprising a (e.g., one or more) phosphorothiolate linkage, and
methods for separating forward and reverse extension products that
comprise a (e.g., one or more) phosphorothiolate linkage. The invention
also encompasses kits for producing and/or determining the sequence of a
modified polynucleotide that comprises a (e.g., one or more)
phosphorothiolate linkage.