The cognitive radio networks or CogNets poses several new challenges to the transport layer protocols, because of many unique features of cognitive radio based devices used to build them. CogNets not only have inherited all features of wireless networks, but also their link connections are intermittent and discontinuous. Exiting transport layer protocols are too slow to respond quickly for utilizing available link capacity. Furthermore, existing self-timed transport layer protocols are neither designed for nor able to provide efficient reliable end-to-end transport service in CogNets, where wide round trip delay variations naturally occur. We identify (i) requirements of protocols for the transport layer of CogNets, (ii) propose a generic architecture for implementing a family of protocols that fulfill desired requirements, (iii) design, implement, and evaluate a family of best-effort transport protocols for serving delay-tolerant applications. Results obtained from ns2 network simulator show that the proposed protocols have potential for significantly improving end-to-end throughput. For instance, at 1% and 5%packet loss rates one of the proposed protocol has shown about 21% and 95% increase in end-to-end throughput for file transfer application.