Methods for reducing nucleic acid damage

Abstract

Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample.

1 . A method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives, or mixtures thereof during the processing step, wherein the contacting inhibits degradation of the nucleic acids. 
     
     
         2 . The method of  claim 1 , wherein the nucleic acids are in an array of nucleic acids attached to a support. 
     
     
         3 . The method of  claim 1 , wherein the gallic acid, analogues, derivatives, or mixtures thereof is present in a concentration ranging from between about 10 mM to about 200 mM. 
     
     
         4 - 6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein the processing step is a detection processing step. 
     
     
         8 . The method of  claim 7 , wherein the detection processing step comprises irradiating the nucleic acids. 
     
     
         9 . The method of  claim 8 , wherein the irradiating is conducted in a range from about 360 nm to about 800 nm. 
     
     
         10 . The method of  claim 8 , wherein the irradiating is conducted with a light source having power in a range between about 5 to about 500 milliwatts. 
     
     
         11 . The method of  claim 8 , wherein the irradiating is conducted for a time period of about 0.1 seconds to about 10 minutes. 
     
     
         12 . The method of  claim 1 , wherein the degradation is light-induced degradation. 
     
     
         13 . The method of  claim 12 , wherein the light-induced degradation comprises removal of a nucleic acid member from the array of nucleic acids. 
     
     
         14 . The method of  claim 7 , further comprising adding a fluorescently tagged nucleotide to the array and repeating the detection processing step. 
     
     
         15 . The method of  claim 14 , wherein the adding the fluorescently tagged nucleotide comprises using a polymerase to add a single fluorescently tagged nucleotide. 
     
     
         16 . The method of  claim 14 , further comprising repeating the detection processing and addition steps for at least 50, 75 or 100 cycles. 
     
     
         17 . The method of  claim 7 , wherein the solution reduces the detection error rate by greater than 20, 40, or 50% compared to a control. 
     
     
         18 . The method of  claim 1 , wherein the processing step is fragmentation. 
     
     
         19 . The method of  claim 18 , wherein the nucleic acids are being prepared for sequencing. 
     
     
         20 . The method of  claim 19 , wherein the fidelity of the sequence information in the nucleic acids is improved as compared to nucleic acids fragmented in the absence of the solution. 
     
     
         21 . The method of  claim 18 , further comprising treating the nucleic acids with an enzyme that cleaves nucleic acid sequences comprising damaged nucleic acids to remove any damaged nucleic acids. 
     
     
         22 . The method of  claim 21 , wherein the enzyme is formamidopyrimidine DNA glycosylase (FPG). 
     
     
         23 . The method of  claim 18 , further comprising treating the sample with an antibody that selectively binds one or more types of damaged nucleic acids to remove any damaged nucleic acids. 
     
     
         24 . The method of  claim 23 , wherein the antibody binds 8-oxo-G. 
     
     
         25 - 27 . (canceled)