Multipart reagents having increased avidity for polymerase binding

A method for nucleic acid processing, comprising:

• (a) providing a surface having coupled thereto at least one polymer layer comprising a polymer coupled to a first nucleic acid molecule:
• and
• fb) contacting said first nucleic acid molecule with a second nucleic acid molecule such that said second nucleic acid molecule couples to said first nucleic acid molecule,
• wherein a first image of said surface subsequent to (b) exhibits a contrast-to-noise ratio of greater than or equal to about 5 when said first image of said surface is obtained using an inverted microscope and a camera under non-signal saturating conditions while said surface is immersed in a buffer and wherein said second nucleic acid molecule comprises a detectable tag that is a fluorescent dye, and
• wherein a second image of said surface exhibits a ratio of foreground fluorescence intensity and nonspecific dye adsorption background (Bimer) fluorescence intensity of at least 3:1 when said second nucleic acid molecule or derivative thereof is amplified and labeled with Cyanine dye 3 and said second image is obtained using an inverted microscope and a camera under non-signal saturating conditions while said surface is immersed in a buffer.

A method for nucleic acid processing, comprising:

• fa) providing a surface having coupled thereto at least one polymer layer comprising a polymer coupled to a first nucleic acid molecule:
• and
• (b) contacting said first nucleic acid molecule with a second nucleic acid molecule such that said second nucleic acid molecule couples to said first nucleic acid molecule,
• wherein a first image of said surface subsequent to fb) exhibits a contrast-to-noise ratio of greater than or equal to about 5 when said first image of said surface is obtained using an inverted microscope and a camera under non-signal saturating conditions while said surface is immersed in a buffer and wherein said second nucleic acid molecule comprises a detectable tag that is a fluorescent dye:
• and
• wherein a second image of said surface exhibits a ratio of foreground fluorescence intensity and a combination of nonspecific dye adsorption background and nonspecific amplification background (Bmter+Bmtra) fluorescence intensity of at least 3:1 when said second nucleic acid molecule or derivative thereof is amplified and labeled with Cyanine dye 3 and said second image is obtained using said inverted microscope and said camera under non-signal saturating conditions while said surface is immersed in a buffer.

A method for nucleic acid processing, comprising:

• (a) providing a surface having coupled thereto at least one polymer layer comprising a polymer coupled to a first nucleic acid molecule:
• (b) contacting said first nucleic acid molecule with a second nucleic acid molecule such that said second nucleic acid molecule couples to said first nucleic acid molecule:
• and
• (c) subsequent to fb), amplifying said second nucleic acid molecule or derivative thereof,
• wherein an image of said surface subsequent to fb) exhibits a contrast-to-noise ratio of greater than or equal to about 5 when said image of said surface is obtained using an inverted microscope and a camera under non-signal saturating conditions while said surface is immersed in a buffer and wherein said second nucleic acid molecule comprises a detectable tag that is a fluorescent dve, and
• wherein a background fluorescence intensity measured at a region of said surface that is laterally-displaced from a discrete region of said surface having said at least one polymer layer is no more than twice an intensity measured at said discrete region prior to said amplifying.