Detection of HIV-1 Nucleic Acids by Northern Blotting

Northern blotting (1 ) is one of many tools used in understanding the human immunodeficiency virus type 1 (HIV-1). In the process of Northern blotting, RNA is first separated by size through a denaturing agarose gel and transferred onto a membrane. With this transfer or blotting, and subsequent hybridization with a DNA or RNA probe, quantitation, expression levels of the RNA, size of the RNA, and mapping of the 5′- and 3′-terminal end of the RNA can be determined from primary and cultured cells, blood, and tissue. For HIV research, Northern blotting has been utilized for determining the expression levels and splicing patterns of HIV RNA regulatory genes (2 –4 ), HIV RNA protease gene (5 ), cytokine effects on the levels of spliced and genomic HIV RNA (6 ,7 ), steady-state transcriptional levels and splicing patterns of HIV RNA as a result of antiviral constructs (8 ), and receptor studies (9 ,10 ). In addition, Northern blotting has be utilized to answer questions on the effect on the HIV RNA level of expression of the envelope protein on calmodulin (11 ) and carbohydrate binding proteins (12 ).